JoaoJunior/formatted-java-preprocessed-code-APR

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); } Vector result = pedFile.check(); Vector indList = pedFile.getUnrelatedIndividuals(); Vector indsInTrio = new Vector(); int numMarkers = 0; numSingletons = 0; numTrios = 0; numPeds = pedFile.getNumFamilies(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); byte[] zeroArray = {0,0}; //first time through we deal with trios. for(int x=0; x < indList.size(); x++){ currentInd = (Individual)indList.get(x); currentFamily = pedFile.getFamily(currentInd.getFamilyID()); if (currentFamily.containsMember(currentInd.getMomID()) && currentFamily.containsMember(currentInd.getDadID())){ //if indiv has both parents Individual mom = currentFamily.getMember(currentInd.getMomID()); Individual dad = currentFamily.getMember(currentInd.getDadID()); if (indList.contains(mom) && indList.contains(dad)){ numMarkers = currentInd.getNumMarkers(); byte[] dadTb = new byte[numMarkers]; byte[] dadUb = new byte[numMarkers]; byte[] momTb = new byte[numMarkers]; byte[] momUb = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } byte kid1 = thisMarker[0]; byte kid2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getMomID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getMomID())).getMarker(i); } byte mom1 = thisMarker[0]; byte mom2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getDadID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getDadID())).getMarker(i); } byte dad1 = thisMarker[0]; byte dad2 = thisMarker[1]; if (kid1 == 0 || kid2 == 0) { //kid missing if (dad1 == dad2) { dadTb[i] = dad1; dadUb[i] = dad1; } else if (dad1 != 0 && dad2 != 0) { dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); } if (mom1 == mom2) { momTb[i] = mom1; momUb[i] = mom1; } else if (mom1 != 0 && mom2 != 0){ momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } else if (kid1 == kid2) { //kid homozygous if (dad1 == 0) { dadTb[i] = kid1; dadUb[i] = 0; } else if (dad1 == kid1) { dadTb[i] = dad1; dadUb[i] = dad2; } else { dadTb[i] = dad2; dadUb[i] = dad1; } if (mom1 == 0) { momTb[i] = kid1; momUb[i] = 0; } else if (mom1 == kid1) { momTb[i] = mom1; momUb[i] = mom2; } else { momTb[i] = mom2; momUb[i] = mom1; } } else { //kid heterozygous and this if tree's a bitch if (dad1 == 0 && mom1 == 0) { //both missing dadTb[i] = 0; dadUb[i] = 0; momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 != mom2) { //dad missing mom het dadTb[i] = 0; dadUb[i] = 0; momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } else if (mom1 == 0 && dad1 != dad2) { //dad het mom missing dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 == mom2) { //dad missing mom hom momTb[i] = mom1; momUb[i] = mom1; dadUb[i] = 0; if (kid1 == mom1) { dadTb[i] = kid2; } else { dadTb[i] = kid1; } } else if (mom1 == 0 && dad1 == dad2) { //mom missing dad hom dadTb[i] = dad1; dadUb[i] = dad1; momUb[i] = 0; if (kid1 == dad1) { momTb[i] = kid2; } else { momTb[i] = kid1; } } else if (dad1 == dad2 && mom1 != mom2) { //dad hom mom het dadTb[i] = dad1; dadUb[i] = dad2; if (kid1 == dad1) { momTb[i] = kid2; momUb[i] = kid1; } else { momTb[i] = kid1; momUb[i] = kid2; } } else if (mom1 == mom2 && dad1 != dad2) { //dad het mom hom momTb[i] = mom1; momUb[i] = mom2; if (kid1 == mom1) { dadTb[i] = kid2; dadUb[i] = kid1; } else { dadTb[i] = kid1; dadUb[i] = kid2; } } else if (dad1 == dad2 && mom1 == mom2) { //mom & dad hom dadTb[i] = dad1; dadUb[i] = dad1; momTb[i] = mom1; momUb[i] = mom1; } else { //everybody het dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadTb, dad.getAffectedStatus(), currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadUb, dad.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momTb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momUb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); numTrios++; indsInTrio.add(mom); indsInTrio.add(dad); indsInTrio.add(currentInd); } } } for (int x=0; x<indList.size(); x++){ currentInd = (Individual)indList.get(x); if (!indsInTrio.contains(currentInd)){ //ind has no parents or kids -- he's a singleton numMarkers = currentInd.getNumMarkers(); byte[] chrom1 = new byte[numMarkers]; byte[] chrom2 = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } if (thisMarker[0] == thisMarker[1] || thisMarker[0] == 0 || thisMarker[1] == 0){ chrom1[i] = thisMarker[0]; chrom2[i] = thisMarker[1]; }else{ chrom1[i] = (byte)(4+thisMarker[0]); chrom2[i] = (byte)(4+thisMarker[1]); } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom1, currentInd.getAffectedStatus(), -1)); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom2,currentInd.getAffectedStatus(), -1)); numSingletons++; } } chromosomes = chrom; //wipe clean any existing marker info so we know we're starting with a new file Chromosome.markers = null; return result; }

1,110,802

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); } Vector result = pedFile.check(); Vector indList = pedFile.getUnrelatedIndividuals(); Vector indsInTrio = new Vector(); int numMarkers = 0; numSingletons = 0; numTrios = 0; numPeds = pedFile.getNumFamilies(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); byte[] zeroArray = {0,0}; //first time through we deal with trios. for(int x=0; x < indList.size(); x++){ currentInd = (Individual)indList.get(x); currentFamily = pedFile.getFamily(currentInd.getFamilyID()); if (currentFamily.containsMember(currentInd.getMomID()) && currentFamily.containsMember(currentInd.getDadID())){ //if indiv has both parents Individual mom = currentFamily.getMember(currentInd.getMomID()); Individual dad = currentFamily.getMember(currentInd.getDadID()); if (indList.contains(mom) && indList.contains(dad)){ numMarkers = currentInd.getNumMarkers(); byte[] dadTb = new byte[numMarkers]; byte[] dadUb = new byte[numMarkers]; byte[] momTb = new byte[numMarkers]; byte[] momUb = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } byte kid1 = thisMarker[0]; byte kid2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getMomID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getMomID())).getMarker(i); } byte mom1 = thisMarker[0]; byte mom2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getDadID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getDadID())).getMarker(i); } byte dad1 = thisMarker[0]; byte dad2 = thisMarker[1]; if (kid1 == 0 || kid2 == 0) { //kid missing if (dad1 == dad2) { dadTb[i] = dad1; dadUb[i] = dad1; } else if (dad1 != 0 && dad2 != 0) { dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); } if (mom1 == mom2) { momTb[i] = mom1; momUb[i] = mom1; } else if (mom1 != 0 && mom2 != 0){ momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } else if (kid1 == kid2) { //kid homozygous if (dad1 == 0) { dadTb[i] = kid1; dadUb[i] = 0; } else if (dad1 == kid1) { dadTb[i] = dad1; dadUb[i] = dad2; } else { dadTb[i] = dad2; dadUb[i] = dad1; } if (mom1 == 0) { momTb[i] = kid1; momUb[i] = 0; } else if (mom1 == kid1) { momTb[i] = mom1; momUb[i] = mom2; } else { momTb[i] = mom2; momUb[i] = mom1; } } else { //kid heterozygous and this if tree's a bitch if (dad1 == 0 && mom1 == 0) { //both missing dadTb[i] = 0; dadUb[i] = 0; momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 != mom2) { //dad missing mom het dadTb[i] = 0; dadUb[i] = 0; momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } else if (mom1 == 0 && dad1 != dad2) { //dad het mom missing dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 == mom2) { //dad missing mom hom momTb[i] = mom1; momUb[i] = mom1; dadUb[i] = 0; if (kid1 == mom1) { dadTb[i] = kid2; } else { dadTb[i] = kid1; } } else if (mom1 == 0 && dad1 == dad2) { //mom missing dad hom dadTb[i] = dad1; dadUb[i] = dad1; momUb[i] = 0; if (kid1 == dad1) { momTb[i] = kid2; } else { momTb[i] = kid1; } } else if (dad1 == dad2 && mom1 != mom2) { //dad hom mom het dadTb[i] = dad1; dadUb[i] = dad2; if (kid1 == dad1) { momTb[i] = kid2; momUb[i] = kid1; } else { momTb[i] = kid1; momUb[i] = kid2; } } else if (mom1 == mom2 && dad1 != dad2) { //dad het mom hom momTb[i] = mom1; momUb[i] = mom2; if (kid1 == mom1) { dadTb[i] = kid2; dadUb[i] = kid1; } else { dadTb[i] = kid1; dadUb[i] = kid2; } } else if (dad1 == dad2 && mom1 == mom2) { //mom & dad hom dadTb[i] = dad1; dadUb[i] = dad1; momTb[i] = mom1; momUb[i] = mom1; } else { //everybody het dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadTb, dad.getAffectedStatus(), currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadUb, dad.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momTb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momUb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); numTrios++; indsInTrio.add(mom); indsInTrio.add(dad); indsInTrio.add(currentInd); } } } for (int x=0; x<indList.size(); x++){ currentInd = (Individual)indList.get(x); if (!indsInTrio.contains(currentInd)){ //ind has no parents or kids -- he's a singleton numMarkers = currentInd.getNumMarkers(); byte[] chrom1 = new byte[numMarkers]; byte[] chrom2 = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } if (thisMarker[0] == thisMarker[1] || thisMarker[0] == 0 || thisMarker[1] == 0){ chrom1[i] = thisMarker[0]; chrom2[i] = thisMarker[1]; }else{ chrom1[i] = (byte)(4+thisMarker[0]); chrom2[i] = (byte)(4+thisMarker[1]); } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom1, currentInd.getAffectedStatus(), -1)); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom2,currentInd.getAffectedStatus(), -1)); numSingletons++; } } chromosomes = chrom; //wipe clean any existing marker info so we know we're starting with a new file Chromosome.markers = null; return result; }

1,110,803

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); } Vector result = pedFile.check(); Vector indList = pedFile.getUnrelatedIndividuals(); Vector indsInTrio = new Vector(); int numMarkers = 0; numSingletons = 0; numTrios = 0; numPeds = pedFile.getNumFamilies(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); byte[] zeroArray = {0,0}; //first time through we deal with trios. for(int x=0; x < indList.size(); x++){ currentInd = (Individual)indList.get(x); currentFamily = pedFile.getFamily(currentInd.getFamilyID()); if (currentFamily.containsMember(currentInd.getMomID()) && currentFamily.containsMember(currentInd.getDadID())){ //if indiv has both parents Individual mom = currentFamily.getMember(currentInd.getMomID()); Individual dad = currentFamily.getMember(currentInd.getDadID()); if (indList.contains(mom) && indList.contains(dad)){ numMarkers = currentInd.getNumMarkers(); byte[] dadTb = new byte[numMarkers]; byte[] dadUb = new byte[numMarkers]; byte[] momTb = new byte[numMarkers]; byte[] momUb = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } byte kid1 = thisMarker[0]; byte kid2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getMomID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getMomID())).getMarker(i); } byte mom1 = thisMarker[0]; byte mom2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getDadID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getDadID())).getMarker(i); } byte dad1 = thisMarker[0]; byte dad2 = thisMarker[1]; if (kid1 == 0 || kid2 == 0) { //kid missing if (dad1 == dad2) { dadTb[i] = dad1; dadUb[i] = dad1; } else if (dad1 != 0 && dad2 != 0) { dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); } if (mom1 == mom2) { momTb[i] = mom1; momUb[i] = mom1; } else if (mom1 != 0 && mom2 != 0){ momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } else if (kid1 == kid2) { //kid homozygous if (dad1 == 0) { dadTb[i] = kid1; dadUb[i] = 0; } else if (dad1 == kid1) { dadTb[i] = dad1; dadUb[i] = dad2; } else { dadTb[i] = dad2; dadUb[i] = dad1; } if (mom1 == 0) { momTb[i] = kid1; momUb[i] = 0; } else if (mom1 == kid1) { momTb[i] = mom1; momUb[i] = mom2; } else { momTb[i] = mom2; momUb[i] = mom1; } } else { //kid heterozygous and this if tree's a bitch if (dad1 == 0 && mom1 == 0) { //both missing dadTb[i] = 0; dadUb[i] = 0; momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 != mom2) { //dad missing mom het dadTb[i] = 0; dadUb[i] = 0; momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } else if (mom1 == 0 && dad1 != dad2) { //dad het mom missing dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 == mom2) { //dad missing mom hom momTb[i] = mom1; momUb[i] = mom1; dadUb[i] = 0; if (kid1 == mom1) { dadTb[i] = kid2; } else { dadTb[i] = kid1; } } else if (mom1 == 0 && dad1 == dad2) { //mom missing dad hom dadTb[i] = dad1; dadUb[i] = dad1; momUb[i] = 0; if (kid1 == dad1) { momTb[i] = kid2; } else { momTb[i] = kid1; } } else if (dad1 == dad2 && mom1 != mom2) { //dad hom mom het dadTb[i] = dad1; dadUb[i] = dad2; if (kid1 == dad1) { momTb[i] = kid2; momUb[i] = kid1; } else { momTb[i] = kid1; momUb[i] = kid2; } } else if (mom1 == mom2 && dad1 != dad2) { //dad het mom hom momTb[i] = mom1; momUb[i] = mom2; if (kid1 == mom1) { dadTb[i] = kid2; dadUb[i] = kid1; } else { dadTb[i] = kid1; dadUb[i] = kid2; } } else if (dad1 == dad2 && mom1 == mom2) { //mom & dad hom dadTb[i] = dad1; dadUb[i] = dad1; momTb[i] = mom1; momUb[i] = mom1; } else { //everybody het dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadTb, dad.getAffectedStatus(), currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadUb, dad.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momTb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momUb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); numTrios++; indsInTrio.add(mom); indsInTrio.add(dad); indsInTrio.add(currentInd); } } } for (int x=0; x<indList.size(); x++){ currentInd = (Individual)indList.get(x); if (!indsInTrio.contains(currentInd)){ //ind has no parents or kids -- he's a singleton numMarkers = currentInd.getNumMarkers(); byte[] chrom1 = new byte[numMarkers]; byte[] chrom2 = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } if (thisMarker[0] == thisMarker[1] || thisMarker[0] == 0 || thisMarker[1] == 0){ chrom1[i] = thisMarker[0]; chrom2[i] = thisMarker[1]; }else{ chrom1[i] = (byte)(4+thisMarker[0]); chrom2[i] = (byte)(4+thisMarker[1]); } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom1, currentInd.getAffectedStatus(), -1)); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom2,currentInd.getAffectedStatus(), -1)); numSingletons++; } } chromosomes = chrom; //wipe clean any existing marker info so we know we're starting with a new file Chromosome.markers = null; return result; }

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); } Vector result = pedFile.check(); Vector indList = pedFile.getUnrelatedIndividuals(); Vector indsInTrio = new Vector(); int numMarkers = 0; numSingletons = 0; numTrios = 0; numPeds = pedFile.getNumFamilies(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); byte[] zeroArray = {0,0}; //first time through we deal with trios. for(int x=0; x < indList.size(); x++){ currentInd = (Individual)indList.get(x); currentFamily = pedFile.getFamily(currentInd.getFamilyID()); if (currentFamily.containsMember(currentInd.getMomID()) && currentFamily.containsMember(currentInd.getDadID())){ //if indiv has both parents Individual mom = currentFamily.getMember(currentInd.getMomID()); Individual dad = currentFamily.getMember(currentInd.getDadID()); if (indList.contains(mom) && indList.contains(dad)){ numMarkers = currentInd.getNumMarkers(); byte[] dadTb = new byte[numMarkers]; byte[] dadUb = new byte[numMarkers]; byte[] momTb = new byte[numMarkers]; byte[] momUb = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte thisMarkerA, thisMarkerB; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } byte kid1 = thisMarker[0]; byte kid2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getMomID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getMomID())).getMarker(i); } byte mom1 = thisMarker[0]; byte mom2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getDadID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getDadID())).getMarker(i); } byte dad1 = thisMarker[0]; byte dad2 = thisMarker[1]; if (kid1 == 0 || kid2 == 0) { //kid missing if (dad1 == dad2) { dadTb[i] = dad1; dadUb[i] = dad1; } else if (dad1 != 0 && dad2 != 0) { dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); } if (mom1 == mom2) { momTb[i] = mom1; momUb[i] = mom1; } else if (mom1 != 0 && mom2 != 0){ momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } else if (kid1 == kid2) { //kid homozygous if (dad1 == 0) { dadTb[i] = kid1; dadUb[i] = 0; } else if (dad1 == kid1) { dadTb[i] = dad1; dadUb[i] = dad2; } else { dadTb[i] = dad2; dadUb[i] = dad1; } if (mom1 == 0) { momTb[i] = kid1; momUb[i] = 0; } else if (mom1 == kid1) { momTb[i] = mom1; momUb[i] = mom2; } else { momTb[i] = mom2; momUb[i] = mom1; } } else { //kid heterozygous and this if tree's a bitch if (dad1 == 0 && mom1 == 0) { //both missing dadTb[i] = 0; dadUb[i] = 0; momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 != mom2) { //dad missing mom het dadTb[i] = 0; dadUb[i] = 0; momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } else if (mom1 == 0 && dad1 != dad2) { //dad het mom missing dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 == mom2) { //dad missing mom hom momTb[i] = mom1; momUb[i] = mom1; dadUb[i] = 0; if (kid1 == mom1) { dadTb[i] = kid2; } else { dadTb[i] = kid1; } } else if (mom1 == 0 && dad1 == dad2) { //mom missing dad hom dadTb[i] = dad1; dadUb[i] = dad1; momUb[i] = 0; if (kid1 == dad1) { momTb[i] = kid2; } else { momTb[i] = kid1; } } else if (dad1 == dad2 && mom1 != mom2) { //dad hom mom het dadTb[i] = dad1; dadUb[i] = dad2; if (kid1 == dad1) { momTb[i] = kid2; momUb[i] = kid1; } else { momTb[i] = kid1; momUb[i] = kid2; } } else if (mom1 == mom2 && dad1 != dad2) { //dad het mom hom momTb[i] = mom1; momUb[i] = mom2; if (kid1 == mom1) { dadTb[i] = kid2; dadUb[i] = kid1; } else { dadTb[i] = kid1; dadUb[i] = kid2; } } else if (dad1 == dad2 && mom1 == mom2) { //mom & dad hom dadTb[i] = dad1; dadUb[i] = dad1; momTb[i] = mom1; momUb[i] = mom1; } else { //everybody het dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadTb, dad.getAffectedStatus(), currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadUb, dad.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momTb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momUb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); numTrios++; indsInTrio.add(mom); indsInTrio.add(dad); indsInTrio.add(currentInd); } } } for (int x=0; x<indList.size(); x++){ currentInd = (Individual)indList.get(x); if (!indsInTrio.contains(currentInd)){ //ind has no parents or kids -- he's a singleton numMarkers = currentInd.getNumMarkers(); byte[] chrom1 = new byte[numMarkers]; byte[] chrom2 = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte thisMarkerA, thisMarkerB; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } if (thisMarker[0] == thisMarker[1] || thisMarker[0] == 0 || thisMarker[1] == 0){ chrom1[i] = thisMarker[0]; chrom2[i] = thisMarker[1]; }else{ chrom1[i] = (byte)(4+thisMarker[0]); chrom2[i] = (byte)(4+thisMarker[1]); } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom1, currentInd.getAffectedStatus(), -1)); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom2,currentInd.getAffectedStatus(), -1)); numSingletons++; } } chromosomes = chrom; //wipe clean any existing marker info so we know we're starting with a new file Chromosome.markers = null; return result; }

1,110,804

public Vector linkageToChrom(File infile, int type) throws IllegalArgumentException, HaploViewException, PedFileException, IOException{ pedFile = new PedFile(); if (type == PED_FILE){ pedFile.parseLinkage(infile); }else{ pedFile.parseHapMap(infile); } Vector result = pedFile.check(); Vector indList = pedFile.getUnrelatedIndividuals(); Vector indsInTrio = new Vector(); int numMarkers = 0; numSingletons = 0; numTrios = 0; numPeds = pedFile.getNumFamilies(); Individual currentInd; Family currentFamily; Vector chrom = new Vector(); byte[] zeroArray = {0,0}; //first time through we deal with trios. for(int x=0; x < indList.size(); x++){ currentInd = (Individual)indList.get(x); currentFamily = pedFile.getFamily(currentInd.getFamilyID()); if (currentFamily.containsMember(currentInd.getMomID()) && currentFamily.containsMember(currentInd.getDadID())){ //if indiv has both parents Individual mom = currentFamily.getMember(currentInd.getMomID()); Individual dad = currentFamily.getMember(currentInd.getDadID()); if (indList.contains(mom) && indList.contains(dad)){ numMarkers = currentInd.getNumMarkers(); byte[] dadTb = new byte[numMarkers]; byte[] dadUb = new byte[numMarkers]; byte[] momTb = new byte[numMarkers]; byte[] momUb = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } byte kid1 = thisMarker[0]; byte kid2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getMomID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getMomID())).getMarker(i); } byte mom1 = thisMarker[0]; byte mom2 = thisMarker[1]; if (currentFamily.getMember(currentInd.getDadID()).getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = (currentFamily.getMember(currentInd.getDadID())).getMarker(i); } byte dad1 = thisMarker[0]; byte dad2 = thisMarker[1]; if (kid1 == 0 || kid2 == 0) { //kid missing if (dad1 == dad2) { dadTb[i] = dad1; dadUb[i] = dad1; } else if (dad1 != 0 && dad2 != 0) { dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); } if (mom1 == mom2) { momTb[i] = mom1; momUb[i] = mom1; } else if (mom1 != 0 && mom2 != 0){ momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } else if (kid1 == kid2) { //kid homozygous if (dad1 == 0) { dadTb[i] = kid1; dadUb[i] = 0; } else if (dad1 == kid1) { dadTb[i] = dad1; dadUb[i] = dad2; } else { dadTb[i] = dad2; dadUb[i] = dad1; } if (mom1 == 0) { momTb[i] = kid1; momUb[i] = 0; } else if (mom1 == kid1) { momTb[i] = mom1; momUb[i] = mom2; } else { momTb[i] = mom2; momUb[i] = mom1; } } else { //kid heterozygous and this if tree's a bitch if (dad1 == 0 && mom1 == 0) { //both missing dadTb[i] = 0; dadUb[i] = 0; momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 != mom2) { //dad missing mom het dadTb[i] = 0; dadUb[i] = 0; momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } else if (mom1 == 0 && dad1 != dad2) { //dad het mom missing dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = 0; momUb[i] = 0; } else if (dad1 == 0 && mom1 == mom2) { //dad missing mom hom momTb[i] = mom1; momUb[i] = mom1; dadUb[i] = 0; if (kid1 == mom1) { dadTb[i] = kid2; } else { dadTb[i] = kid1; } } else if (mom1 == 0 && dad1 == dad2) { //mom missing dad hom dadTb[i] = dad1; dadUb[i] = dad1; momUb[i] = 0; if (kid1 == dad1) { momTb[i] = kid2; } else { momTb[i] = kid1; } } else if (dad1 == dad2 && mom1 != mom2) { //dad hom mom het dadTb[i] = dad1; dadUb[i] = dad2; if (kid1 == dad1) { momTb[i] = kid2; momUb[i] = kid1; } else { momTb[i] = kid1; momUb[i] = kid2; } } else if (mom1 == mom2 && dad1 != dad2) { //dad het mom hom momTb[i] = mom1; momUb[i] = mom2; if (kid1 == mom1) { dadTb[i] = kid2; dadUb[i] = kid1; } else { dadTb[i] = kid1; dadUb[i] = kid2; } } else if (dad1 == dad2 && mom1 == mom2) { //mom & dad hom dadTb[i] = dad1; dadUb[i] = dad1; momTb[i] = mom1; momUb[i] = mom1; } else { //everybody het dadTb[i] = (byte)(4+dad1); dadUb[i] = (byte)(4+dad2); momTb[i] = (byte)(4+mom1); momUb[i] = (byte)(4+mom2); } } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadTb, dad.getAffectedStatus(), currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),dadUb, dad.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momTb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),momUb, mom.getAffectedStatus(),currentInd.getAffectedStatus())); numTrios++; indsInTrio.add(mom); indsInTrio.add(dad); indsInTrio.add(currentInd); } } } for (int x=0; x<indList.size(); x++){ currentInd = (Individual)indList.get(x); if (!indsInTrio.contains(currentInd)){ //ind has no parents or kids -- he's a singleton numMarkers = currentInd.getNumMarkers(); byte[] chrom1 = new byte[numMarkers]; byte[] chrom2 = new byte[numMarkers]; for (int i = 0; i < numMarkers; i++){ byte[] thisMarker; if (currentInd.getZeroed(i)){ thisMarker = zeroArray; }else{ thisMarker = currentInd.getMarker(i); } if (thisMarker[0] == thisMarker[1] || thisMarker[0] == 0 || thisMarker[1] == 0){ chrom1[i] = thisMarker[0]; chrom2[i] = thisMarker[1]; }else{ chrom1[i] = (byte)(4+thisMarker[0]); chrom2[i] = (byte)(4+thisMarker[1]); } } chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom1, currentInd.getAffectedStatus(), -1)); chrom.add(new Chromosome(currentInd.getFamilyID(),currentInd.getIndividualID(),chrom2,currentInd.getAffectedStatus(), -1)); numSingletons++; } } chromosomes = chrom; //wipe clean any existing marker info so we know we're starting with a new file Chromosome.markers = null; return result; }

1,110,805

void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist is //used to determine beyond what distance comparisons will not be //made. if the infile param is null, loads up "dummy info" for //situation where no info file exists //An optional third column is supported which is designed to hold //association study data. If there is a third column there will be //a visual indicator in the D' display that there is additional data //and the detailed data can be viewed with a mouse press. Vector names = new Vector(); HashSet nameSearch = new HashSet(); HashSet dupCheck = new HashSet(); Vector positions = new Vector(); Vector extras = new Vector(); dupsToBeFlagged = false; dupNames = false; try{ if (infile != null){ if (infile.length() < 1){ throw new HaploViewException("Info file is empty or does not exist: " + infile.getName()); } String currentLine; long prevloc = -1000000000; //read the input file: BufferedReader in = new BufferedReader(new FileReader(infile)); int lineCount = 0; while ((currentLine = in.readLine()) != null){ StringTokenizer st = new StringTokenizer(currentLine); if (st.countTokens() > 1){ lineCount++; }else if (st.countTokens() == 1){ //complain if only one field found throw new HaploViewException("Info file format error on line "+lineCount+ ":\n Info file must be of format: <markername> <markerposition>"); }else{ //skip blank lines continue; } String name = st.nextToken(); String l = st.nextToken(); String extra = null; if (st.hasMoreTokens()) extra = st.nextToken(); long loc; try{ loc = Long.parseLong(l); }catch (NumberFormatException nfe){ throw new HaploViewException("Info file format error on line "+lineCount+ ":\n\"" + l + "\" should be of type long." + "\n Info file must be of format: <markername> <markerposition>"); } //basically if anyone is crazy enough to load a dataset, then go back and load //an out-of-order info file we tell them to bugger off and start over. if (loc < prevloc && Chromosome.markers != null){ throw new HaploViewException("Info file out of order with preloaded dataset:\n"+ name + "\nPlease reload data file and info file together."); } prevloc = loc; if (nameSearch.contains(name)){ dupCheck.add(name); } names.add(name); nameSearch.add(name); positions.add(l); extras.add(extra); } if (lineCount > Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too many\nmarkers in info file compared to data file.")); } if (lineCount < Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too few\nmarkers in info file compared to data file.")); } infoKnown=true; } if (hapmapGoodies != null){ //we know some stuff from the hapmap so we'll add it here for (int x=0; x < hapmapGoodies.length; x++){ if (nameSearch.contains(hapmapGoodies[x][0])){ dupCheck.add(hapmapGoodies[x][0]); } names.add(hapmapGoodies[x][0]); nameSearch.add(hapmapGoodies[x][0]); positions.add(hapmapGoodies[x][1]); extras.add(null); } infoKnown = true; } if(dupCheck.size() > 0) { int nameCount = names.size(); Hashtable dupCounts = new Hashtable(); for(int i=0;i<nameCount;i++) { if(dupCheck.contains(names.get(i))){ String n = (String) names.get(i); if(dupCounts.containsKey(n)){ int numDups = ((Integer) dupCounts.get(n)).intValue(); String newName = n + "." + numDups; while (nameSearch.contains(newName)){ numDups++; newName = n + "." + numDups; } names.setElementAt(newName,i); nameSearch.add(newName); dupCounts.put(n,new Integer(numDups)) ; }else { //we leave the first instance with its original name dupCounts.put(n,new Integer(1)); } dupNames = true; } } } //sort the markers int numLines = names.size(); class SortingHelper implements Comparable{ long pos; int orderInFile; public SortingHelper(long pos, int order){ this.pos = pos; this.orderInFile = order; } public int compareTo(Object o) { SortingHelper sh = (SortingHelper)o; if (sh.pos > pos){ return -1; }else if (sh.pos < pos){ return 1; }else{ return 0; } } } boolean needSort = false; Vector sortHelpers = new Vector(); for (int k = 0; k < (numLines); k++){ sortHelpers.add(new SortingHelper(Long.parseLong((String)positions.get(k)),k)); } //loop through and check if any markers are out of order for (int k = 1; k < (numLines); k++){ if(((SortingHelper)sortHelpers.get(k)).compareTo(sortHelpers.get(k-1)) < 0) { needSort = true; break; } } //if any were out of order, then we need to put them in order if(needSort){ //sort the positions Collections.sort(sortHelpers); Vector newNames = new Vector(); Vector newExtras = new Vector(); Vector newPositions = new Vector(); int[] realPos = new int[numLines]; //reorder the vectors names and extras so that they have the same order as the sorted markers for (int i = 0; i < sortHelpers.size(); i++){ realPos[i] = ((SortingHelper)sortHelpers.get(i)).orderInFile; newNames.add(names.get(realPos[i])); newPositions.add(positions.get(realPos[i])); newExtras.add(extras.get(realPos[i])); } names = newNames; extras = newExtras; positions = newPositions; byte[] tempGenotype = new byte[sortHelpers.size()]; //now we reorder all the individuals genotypes according to the sorted marker order for(int j=0;j<chromosomes.size();j++){ Chromosome tempChrom = (Chromosome)chromosomes.elementAt(j); for(int i =0;i<sortHelpers.size();i++){ tempGenotype[i] = tempChrom.getUnfilteredGenotype(realPos[i]); } for(int i=0;i<sortHelpers.size();i++){ tempChrom.setGenotype(tempGenotype[i],i); } } //sort pedfile objects //todo: this should really be done before pedfile is subjected to any processing. //todo: that would require altering some order of operations in dealing with inputs //todo: this will fry an out-of-order haps file...grr Vector unsortedRes = pedFile.getResults(); Vector sortedRes = new Vector(); for (int i = 0; i < realPos.length; i++){ sortedRes.add(unsortedRes.elementAt(realPos[i])); } pedFile.setResults(sortedRes); Vector o = pedFile.getAllIndividuals(); for (int i = 0; i < o.size(); i++){ Individual ind = (Individual) o.get(i); Vector unsortedMarkers = ind.getMarkers(); boolean[] unsortedZeroed = ind.getZeroedArray(); boolean[] sortedZeroed = new boolean[unsortedMarkers.size()]; Vector sortedMarkers = new Vector(); for (int j = 0; j < unsortedMarkers.size(); j++){ sortedMarkers.add(unsortedMarkers.get(realPos[j])); sortedZeroed[j] = unsortedZeroed[realPos[j]]; } ind.setMarkers(new Vector(sortedMarkers)); ind.setZeroedArray(sortedZeroed); } } }catch (HaploViewException e){ throw(e); }finally{ double numChroms = chromosomes.size(); Vector markerInfo = new Vector(); double[] numBadGenotypes = new double[Chromosome.getUnfilteredSize()]; percentBadGenotypes = new double[Chromosome.getUnfilteredSize()]; Vector results = null; if (pedFile != null){ results = pedFile.getResults(); } long prevPosition = Long.MIN_VALUE; SNP prevMarker = null; MarkerResult pmr = null; for (int i = 0; i < Chromosome.getUnfilteredSize(); i++){ MarkerResult mr = null; if (results != null){ mr = (MarkerResult)results.elementAt(i); } //to compute minor/major alleles, browse chrom list and count instances of each allele byte a1 = 0; byte a2 = 0; double numa1 = 0; double numa2 = 0; for (int j = 0; j < chromosomes.size(); j++){ //if there is a data point for this marker on this chromosome byte thisAllele = ((Chromosome)chromosomes.elementAt(j)).getUnfilteredGenotype(i); if (!(thisAllele == 0)){ if (thisAllele >= 5){ numa1+=0.5; numa2+=0.5; if (thisAllele < 9){ if (a1==0){ a1 = (byte)(thisAllele-4); }else if (a2 == 0){ if (!(thisAllele-4 == a1)){ a2 = (byte)(thisAllele-4); } } } }else if (a1 == 0){ a1 = thisAllele; numa1++; }else if (thisAllele == a1){ numa1++; }else{ numa2++; a2 = thisAllele; } } else { numBadGenotypes[i]++; } } if (numa2 > numa1){ byte temp = a1; double tempnum = numa1; numa1 = numa2; a1 = a2; numa2 = tempnum; a2 = temp; } double maf; if (mr != null){ maf = Util.roundDouble(mr.getMAF(),3); }else{ maf = Util.roundDouble((numa2/(numa1+numa2)),3); } if (infoKnown){ long pos = Long.parseLong((String)positions.elementAt(i)); SNP thisMarker = (new SNP((String)names.elementAt(i), pos, maf, a1, a2, (String)extras.elementAt(i))); markerInfo.add(thisMarker); if (mr != null){ double genoPC = mr.getGenoPercent(); //check to make sure adjacent SNPs do not have identical positions if (prevPosition != Long.MIN_VALUE){ //only do this for markers 2..N, since we're comparing to the previous location if (pos == prevPosition){ dupsToBeFlagged = true; if (genoPC >= pmr.getGenoPercent()){ //use this one because it has more genotypes thisMarker.setDup(1); prevMarker.setDup(2); }else{ //use the other one because it has more genotypes thisMarker.setDup(2); prevMarker.setDup(1); } } } prevPosition = pos; prevMarker = thisMarker; pmr = mr; } }else{ markerInfo.add(new SNP("Marker " + String.valueOf(i+1), (i*4000), maf,a1,a2)); } percentBadGenotypes[i] = numBadGenotypes[i]/numChroms; } Chromosome.markers = markerInfo; } }

void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist is //used to determine beyond what distance comparisons will not be //made. if the infile param is null, loads up "dummy info" for //situation where no info file exists //An optional third column is supported which is designed to hold //association study data. If there is a third column there will be //a visual indicator in the D' display that there is additional data //and the detailed data can be viewed with a mouse press. Vector names = new Vector(); HashSet nameSearch = new HashSet(); HashSet dupCheck = new HashSet(); Vector positions = new Vector(); Vector extras = new Vector(); dupsToBeFlagged = false; dupNames = false; try{ if (infile != null){ if (infile.length() < 1){ throw new HaploViewException("Info file is empty or does not exist: " + infile.getName()); } String currentLine; long prevloc = -1000000000; //read the input file: BufferedReader in = new BufferedReader(new FileReader(infile)); int lineCount = 0; while ((currentLine = in.readLine()) != null){ StringTokenizer st = new StringTokenizer(currentLine); if (st.countTokens() > 1){ lineCount++; }else if (st.countTokens() == 1){ //complain if only one field found throw new HaploViewException("Info file format error on line "+lineCount+ ":\n Info file must be of format: <markername> <markerposition>"); }else{ //skip blank lines continue; } String name = st.nextToken(); String l = st.nextToken(); String extra = null; if (st.hasMoreTokens()) extra = st.nextToken(); long loc; try{ loc = Long.parseLong(l); }catch (NumberFormatException nfe){ throw new HaploViewException("Info file format error on line "+lineCount+ ":\n\"" + l + "\" should be of type long." + "\n Info file must be of format: <markername> <markerposition>"); } //basically if anyone is crazy enough to load a dataset, then go back and load //an out-of-order info file we tell them to bugger off and start over. if (loc < prevloc && Chromosome.markers != null){ throw new HaploViewException("Info file out of order with preloaded dataset:\n"+ name + "\nPlease reload data file and info file together."); } prevloc = loc; if (nameSearch.contains(name)){ dupCheck.add(name); } names.add(name); nameSearch.add(name); positions.add(l); extras.add(extra); } if (lineCount > Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too many\nmarkers in info file compared to data file.")); } if (lineCount < Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too few\nmarkers in info file compared to data file.")); } infoKnown=true; } if (hapmapGoodies != null){ //we know some stuff from the hapmap so we'll add it here for (int x=0; x < hapmapGoodies.length; x++){ if (nameSearch.contains(hapmapGoodies[x][0])){ dupCheck.add(hapmapGoodies[x][0]); } names.add(hapmapGoodies[x][0]); nameSearch.add(hapmapGoodies[x][0]); positions.add(hapmapGoodies[x][1]); extras.add(null); } infoKnown = true; } if(dupCheck.size() > 0) { int nameCount = names.size(); Hashtable dupCounts = new Hashtable(); for(int i=0;i<nameCount;i++) { if(dupCheck.contains(names.get(i))){ String n = (String) names.get(i); if(dupCounts.containsKey(n)){ int numDups = ((Integer) dupCounts.get(n)).intValue(); String newName = n + "." + numDups; while (nameSearch.contains(newName)){ numDups++; newName = n + "." + numDups; } names.setElementAt(newName,i); nameSearch.add(newName); dupCounts.put(n,new Integer(numDups)) ; }else { //we leave the first instance with its original name dupCounts.put(n,new Integer(1)); } dupNames = true; } } } //sort the markers int numLines = names.size(); class SortingHelper implements Comparable{ long pos; int orderInFile; public SortingHelper(long pos, int order){ this.pos = pos; this.orderInFile = order; } public int compareTo(Object o) { SortingHelper sh = (SortingHelper)o; if (sh.pos > pos){ return -1; }else if (sh.pos < pos){ return 1; }else{ return 0; } } } boolean needSort = false; Vector sortHelpers = new Vector(); for (int k = 0; k < (numLines); k++){ sortHelpers.add(new SortingHelper(Long.parseLong((String)positions.get(k)),k)); } //loop through and check if any markers are out of order for (int k = 1; k < (numLines); k++){ if(((SortingHelper)sortHelpers.get(k)).compareTo(sortHelpers.get(k-1)) < 0) { needSort = true; break; } } //if any were out of order, then we need to put them in order if(needSort){ //sort the positions Collections.sort(sortHelpers); Vector newNames = new Vector(); Vector newExtras = new Vector(); Vector newPositions = new Vector(); int[] realPos = new int[numLines]; //reorder the vectors names and extras so that they have the same order as the sorted markers for (int i = 0; i < sortHelpers.size(); i++){ realPos[i] = ((SortingHelper)sortHelpers.get(i)).orderInFile; newNames.add(names.get(realPos[i])); newPositions.add(positions.get(realPos[i])); newExtras.add(extras.get(realPos[i])); } names = newNames; extras = newExtras; positions = newPositions; byte[] tempGenotype = new byte[sortHelpers.size()]; //now we reorder all the individuals genotypes according to the sorted marker order for(int j=0;j<chromosomes.size();j++){ Chromosome tempChrom = (Chromosome)chromosomes.elementAt(j); for(int i =0;i<sortHelpers.size();i++){ tempGenotype[i] = tempChrom.getUnfilteredGenotype(realPos[i]); } for(int i=0;i<sortHelpers.size();i++){ tempChrom.setGenotype(tempGenotype[i],i); } } //sort pedfile objects //todo: this should really be done before pedfile is subjected to any processing. //todo: that would require altering some order of operations in dealing with inputs //todo: this will fry an out-of-order haps file...grr Vector unsortedRes = pedFile.getResults(); Vector sortedRes = new Vector(); for (int i = 0; i < realPos.length; i++){ sortedRes.add(unsortedRes.elementAt(realPos[i])); } pedFile.setResults(sortedRes); Vector o = pedFile.getAllIndividuals(); for (int i = 0; i < o.size(); i++){ Individual ind = (Individual) o.get(i); byte[] sortedMarkersa = new byte[ind.getNumMarkers()]; byte[] sortedMarkersb = new byte[ind.getNumMarkers()]; boolean[] unsortedZeroed = ind.getZeroedArray(); boolean[] sortedZeroed = new boolean[unsortedMarkers.size()]; Vector sortedMarkers = new Vector(); for (int j = 0; j < unsortedMarkers.size(); j++){ sortedMarkers.add(unsortedMarkers.get(realPos[j])); sortedZeroed[j] = unsortedZeroed[realPos[j]]; } ind.setMarkers(new Vector(sortedMarkers)); ind.setZeroedArray(sortedZeroed); } } }catch (HaploViewException e){ throw(e); }finally{ double numChroms = chromosomes.size(); Vector markerInfo = new Vector(); double[] numBadGenotypes = new double[Chromosome.getUnfilteredSize()]; percentBadGenotypes = new double[Chromosome.getUnfilteredSize()]; Vector results = null; if (pedFile != null){ results = pedFile.getResults(); } long prevPosition = Long.MIN_VALUE; SNP prevMarker = null; MarkerResult pmr = null; for (int i = 0; i < Chromosome.getUnfilteredSize(); i++){ MarkerResult mr = null; if (results != null){ mr = (MarkerResult)results.elementAt(i); } //to compute minor/major alleles, browse chrom list and count instances of each allele byte a1 = 0; byte a2 = 0; double numa1 = 0; double numa2 = 0; for (int j = 0; j < chromosomes.size(); j++){ //if there is a data point for this marker on this chromosome byte thisAllele = ((Chromosome)chromosomes.elementAt(j)).getUnfilteredGenotype(i); if (!(thisAllele == 0)){ if (thisAllele >= 5){ numa1+=0.5; numa2+=0.5; if (thisAllele < 9){ if (a1==0){ a1 = (byte)(thisAllele-4); }else if (a2 == 0){ if (!(thisAllele-4 == a1)){ a2 = (byte)(thisAllele-4); } } } }else if (a1 == 0){ a1 = thisAllele; numa1++; }else if (thisAllele == a1){ numa1++; }else{ numa2++; a2 = thisAllele; } } else { numBadGenotypes[i]++; } } if (numa2 > numa1){ byte temp = a1; double tempnum = numa1; numa1 = numa2; a1 = a2; numa2 = tempnum; a2 = temp; } double maf; if (mr != null){ maf = Util.roundDouble(mr.getMAF(),3); }else{ maf = Util.roundDouble((numa2/(numa1+numa2)),3); } if (infoKnown){ long pos = Long.parseLong((String)positions.elementAt(i)); SNP thisMarker = (new SNP((String)names.elementAt(i), pos, maf, a1, a2, (String)extras.elementAt(i))); markerInfo.add(thisMarker); if (mr != null){ double genoPC = mr.getGenoPercent(); //check to make sure adjacent SNPs do not have identical positions if (prevPosition != Long.MIN_VALUE){ //only do this for markers 2..N, since we're comparing to the previous location if (pos == prevPosition){ dupsToBeFlagged = true; if (genoPC >= pmr.getGenoPercent()){ //use this one because it has more genotypes thisMarker.setDup(1); prevMarker.setDup(2); }else{ //use the other one because it has more genotypes thisMarker.setDup(2); prevMarker.setDup(1); } } } prevPosition = pos; prevMarker = thisMarker; pmr = mr; } }else{ markerInfo.add(new SNP("Marker " + String.valueOf(i+1), (i*4000), maf,a1,a2)); } percentBadGenotypes[i] = numBadGenotypes[i]/numChroms; } Chromosome.markers = markerInfo; } }

1,110,806

void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist is //used to determine beyond what distance comparisons will not be //made. if the infile param is null, loads up "dummy info" for //situation where no info file exists //An optional third column is supported which is designed to hold //association study data. If there is a third column there will be //a visual indicator in the D' display that there is additional data //and the detailed data can be viewed with a mouse press. Vector names = new Vector(); HashSet nameSearch = new HashSet(); HashSet dupCheck = new HashSet(); Vector positions = new Vector(); Vector extras = new Vector(); dupsToBeFlagged = false; dupNames = false; try{ if (infile != null){ if (infile.length() < 1){ throw new HaploViewException("Info file is empty or does not exist: " + infile.getName()); } String currentLine; long prevloc = -1000000000; //read the input file: BufferedReader in = new BufferedReader(new FileReader(infile)); int lineCount = 0; while ((currentLine = in.readLine()) != null){ StringTokenizer st = new StringTokenizer(currentLine); if (st.countTokens() > 1){ lineCount++; }else if (st.countTokens() == 1){ //complain if only one field found throw new HaploViewException("Info file format error on line "+lineCount+ ":\n Info file must be of format: <markername> <markerposition>"); }else{ //skip blank lines continue; } String name = st.nextToken(); String l = st.nextToken(); String extra = null; if (st.hasMoreTokens()) extra = st.nextToken(); long loc; try{ loc = Long.parseLong(l); }catch (NumberFormatException nfe){ throw new HaploViewException("Info file format error on line "+lineCount+ ":\n\"" + l + "\" should be of type long." + "\n Info file must be of format: <markername> <markerposition>"); } //basically if anyone is crazy enough to load a dataset, then go back and load //an out-of-order info file we tell them to bugger off and start over. if (loc < prevloc && Chromosome.markers != null){ throw new HaploViewException("Info file out of order with preloaded dataset:\n"+ name + "\nPlease reload data file and info file together."); } prevloc = loc; if (nameSearch.contains(name)){ dupCheck.add(name); } names.add(name); nameSearch.add(name); positions.add(l); extras.add(extra); } if (lineCount > Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too many\nmarkers in info file compared to data file.")); } if (lineCount < Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too few\nmarkers in info file compared to data file.")); } infoKnown=true; } if (hapmapGoodies != null){ //we know some stuff from the hapmap so we'll add it here for (int x=0; x < hapmapGoodies.length; x++){ if (nameSearch.contains(hapmapGoodies[x][0])){ dupCheck.add(hapmapGoodies[x][0]); } names.add(hapmapGoodies[x][0]); nameSearch.add(hapmapGoodies[x][0]); positions.add(hapmapGoodies[x][1]); extras.add(null); } infoKnown = true; } if(dupCheck.size() > 0) { int nameCount = names.size(); Hashtable dupCounts = new Hashtable(); for(int i=0;i<nameCount;i++) { if(dupCheck.contains(names.get(i))){ String n = (String) names.get(i); if(dupCounts.containsKey(n)){ int numDups = ((Integer) dupCounts.get(n)).intValue(); String newName = n + "." + numDups; while (nameSearch.contains(newName)){ numDups++; newName = n + "." + numDups; } names.setElementAt(newName,i); nameSearch.add(newName); dupCounts.put(n,new Integer(numDups)) ; }else { //we leave the first instance with its original name dupCounts.put(n,new Integer(1)); } dupNames = true; } } } //sort the markers int numLines = names.size(); class SortingHelper implements Comparable{ long pos; int orderInFile; public SortingHelper(long pos, int order){ this.pos = pos; this.orderInFile = order; } public int compareTo(Object o) { SortingHelper sh = (SortingHelper)o; if (sh.pos > pos){ return -1; }else if (sh.pos < pos){ return 1; }else{ return 0; } } } boolean needSort = false; Vector sortHelpers = new Vector(); for (int k = 0; k < (numLines); k++){ sortHelpers.add(new SortingHelper(Long.parseLong((String)positions.get(k)),k)); } //loop through and check if any markers are out of order for (int k = 1; k < (numLines); k++){ if(((SortingHelper)sortHelpers.get(k)).compareTo(sortHelpers.get(k-1)) < 0) { needSort = true; break; } } //if any were out of order, then we need to put them in order if(needSort){ //sort the positions Collections.sort(sortHelpers); Vector newNames = new Vector(); Vector newExtras = new Vector(); Vector newPositions = new Vector(); int[] realPos = new int[numLines]; //reorder the vectors names and extras so that they have the same order as the sorted markers for (int i = 0; i < sortHelpers.size(); i++){ realPos[i] = ((SortingHelper)sortHelpers.get(i)).orderInFile; newNames.add(names.get(realPos[i])); newPositions.add(positions.get(realPos[i])); newExtras.add(extras.get(realPos[i])); } names = newNames; extras = newExtras; positions = newPositions; byte[] tempGenotype = new byte[sortHelpers.size()]; //now we reorder all the individuals genotypes according to the sorted marker order for(int j=0;j<chromosomes.size();j++){ Chromosome tempChrom = (Chromosome)chromosomes.elementAt(j); for(int i =0;i<sortHelpers.size();i++){ tempGenotype[i] = tempChrom.getUnfilteredGenotype(realPos[i]); } for(int i=0;i<sortHelpers.size();i++){ tempChrom.setGenotype(tempGenotype[i],i); } } //sort pedfile objects //todo: this should really be done before pedfile is subjected to any processing. //todo: that would require altering some order of operations in dealing with inputs //todo: this will fry an out-of-order haps file...grr Vector unsortedRes = pedFile.getResults(); Vector sortedRes = new Vector(); for (int i = 0; i < realPos.length; i++){ sortedRes.add(unsortedRes.elementAt(realPos[i])); } pedFile.setResults(sortedRes); Vector o = pedFile.getAllIndividuals(); for (int i = 0; i < o.size(); i++){ Individual ind = (Individual) o.get(i); Vector unsortedMarkers = ind.getMarkers(); boolean[] unsortedZeroed = ind.getZeroedArray(); boolean[] sortedZeroed = new boolean[unsortedMarkers.size()]; Vector sortedMarkers = new Vector(); for (int j = 0; j < unsortedMarkers.size(); j++){ sortedMarkers.add(unsortedMarkers.get(realPos[j])); sortedZeroed[j] = unsortedZeroed[realPos[j]]; } ind.setMarkers(new Vector(sortedMarkers)); ind.setZeroedArray(sortedZeroed); } } }catch (HaploViewException e){ throw(e); }finally{ double numChroms = chromosomes.size(); Vector markerInfo = new Vector(); double[] numBadGenotypes = new double[Chromosome.getUnfilteredSize()]; percentBadGenotypes = new double[Chromosome.getUnfilteredSize()]; Vector results = null; if (pedFile != null){ results = pedFile.getResults(); } long prevPosition = Long.MIN_VALUE; SNP prevMarker = null; MarkerResult pmr = null; for (int i = 0; i < Chromosome.getUnfilteredSize(); i++){ MarkerResult mr = null; if (results != null){ mr = (MarkerResult)results.elementAt(i); } //to compute minor/major alleles, browse chrom list and count instances of each allele byte a1 = 0; byte a2 = 0; double numa1 = 0; double numa2 = 0; for (int j = 0; j < chromosomes.size(); j++){ //if there is a data point for this marker on this chromosome byte thisAllele = ((Chromosome)chromosomes.elementAt(j)).getUnfilteredGenotype(i); if (!(thisAllele == 0)){ if (thisAllele >= 5){ numa1+=0.5; numa2+=0.5; if (thisAllele < 9){ if (a1==0){ a1 = (byte)(thisAllele-4); }else if (a2 == 0){ if (!(thisAllele-4 == a1)){ a2 = (byte)(thisAllele-4); } } } }else if (a1 == 0){ a1 = thisAllele; numa1++; }else if (thisAllele == a1){ numa1++; }else{ numa2++; a2 = thisAllele; } } else { numBadGenotypes[i]++; } } if (numa2 > numa1){ byte temp = a1; double tempnum = numa1; numa1 = numa2; a1 = a2; numa2 = tempnum; a2 = temp; } double maf; if (mr != null){ maf = Util.roundDouble(mr.getMAF(),3); }else{ maf = Util.roundDouble((numa2/(numa1+numa2)),3); } if (infoKnown){ long pos = Long.parseLong((String)positions.elementAt(i)); SNP thisMarker = (new SNP((String)names.elementAt(i), pos, maf, a1, a2, (String)extras.elementAt(i))); markerInfo.add(thisMarker); if (mr != null){ double genoPC = mr.getGenoPercent(); //check to make sure adjacent SNPs do not have identical positions if (prevPosition != Long.MIN_VALUE){ //only do this for markers 2..N, since we're comparing to the previous location if (pos == prevPosition){ dupsToBeFlagged = true; if (genoPC >= pmr.getGenoPercent()){ //use this one because it has more genotypes thisMarker.setDup(1); prevMarker.setDup(2); }else{ //use the other one because it has more genotypes thisMarker.setDup(2); prevMarker.setDup(1); } } } prevPosition = pos; prevMarker = thisMarker; pmr = mr; } }else{ markerInfo.add(new SNP("Marker " + String.valueOf(i+1), (i*4000), maf,a1,a2)); } percentBadGenotypes[i] = numBadGenotypes[i]/numChroms; } Chromosome.markers = markerInfo; } }

1,110,807

void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist is //used to determine beyond what distance comparisons will not be //made. if the infile param is null, loads up "dummy info" for //situation where no info file exists //An optional third column is supported which is designed to hold //association study data. If there is a third column there will be //a visual indicator in the D' display that there is additional data //and the detailed data can be viewed with a mouse press. Vector names = new Vector(); HashSet nameSearch = new HashSet(); HashSet dupCheck = new HashSet(); Vector positions = new Vector(); Vector extras = new Vector(); dupsToBeFlagged = false; dupNames = false; try{ if (infile != null){ if (infile.length() < 1){ throw new HaploViewException("Info file is empty or does not exist: " + infile.getName()); } String currentLine; long prevloc = -1000000000; //read the input file: BufferedReader in = new BufferedReader(new FileReader(infile)); int lineCount = 0; while ((currentLine = in.readLine()) != null){ StringTokenizer st = new StringTokenizer(currentLine); if (st.countTokens() > 1){ lineCount++; }else if (st.countTokens() == 1){ //complain if only one field found throw new HaploViewException("Info file format error on line "+lineCount+ ":\n Info file must be of format: <markername> <markerposition>"); }else{ //skip blank lines continue; } String name = st.nextToken(); String l = st.nextToken(); String extra = null; if (st.hasMoreTokens()) extra = st.nextToken(); long loc; try{ loc = Long.parseLong(l); }catch (NumberFormatException nfe){ throw new HaploViewException("Info file format error on line "+lineCount+ ":\n\"" + l + "\" should be of type long." + "\n Info file must be of format: <markername> <markerposition>"); } //basically if anyone is crazy enough to load a dataset, then go back and load //an out-of-order info file we tell them to bugger off and start over. if (loc < prevloc && Chromosome.markers != null){ throw new HaploViewException("Info file out of order with preloaded dataset:\n"+ name + "\nPlease reload data file and info file together."); } prevloc = loc; if (nameSearch.contains(name)){ dupCheck.add(name); } names.add(name); nameSearch.add(name); positions.add(l); extras.add(extra); } if (lineCount > Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too many\nmarkers in info file compared to data file.")); } if (lineCount < Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too few\nmarkers in info file compared to data file.")); } infoKnown=true; } if (hapmapGoodies != null){ //we know some stuff from the hapmap so we'll add it here for (int x=0; x < hapmapGoodies.length; x++){ if (nameSearch.contains(hapmapGoodies[x][0])){ dupCheck.add(hapmapGoodies[x][0]); } names.add(hapmapGoodies[x][0]); nameSearch.add(hapmapGoodies[x][0]); positions.add(hapmapGoodies[x][1]); extras.add(null); } infoKnown = true; } if(dupCheck.size() > 0) { int nameCount = names.size(); Hashtable dupCounts = new Hashtable(); for(int i=0;i<nameCount;i++) { if(dupCheck.contains(names.get(i))){ String n = (String) names.get(i); if(dupCounts.containsKey(n)){ int numDups = ((Integer) dupCounts.get(n)).intValue(); String newName = n + "." + numDups; while (nameSearch.contains(newName)){ numDups++; newName = n + "." + numDups; } names.setElementAt(newName,i); nameSearch.add(newName); dupCounts.put(n,new Integer(numDups)) ; }else { //we leave the first instance with its original name dupCounts.put(n,new Integer(1)); } dupNames = true; } } } //sort the markers int numLines = names.size(); class SortingHelper implements Comparable{ long pos; int orderInFile; public SortingHelper(long pos, int order){ this.pos = pos; this.orderInFile = order; } public int compareTo(Object o) { SortingHelper sh = (SortingHelper)o; if (sh.pos > pos){ return -1; }else if (sh.pos < pos){ return 1; }else{ return 0; } } } boolean needSort = false; Vector sortHelpers = new Vector(); for (int k = 0; k < (numLines); k++){ sortHelpers.add(new SortingHelper(Long.parseLong((String)positions.get(k)),k)); } //loop through and check if any markers are out of order for (int k = 1; k < (numLines); k++){ if(((SortingHelper)sortHelpers.get(k)).compareTo(sortHelpers.get(k-1)) < 0) { needSort = true; break; } } //if any were out of order, then we need to put them in order if(needSort){ //sort the positions Collections.sort(sortHelpers); Vector newNames = new Vector(); Vector newExtras = new Vector(); Vector newPositions = new Vector(); int[] realPos = new int[numLines]; //reorder the vectors names and extras so that they have the same order as the sorted markers for (int i = 0; i < sortHelpers.size(); i++){ realPos[i] = ((SortingHelper)sortHelpers.get(i)).orderInFile; newNames.add(names.get(realPos[i])); newPositions.add(positions.get(realPos[i])); newExtras.add(extras.get(realPos[i])); } names = newNames; extras = newExtras; positions = newPositions; byte[] tempGenotype = new byte[sortHelpers.size()]; //now we reorder all the individuals genotypes according to the sorted marker order for(int j=0;j<chromosomes.size();j++){ Chromosome tempChrom = (Chromosome)chromosomes.elementAt(j); for(int i =0;i<sortHelpers.size();i++){ tempGenotype[i] = tempChrom.getUnfilteredGenotype(realPos[i]); } for(int i=0;i<sortHelpers.size();i++){ tempChrom.setGenotype(tempGenotype[i],i); } } //sort pedfile objects //todo: this should really be done before pedfile is subjected to any processing. //todo: that would require altering some order of operations in dealing with inputs //todo: this will fry an out-of-order haps file...grr Vector unsortedRes = pedFile.getResults(); Vector sortedRes = new Vector(); for (int i = 0; i < realPos.length; i++){ sortedRes.add(unsortedRes.elementAt(realPos[i])); } pedFile.setResults(sortedRes); Vector o = pedFile.getAllIndividuals(); for (int i = 0; i < o.size(); i++){ Individual ind = (Individual) o.get(i); Vector unsortedMarkers = ind.getMarkers(); boolean[] unsortedZeroed = ind.getZeroedArray(); boolean[] sortedZeroed = new boolean[unsortedMarkers.size()]; Vector sortedMarkers = new Vector(); for (int j = 0; j < unsortedMarkers.size(); j++){ sortedMarkers.add(unsortedMarkers.get(realPos[j])); sortedZeroed[j] = unsortedZeroed[realPos[j]]; } ind.setMarkers(new Vector(sortedMarkers)); ind.setZeroedArray(sortedZeroed); } } }catch (HaploViewException e){ throw(e); }finally{ double numChroms = chromosomes.size(); Vector markerInfo = new Vector(); double[] numBadGenotypes = new double[Chromosome.getUnfilteredSize()]; percentBadGenotypes = new double[Chromosome.getUnfilteredSize()]; Vector results = null; if (pedFile != null){ results = pedFile.getResults(); } long prevPosition = Long.MIN_VALUE; SNP prevMarker = null; MarkerResult pmr = null; for (int i = 0; i < Chromosome.getUnfilteredSize(); i++){ MarkerResult mr = null; if (results != null){ mr = (MarkerResult)results.elementAt(i); } //to compute minor/major alleles, browse chrom list and count instances of each allele byte a1 = 0; byte a2 = 0; double numa1 = 0; double numa2 = 0; for (int j = 0; j < chromosomes.size(); j++){ //if there is a data point for this marker on this chromosome byte thisAllele = ((Chromosome)chromosomes.elementAt(j)).getUnfilteredGenotype(i); if (!(thisAllele == 0)){ if (thisAllele >= 5){ numa1+=0.5; numa2+=0.5; if (thisAllele < 9){ if (a1==0){ a1 = (byte)(thisAllele-4); }else if (a2 == 0){ if (!(thisAllele-4 == a1)){ a2 = (byte)(thisAllele-4); } } } }else if (a1 == 0){ a1 = thisAllele; numa1++; }else if (thisAllele == a1){ numa1++; }else{ numa2++; a2 = thisAllele; } } else { numBadGenotypes[i]++; } } if (numa2 > numa1){ byte temp = a1; double tempnum = numa1; numa1 = numa2; a1 = a2; numa2 = tempnum; a2 = temp; } double maf; if (mr != null){ maf = Util.roundDouble(mr.getMAF(),3); }else{ maf = Util.roundDouble((numa2/(numa1+numa2)),3); } if (infoKnown){ long pos = Long.parseLong((String)positions.elementAt(i)); SNP thisMarker = (new SNP((String)names.elementAt(i), pos, maf, a1, a2, (String)extras.elementAt(i))); markerInfo.add(thisMarker); if (mr != null){ double genoPC = mr.getGenoPercent(); //check to make sure adjacent SNPs do not have identical positions if (prevPosition != Long.MIN_VALUE){ //only do this for markers 2..N, since we're comparing to the previous location if (pos == prevPosition){ dupsToBeFlagged = true; if (genoPC >= pmr.getGenoPercent()){ //use this one because it has more genotypes thisMarker.setDup(1); prevMarker.setDup(2); }else{ //use the other one because it has more genotypes thisMarker.setDup(2); prevMarker.setDup(1); } } } prevPosition = pos; prevMarker = thisMarker; pmr = mr; } }else{ markerInfo.add(new SNP("Marker " + String.valueOf(i+1), (i*4000), maf,a1,a2)); } percentBadGenotypes[i] = numBadGenotypes[i]/numChroms; } Chromosome.markers = markerInfo; } }

void prepareMarkerInput(File infile, String[][] hapmapGoodies) throws IOException, HaploViewException{ //this method is called to gather data about the markers used. //It is assumed that the input file is two columns, the first being //the name and the second the absolute position. the maxdist is //used to determine beyond what distance comparisons will not be //made. if the infile param is null, loads up "dummy info" for //situation where no info file exists //An optional third column is supported which is designed to hold //association study data. If there is a third column there will be //a visual indicator in the D' display that there is additional data //and the detailed data can be viewed with a mouse press. Vector names = new Vector(); HashSet nameSearch = new HashSet(); HashSet dupCheck = new HashSet(); Vector positions = new Vector(); Vector extras = new Vector(); dupsToBeFlagged = false; dupNames = false; try{ if (infile != null){ if (infile.length() < 1){ throw new HaploViewException("Info file is empty or does not exist: " + infile.getName()); } String currentLine; long prevloc = -1000000000; //read the input file: BufferedReader in = new BufferedReader(new FileReader(infile)); int lineCount = 0; while ((currentLine = in.readLine()) != null){ StringTokenizer st = new StringTokenizer(currentLine); if (st.countTokens() > 1){ lineCount++; }else if (st.countTokens() == 1){ //complain if only one field found throw new HaploViewException("Info file format error on line "+lineCount+ ":\n Info file must be of format: <markername> <markerposition>"); }else{ //skip blank lines continue; } String name = st.nextToken(); String l = st.nextToken(); String extra = null; if (st.hasMoreTokens()) extra = st.nextToken(); long loc; try{ loc = Long.parseLong(l); }catch (NumberFormatException nfe){ throw new HaploViewException("Info file format error on line "+lineCount+ ":\n\"" + l + "\" should be of type long." + "\n Info file must be of format: <markername> <markerposition>"); } //basically if anyone is crazy enough to load a dataset, then go back and load //an out-of-order info file we tell them to bugger off and start over. if (loc < prevloc && Chromosome.markers != null){ throw new HaploViewException("Info file out of order with preloaded dataset:\n"+ name + "\nPlease reload data file and info file together."); } prevloc = loc; if (nameSearch.contains(name)){ dupCheck.add(name); } names.add(name); nameSearch.add(name); positions.add(l); extras.add(extra); } if (lineCount > Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too many\nmarkers in info file compared to data file.")); } if (lineCount < Chromosome.getUnfilteredSize()){ throw(new HaploViewException("Info file error:\nMarker number mismatch: too few\nmarkers in info file compared to data file.")); } infoKnown=true; } if (hapmapGoodies != null){ //we know some stuff from the hapmap so we'll add it here for (int x=0; x < hapmapGoodies.length; x++){ if (nameSearch.contains(hapmapGoodies[x][0])){ dupCheck.add(hapmapGoodies[x][0]); } names.add(hapmapGoodies[x][0]); nameSearch.add(hapmapGoodies[x][0]); positions.add(hapmapGoodies[x][1]); extras.add(null); } infoKnown = true; } if(dupCheck.size() > 0) { int nameCount = names.size(); Hashtable dupCounts = new Hashtable(); for(int i=0;i<nameCount;i++) { if(dupCheck.contains(names.get(i))){ String n = (String) names.get(i); if(dupCounts.containsKey(n)){ int numDups = ((Integer) dupCounts.get(n)).intValue(); String newName = n + "." + numDups; while (nameSearch.contains(newName)){ numDups++; newName = n + "." + numDups; } names.setElementAt(newName,i); nameSearch.add(newName); dupCounts.put(n,new Integer(numDups)) ; }else { //we leave the first instance with its original name dupCounts.put(n,new Integer(1)); } dupNames = true; } } } //sort the markers int numLines = names.size(); class SortingHelper implements Comparable{ long pos; int orderInFile; public SortingHelper(long pos, int order){ this.pos = pos; this.orderInFile = order; } public int compareTo(Object o) { SortingHelper sh = (SortingHelper)o; if (sh.pos > pos){ return -1; }else if (sh.pos < pos){ return 1; }else{ return 0; } } } boolean needSort = false; Vector sortHelpers = new Vector(); for (int k = 0; k < (numLines); k++){ sortHelpers.add(new SortingHelper(Long.parseLong((String)positions.get(k)),k)); } //loop through and check if any markers are out of order for (int k = 1; k < (numLines); k++){ if(((SortingHelper)sortHelpers.get(k)).compareTo(sortHelpers.get(k-1)) < 0) { needSort = true; break; } } //if any were out of order, then we need to put them in order if(needSort){ //sort the positions Collections.sort(sortHelpers); Vector newNames = new Vector(); Vector newExtras = new Vector(); Vector newPositions = new Vector(); int[] realPos = new int[numLines]; //reorder the vectors names and extras so that they have the same order as the sorted markers for (int i = 0; i < sortHelpers.size(); i++){ realPos[i] = ((SortingHelper)sortHelpers.get(i)).orderInFile; newNames.add(names.get(realPos[i])); newPositions.add(positions.get(realPos[i])); newExtras.add(extras.get(realPos[i])); } names = newNames; extras = newExtras; positions = newPositions; byte[] tempGenotype = new byte[sortHelpers.size()]; //now we reorder all the individuals genotypes according to the sorted marker order for(int j=0;j<chromosomes.size();j++){ Chromosome tempChrom = (Chromosome)chromosomes.elementAt(j); for(int i =0;i<sortHelpers.size();i++){ tempGenotype[i] = tempChrom.getUnfilteredGenotype(realPos[i]); } for(int i=0;i<sortHelpers.size();i++){ tempChrom.setGenotype(tempGenotype[i],i); } } //sort pedfile objects //todo: this should really be done before pedfile is subjected to any processing. //todo: that would require altering some order of operations in dealing with inputs //todo: this will fry an out-of-order haps file...grr Vector unsortedRes = pedFile.getResults(); Vector sortedRes = new Vector(); for (int i = 0; i < realPos.length; i++){ sortedRes.add(unsortedRes.elementAt(realPos[i])); } pedFile.setResults(sortedRes); Vector o = pedFile.getAllIndividuals(); for (int i = 0; i < o.size(); i++){ Individual ind = (Individual) o.get(i); Vector unsortedMarkers = ind.getMarkers(); boolean[] unsortedZeroed = ind.getZeroedArray(); boolean[] sortedZeroed = new boolean[unsortedMarkers.size()]; Vector sortedMarkers = new Vector(); for (int j = 0; j < unsortedMarkers.size(); j++){ sortedMarkers.add(unsortedMarkers.get(realPos[j])); sortedZeroed[j] = unsortedZeroed[realPos[j]]; } ind.setMarkers(sortedMarkersa, sortedMarkersb); ind.setZeroedArray(sortedZeroed); } } }catch (HaploViewException e){ throw(e); }finally{ double numChroms = chromosomes.size(); Vector markerInfo = new Vector(); double[] numBadGenotypes = new double[Chromosome.getUnfilteredSize()]; percentBadGenotypes = new double[Chromosome.getUnfilteredSize()]; Vector results = null; if (pedFile != null){ results = pedFile.getResults(); } long prevPosition = Long.MIN_VALUE; SNP prevMarker = null; MarkerResult pmr = null; for (int i = 0; i < Chromosome.getUnfilteredSize(); i++){ MarkerResult mr = null; if (results != null){ mr = (MarkerResult)results.elementAt(i); } //to compute minor/major alleles, browse chrom list and count instances of each allele byte a1 = 0; byte a2 = 0; double numa1 = 0; double numa2 = 0; for (int j = 0; j < chromosomes.size(); j++){ //if there is a data point for this marker on this chromosome byte thisAllele = ((Chromosome)chromosomes.elementAt(j)).getUnfilteredGenotype(i); if (!(thisAllele == 0)){ if (thisAllele >= 5){ numa1+=0.5; numa2+=0.5; if (thisAllele < 9){ if (a1==0){ a1 = (byte)(thisAllele-4); }else if (a2 == 0){ if (!(thisAllele-4 == a1)){ a2 = (byte)(thisAllele-4); } } } }else if (a1 == 0){ a1 = thisAllele; numa1++; }else if (thisAllele == a1){ numa1++; }else{ numa2++; a2 = thisAllele; } } else { numBadGenotypes[i]++; } } if (numa2 > numa1){ byte temp = a1; double tempnum = numa1; numa1 = numa2; a1 = a2; numa2 = tempnum; a2 = temp; } double maf; if (mr != null){ maf = Util.roundDouble(mr.getMAF(),3); }else{ maf = Util.roundDouble((numa2/(numa1+numa2)),3); } if (infoKnown){ long pos = Long.parseLong((String)positions.elementAt(i)); SNP thisMarker = (new SNP((String)names.elementAt(i), pos, maf, a1, a2, (String)extras.elementAt(i))); markerInfo.add(thisMarker); if (mr != null){ double genoPC = mr.getGenoPercent(); //check to make sure adjacent SNPs do not have identical positions if (prevPosition != Long.MIN_VALUE){ //only do this for markers 2..N, since we're comparing to the previous location if (pos == prevPosition){ dupsToBeFlagged = true; if (genoPC >= pmr.getGenoPercent()){ //use this one because it has more genotypes thisMarker.setDup(1); prevMarker.setDup(2); }else{ //use the other one because it has more genotypes thisMarker.setDup(2); prevMarker.setDup(1); } } } prevPosition = pos; prevMarker = thisMarker; pmr = mr; } }else{ markerInfo.add(new SNP("Marker " + String.valueOf(i+1), (i*4000), maf,a1,a2)); } percentBadGenotypes[i] = numBadGenotypes[i]/numChroms; } Chromosome.markers = markerInfo; } }

1,110,808

public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } // lets create a child context final JellyContext newContext = new JellyContext(context); Thread thread = new Thread( new Runnable() { public void run() { try { getBody().run(newContext, xmlOutput); xmlOutput.close(); } catch (Exception e) { e.printStackTrace(); } } } ); if ( name != null ) { thread.setName( name ); } thread.start(); }

public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } // lets create a child context final JellyContext newContext = context.newJellyContext(); Thread thread = new Thread( new Runnable() { public void run() { try { getBody().run(newContext, xmlOutput); xmlOutput.close(); } catch (Exception e) { e.printStackTrace(); } } } ); if ( name != null ) { thread.setName( name ); } thread.start(); }

1,110,813

public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } // lets create a child context final JellyContext newContext = new JellyContext(context); Thread thread = new Thread( new Runnable() { public void run() { try { getBody().run(newContext, xmlOutput); xmlOutput.close(); } catch (Exception e) { e.printStackTrace(); } } } ); if ( name != null ) { thread.setName( name ); } thread.start(); }

public void doTag(final XMLOutput output) throws Exception { if ( xmlOutput == null ) { // lets default to system.out xmlOutput = XMLOutput.createXMLOutput( System.out ); } // lets create a child context final JellyContext newContext = new JellyContext(context); Thread thread = new Thread( new Runnable() { public void run() { try { getBody().run(newContext, xmlOutput); if (closeOutput) { xmlOutput.close(); } else { xmlOutput.flush(); } } catch (Exception e) { e.printStackTrace(); } } } ); if ( name != null ) { thread.setName( name ); } thread.start(); }

1,110,814

public void run() { try { getBody().run(newContext, xmlOutput); xmlOutput.close(); } catch (Exception e) { e.printStackTrace(); } }

public void run() { try { getBody().run(newContext, xmlOutput); if (closeOutput) { xmlOutput.close(); } else { xmlOutput.flush(); } } catch (Exception e) { e.printStackTrace(); } }

1,110,815

public void upgradeDatabase() { fireStatusChangeEvent( new SchemaUpdateEvent( PHASE_ALTERING_SCHEMA, 0 ) ); int oldVersion = db.getSchemaVersion(); // Find needed information fr DdlUtils ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcConnectionDescriptor connDesc = cr.getDescriptor( connKey ); DataSource src = connDesc.getDataSource(); String jdbcDriver = connDesc.getDriver(); Platform platform = null; if ( jdbcDriver.equals( "org.apache.derby.jdbc.EmbeddedDriver" ) ) { platform = PlatformFactory.createNewPlatformInstance( "derby" ); } else if ( jdbcDriver.equals( "com.mysql.jdbc.Driver" ) ){ platform = PlatformFactory.createNewPlatformInstance( "mysql" ); } platform.getPlatformInfo().setDelimiterToken( "" ); // Get the database schema XML file InputStream schemaIS = getClass().getClassLoader().getResourceAsStream( "photovault_schema.xml" ); Database dbModel = new DatabaseIO().read( new InputStreamReader( schemaIS ) ); // Alter tables to match corrent schema PersistenceBroker broker = PersistenceBrokerFactory.createPersistenceBroker( connKey ); broker.beginTransaction(); try { Connection con = broker.serviceConnectionManager().getConnection(); /* TODO: Derby alter table statements created by DdlUtils have wrong syntax. Luckily we do not need to do such modifications for now. There is error report for DdlUtils (http://issues.apache.org/jira/browse/DDLUTILS-53), after it has been corrected the alterColumns flag should be set to true. */ System.out.println( platform.getAlterTablesSql( con, dbModel, false, true, true ) ); platform.alterTables( con, dbModel, false, true, true ); } catch (DynaSqlException ex) { ex.printStackTrace(); } catch ( LookupException ex ) { ex.printStackTrace(); } broker.commitTransaction(); broker.close(); if ( oldVersion < 4 ) { // In older version hashcolumn was not included in schema so we must fill it. createHashes(); } DbInfo info = DbInfo.getDbInfo(); info.setVersion( db.CURRENT_SCHEMA_VERSION ); fireStatusChangeEvent( new SchemaUpdateEvent( PHASE_COMPLETE, 100 ) ); }

public void upgradeDatabase() { fireStatusChangeEvent( new SchemaUpdateEvent( PHASE_ALTERING_SCHEMA, 0 ) ); int oldVersion = db.getSchemaVersion(); // Find needed information fr DdlUtils ConnectionRepository cr = MetadataManager.getInstance().connectionRepository(); PBKey connKey = cr.getStandardPBKeyForJcdAlias( "pv" ); JdbcConnectionDescriptor connDesc = cr.getDescriptor( connKey ); String jdbcDriver = connDesc.getDriver(); Platform platform = null; if ( jdbcDriver.equals( "org.apache.derby.jdbc.EmbeddedDriver" ) ) { platform = PlatformFactory.createNewPlatformInstance( "derby" ); } else if ( jdbcDriver.equals( "com.mysql.jdbc.Driver" ) ){ platform = PlatformFactory.createNewPlatformInstance( "mysql" ); } platform.getPlatformInfo().setDelimiterToken( "" ); // Get the database schema XML file InputStream schemaIS = getClass().getClassLoader().getResourceAsStream( "photovault_schema.xml" ); Database dbModel = new DatabaseIO().read( new InputStreamReader( schemaIS ) ); // Alter tables to match corrent schema PersistenceBroker broker = PersistenceBrokerFactory.createPersistenceBroker( connKey ); broker.beginTransaction(); try { Connection con = broker.serviceConnectionManager().getConnection(); /* TODO: Derby alter table statements created by DdlUtils have wrong syntax. Luckily we do not need to do such modifications for now. There is error report for DdlUtils (http://issues.apache.org/jira/browse/DDLUTILS-53), after it has been corrected the alterColumns flag should be set to true. */ System.out.println( platform.getAlterTablesSql( con, dbModel, false, true, true ) ); platform.alterTables( con, dbModel, false, true, true ); } catch (DynaSqlException ex) { ex.printStackTrace(); } catch ( LookupException ex ) { ex.printStackTrace(); } broker.commitTransaction(); broker.close(); if ( oldVersion < 4 ) { // In older version hashcolumn was not included in schema so we must fill it. createHashes(); } DbInfo info = DbInfo.getDbInfo(); info.setVersion( db.CURRENT_SCHEMA_VERSION ); fireStatusChangeEvent( new SchemaUpdateEvent( PHASE_COMPLETE, 100 ) ); }

1,110,818

Haplotype[][] generateHaplotypes(Vector blocks, int hapthresh, boolean crossover) throws HaploViewException{ //TODO: output indiv hap estimates Haplotype[][] results = new Haplotype[blocks.size()][]; //String raw = new String(); //String currentLine; this.totalBlocks = blocks.size(); this.blocksDone = 0; for (int k = 0; k < blocks.size(); k++){ this.blocksDone++; int[] preFiltBlock = (int[])blocks.elementAt(k); int[] theBlock; int[] selectedMarkers = new int[0]; int[] equivClass = new int[0]; if (preFiltBlock.length > 30){ equivClass = new int[preFiltBlock.length]; int classCounter = 0; for (int x = 0; x < preFiltBlock.length; x++){ int marker1 = preFiltBlock[x]; //already been lumped into an equivalency class if (equivClass[x] != 0){ continue; } //start a new equivalency class for this SNP classCounter ++; equivClass[x] = classCounter; for (int y = x+1; y < preFiltBlock.length; y++){ int marker2 = preFiltBlock[y]; if (marker1 > marker2){ int tmp = marker1; marker1 = marker2; marker2 = tmp; } if ( dpTable.getLDStats(marker1,marker2).getRSquared() == 1.0){ //these two SNPs are redundant equivClass[y] = classCounter; } } } //parse equivalency classes selectedMarkers = new int[classCounter]; for (int x = 0; x < selectedMarkers.length; x++){ selectedMarkers[x] = -1; } for (int x = 0; x < classCounter; x++){ double genoPC = 1.0; for (int y = 0; y < equivClass.length; y++){ if (equivClass[y] == x+1){ if (percentBadGenotypes[Chromosome.realIndex[preFiltBlock[y]]] <= genoPC){ selectedMarkers[x] = preFiltBlock[y]; genoPC = percentBadGenotypes[Chromosome.realIndex[preFiltBlock[y]]]; } } } } theBlock = selectedMarkers; }else{ theBlock = preFiltBlock; } //kirby patch EM theEM = new EM(chromosomes,numTrios); theEM.doEM(theBlock); int p = 0; Haplotype[] tempArray = new Haplotype[theEM.numHaplos()]; int[][] returnedHaplos = theEM.getHaplotypes(); double[] returnedFreqs = theEM.getFrequencies(); for (int i = 0; i < theEM.numHaplos(); i++){ int[] genos = new int[returnedHaplos[i].length]; for (int j = 0; j < genos.length; j++){ if (returnedHaplos[i][j] == 1){ genos[j] = Chromosome.getMarker(theBlock[j]).getMajor(); }else{ if (Chromosome.getMarker(theBlock[j]).getMinor() == 0){ genos[j] = 8; }else{ genos[j] = Chromosome.getMarker(theBlock[j]).getMinor(); } } } if (selectedMarkers.length > 0){ //we need to reassemble the haplotypes Hashtable hapsHash = new Hashtable(); //add to hash all the genotypes we phased for (int q = 0; q < genos.length; q++){ hapsHash.put(new Integer(theBlock[q]), new Integer(genos[q])); } //now add all the genotypes we didn't bother phasing, based on //which marker they are identical to for (int q = 0; q < equivClass.length; q++){ int currentClass = equivClass[q]-1; if (selectedMarkers[currentClass] == preFiltBlock[q]){ //we alredy added the phased genotypes above continue; } int indexIntoBlock=0; for (int x = 0; x < theBlock.length; x++){ if (theBlock[x] == selectedMarkers[currentClass]){ indexIntoBlock = x; break; } } //this (somewhat laboriously) reconstructs whether to add the minor or major allele //for markers with MAF close to 0.50 we can't use major/minor alleles to match //'em up 'cause these might change given missing data if (Chromosome.getMarker(selectedMarkers[currentClass]).getMAF() > 0.4){ for (int z = 0; z < chromosomes.size(); z++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(z); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++z); int theGeno = thisChrom.getGenotype(selectedMarkers[currentClass]); int nextGeno = nextChrom.getGenotype(selectedMarkers[currentClass]); if (theGeno == nextGeno && theGeno == genos[indexIntoBlock] && thisChrom.getGenotype(preFiltBlock[q]) != 0){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(thisChrom.getGenotype(preFiltBlock[q]))); } } }else{ if (Chromosome.getMarker(selectedMarkers[currentClass]).getMajor() == genos[indexIntoBlock]){ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMajor())); }else{ hapsHash.put(new Integer(preFiltBlock[q]), new Integer(Chromosome.getMarker(preFiltBlock[q]).getMinor())); } } } genos = new int[preFiltBlock.length]; for (int q = 0; q < preFiltBlock.length; q++){ genos[q] = ((Integer)hapsHash.get(new Integer(preFiltBlock[q]))).intValue(); } } double tempPerc = returnedFreqs[i]; if (tempPerc*100 > hapthresh){ tempArray[p] = new Haplotype(genos, tempPerc, preFiltBlock); p++; } } //make the results array only large enough to hold haps //which pass threshold above results[k] = new Haplotype[p]; for (int z = 0; z < p; z++){ results[k][z] = tempArray[z]; if (Options.getAssocTest() == ASSOC_TRIO){ results[k][z].setTransCount(theEM.getTransCount(z)); results[k][z].setUntransCount(theEM.getUntransCount(z)); }else if (Options.getAssocTest() == ASSOC_CC){ results[k][z].setCaseFreq(theEM.getCaseFreq(z)); results[k][z].setControlFreq(theEM.getControlFreq(z)); } } } if (!crossover){ haplotypes = results; } return results; }

1,110,819

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); } } else { throw new MissingAttributeException("test"); } }

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { try { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); } } catch (BreakException e) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); } } else { throw new MissingAttributeException("test"); } }

1,110,820

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); } } else { throw new MissingAttributeException("test"); } }

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("loop terminated by break: " + e, e); } invokeBody(output); } } else { throw new MissingAttributeException("test"); } }

1,110,821

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } invokeBody(output); } } else { throw new MissingAttributeException("test"); } }

public void doTag(XMLOutput output) throws MissingAttributeException, Exception { if (test != null) { while (test.evaluateAsBoolean(getContext())) { if (log.isDebugEnabled()) { log.debug("evaluated to true! gonna keep on chuggin!"); } } } else { throw new MissingAttributeException("test"); } }

1,110,822

public Relationship(PlayPen pp, SQLRelationship model) throws ArchitectException { this (pp, pp.findTablePane(model.getPkTable()), pp.findTablePane(model.getFkTable())); }

public Relationship(PlayPen pp, SQLRelationship model) throws ArchitectException { this.pp = pp; this.model = model; setPkTable(pp.findTablePane(model.getPkTable())); setFkTable(pp.findTablePane(model.getFkTable())); setup(); }

1,110,823

public void stateChanged(ChangeEvent e) { viewMenuItems[tabs.getSelectedIndex()].setSelected(true); if (checkPanel != null && checkPanel.changed){ window.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); JTable table = checkPanel.getTable(); boolean[] markerResults = new boolean[table.getRowCount()]; for (int i = 0; i < table.getRowCount(); i++){ markerResults[i] = ((Boolean)table.getValueAt(i,7)).booleanValue(); } int count = 0; for (int i = 0; i < Chromosome.getSize(); i++){ if (markerResults[i]){ count++; } } Chromosome.realIndex = new int[count]; int k = 0; for (int i =0; i < Chromosome.getSize(); i++){ if (markerResults[i]){ Chromosome.realIndex[k] = i; k++; } } theData.filteredDPrimeTable = theData.getFilteredTable(); theData.guessBlocks(currentBlockDef); //hack-y way to refresh the image dPrimeDisplay.setVisible(false); dPrimeDisplay.setVisible(true); hapDisplay.theData = theData; try{ hapDisplay.getHaps(); }catch(HaploViewException hv){ JOptionPane.showMessageDialog(window, hv.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } tdtPanel.refreshTable(); //System.out.println(tabs.getComponentAt(VIEW_TDT_NUM)); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); checkPanel.changed=false; } }

1,110,824

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploSingletons = new Vector(); Vector inputHaploTrios = new Vector(); Vector affSingletons = new Vector(); Vector affTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploSingletons (singletons), 2 indicates inputHaploTrios, //3 indicates a person from a broken trio who is treated as a singleton //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= MISSINGLIMIT){ tooManyMissingInASegmentA = true; } if (missingB >= MISSINGLIMIT){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //both parents are good so all 4 chroms are added as a trio whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { //first person good, so he's added as a singleton, other parent is dropped whichVector[i] = 3; whichVector[i+1] =3; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //second person good, so he's added as a singleton, other parent is dropped whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =3; whichVector[i+3]=3; } else { //both people have too much missing data so neither is used whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= MISSINGLIMIT){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] > 0) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(thisChrom.getAffected())); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); affTrios.add(new Integer(thisChrom.getAffected())); }else if (whichVector[i] == 3){ inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(0)); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploSingletons); affTrios.addAll(affSingletons); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); full_em_breakup(input_haplos, block_size, trioCount, affTrios); }

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploSingletons = new Vector(); Vector inputHaploTrios = new Vector(); Vector affSingletons = new Vector(); Vector affTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploSingletons (singletons), 2 indicates inputHaploTrios, //3 indicates a person from a broken trio who is treated as a singleton //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= MISSINGLIMIT){ tooManyMissingInASegmentA = true; } if (missingB >= MISSINGLIMIT){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //both parents are good so all 4 chroms are added as a trio whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { //first person good, so he's added as a singleton, other parent is dropped whichVector[i] = 3; whichVector[i+1] =3; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //second person good, so he's added as a singleton, other parent is dropped whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =3; whichVector[i+3]=3; } else { //both people have too much missing data so neither is used whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= MISSINGLIMIT){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] > 0) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploSingletons.add(thisHap); if(addAff) { affSingletons.add(new Integer(thisChrom.getAffected())); } } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); affTrios.add(new Integer(thisChrom.getAffected())); }else if (whichVector[i] == 3){ inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(0)); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploSingletons); affTrios.addAll(affSingletons); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); full_em_breakup(input_haplos, block_size, trioCount, affTrios); }

1,110,826

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploSingletons = new Vector(); Vector inputHaploTrios = new Vector(); Vector affSingletons = new Vector(); Vector affTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploSingletons (singletons), 2 indicates inputHaploTrios, //3 indicates a person from a broken trio who is treated as a singleton //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= MISSINGLIMIT){ tooManyMissingInASegmentA = true; } if (missingB >= MISSINGLIMIT){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //both parents are good so all 4 chroms are added as a trio whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { //first person good, so he's added as a singleton, other parent is dropped whichVector[i] = 3; whichVector[i+1] =3; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //second person good, so he's added as a singleton, other parent is dropped whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =3; whichVector[i+3]=3; } else { //both people have too much missing data so neither is used whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= MISSINGLIMIT){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] > 0) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(thisChrom.getAffected())); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); affTrios.add(new Integer(thisChrom.getAffected())); }else if (whichVector[i] == 3){ inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(0)); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploSingletons); affTrios.addAll(affSingletons); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); full_em_breakup(input_haplos, block_size, trioCount, affTrios); }

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploSingletons = new Vector(); Vector inputHaploTrios = new Vector(); Vector affSingletons = new Vector(); Vector affTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploSingletons (singletons), 2 indicates inputHaploTrios, //3 indicates a person from a broken trio who is treated as a singleton //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= MISSINGLIMIT){ tooManyMissingInASegmentA = true; } if (missingB >= MISSINGLIMIT){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //both parents are good so all 4 chroms are added as a trio whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { //first person good, so he's added as a singleton, other parent is dropped whichVector[i] = 3; whichVector[i+1] =3; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //second person good, so he's added as a singleton, other parent is dropped whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =3; whichVector[i+3]=3; } else { //both people have too much missing data so neither is used whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= MISSINGLIMIT){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] > 0) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(thisChrom.getAffected())); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); if(addAff) { affTrios.add(new Integer(thisChrom.getAffected())); } }else if (whichVector[i] == 3){ inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(0)); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploSingletons); affTrios.addAll(affSingletons); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); full_em_breakup(input_haplos, block_size, trioCount, affTrios); }

1,110,827

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploSingletons = new Vector(); Vector inputHaploTrios = new Vector(); Vector affSingletons = new Vector(); Vector affTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploSingletons (singletons), 2 indicates inputHaploTrios, //3 indicates a person from a broken trio who is treated as a singleton //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= MISSINGLIMIT){ tooManyMissingInASegmentA = true; } if (missingB >= MISSINGLIMIT){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //both parents are good so all 4 chroms are added as a trio whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { //first person good, so he's added as a singleton, other parent is dropped whichVector[i] = 3; whichVector[i+1] =3; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //second person good, so he's added as a singleton, other parent is dropped whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =3; whichVector[i+3]=3; } else { //both people have too much missing data so neither is used whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= MISSINGLIMIT){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] > 0) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(thisChrom.getAffected())); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); affTrios.add(new Integer(thisChrom.getAffected())); }else if (whichVector[i] == 3){ inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(0)); } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploSingletons); affTrios.addAll(affSingletons); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); full_em_breakup(input_haplos, block_size, trioCount, affTrios); }

public void doEM(int[] theBlock) throws HaploViewException{ //break up large blocks if needed int[] block_size; if (theBlock.length < 9){ block_size = new int[1]; block_size[0] = theBlock.length; } else { //some base-8 arithmetic int ones = theBlock.length%8; int eights = (theBlock.length - ones)/8; if (ones == 0){ block_size = new int[eights]; for (int i = 0; i < eights; i++){ block_size[i]=8; } } else { block_size = new int[eights+1]; for (int i = 0; i < eights-1; i++){ block_size[i]=8; } block_size[eights-1] = (8+ones)/2; block_size[eights] = 8+ones-block_size[eights-1]; } } byte[] thisHap; Vector inputHaploSingletons = new Vector(); Vector inputHaploTrios = new Vector(); Vector affSingletons = new Vector(); Vector affTrios = new Vector(); //whichVector[i] stores a value which indicates which vector chromosome i's genotype should go in //1 indicates inputHaploSingletons (singletons), 2 indicates inputHaploTrios, //3 indicates a person from a broken trio who is treated as a singleton //0 indicates none (too much missing data) int[] whichVector = new int[chromosomes.size()]; for(int i=0;i<numTrios*4; i+=4) { Chromosome parentAFirst = (Chromosome) chromosomes.elementAt(i); Chromosome parentASecond = (Chromosome) chromosomes.elementAt(i+1); Chromosome parentBFirst = (Chromosome) chromosomes.elementAt(i+2); Chromosome parentBSecond = (Chromosome) chromosomes.elementAt(i+3); boolean tooManyMissingInASegmentA = false; boolean tooManyMissingInASegmentB = false; int totalMissingA = 0; int totalMissingB = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missingA = 0; int missingB = 0; for (int j = 0; j < block_size[n]; j++){ byte AFirstGeno = parentAFirst.getGenotype(theBlock[segmentShift+j]); byte ASecondGeno = parentASecond.getGenotype(theBlock[segmentShift+j]); byte BFirstGeno = parentBFirst.getGenotype(theBlock[segmentShift+j]); byte BSecondGeno = parentBSecond.getGenotype(theBlock[segmentShift+j]); if(AFirstGeno == 0 || ASecondGeno == 0) missingA++; if(BFirstGeno == 0 || BSecondGeno == 0) missingB++; } segmentShift += block_size[n]; if (missingA >= MISSINGLIMIT){ tooManyMissingInASegmentA = true; } if (missingB >= MISSINGLIMIT){ tooManyMissingInASegmentB = true; } totalMissingA += missingA; totalMissingB += missingB; } if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3 && !tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //both parents are good so all 4 chroms are added as a trio whichVector[i] = 2; whichVector[i+1] = 2; whichVector[i+2] = 2; whichVector[i+3] = 2; } else if(!tooManyMissingInASegmentA && totalMissingA <= 1+theBlock.length/3) { //first person good, so he's added as a singleton, other parent is dropped whichVector[i] = 3; whichVector[i+1] =3; whichVector[i+2] =0; whichVector[i+3]=0; } else if(!tooManyMissingInASegmentB && totalMissingB <= 1+theBlock.length/3) { //second person good, so he's added as a singleton, other parent is dropped whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =3; whichVector[i+3]=3; } else { //both people have too much missing data so neither is used whichVector[i] = 0; whichVector[i+1] =0; whichVector[i+2] =0; whichVector[i+3]=0; } } for (int i = numTrios*4; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); Chromosome nextChrom = (Chromosome)chromosomes.elementAt(++i); boolean tooManyMissingInASegment = false; int totalMissing = 0; int segmentShift = 0; for (int n = 0; n < block_size.length; n++){ int missing = 0; for (int j = 0; j < block_size[n]; j++){ byte theGeno = thisChrom.getGenotype(theBlock[segmentShift+j]); byte nextGeno = nextChrom.getGenotype(theBlock[segmentShift+j]); if(theGeno == 0 || nextGeno == 0) missing++; } segmentShift += block_size[n]; if (missing >= MISSINGLIMIT){ tooManyMissingInASegment = true; } totalMissing += missing; } //we want to use chromosomes without too many missing genotypes in a given //subsegment (first term) or without too many missing genotypes in the //whole block (second term) if (!tooManyMissingInASegment && totalMissing <= 1+theBlock.length/3){ whichVector[i-1] = 1; whichVector[i] = 1; } } for (int i = 0; i < chromosomes.size(); i++){ Chromosome thisChrom = (Chromosome)chromosomes.elementAt(i); if(whichVector[i] > 0) { thisHap = new byte[theBlock.length]; for (int j = 0; j < theBlock.length; j++){ byte a1 = Chromosome.getMarker(theBlock[j]).getMajor(); byte a2 = Chromosome.getMarker(theBlock[j]).getMinor(); byte theGeno = thisChrom.getGenotype(theBlock[j]); if (theGeno >= 5){ thisHap[j] = 'h'; } else { if (theGeno == a1){ thisHap[j] = '1'; }else if (theGeno == a2){ thisHap[j] = '2'; }else{ thisHap[j] = '0'; } } } if(whichVector[i] == 1) { inputHaploSingletons.add(thisHap); affSingletons.add(new Integer(thisChrom.getAffected())); } else if(whichVector[i] ==2) { inputHaploTrios.add(thisHap); affTrios.add(new Integer(thisChrom.getAffected())); }else if (whichVector[i] == 3){ inputHaploSingletons.add(thisHap); if(addAff) { affSingletons.add(new Integer(0)); } } if(addAff) { addAff = false; } else { addAff =true; } } } int trioCount = inputHaploTrios.size() / 4; inputHaploTrios.addAll(inputHaploSingletons); affTrios.addAll(affSingletons); byte[][] input_haplos = (byte[][])inputHaploTrios.toArray(new byte[0][0]); full_em_breakup(input_haplos, block_size, trioCount, affTrios); }

1,110,828

boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,num_blocks,block_size,hlist,num_hlist); retval=false; for (i=0; i<num_loci; i++) { if (ambighet[this_trio][i] == 0) { //TODO:ask mark if this if statement should break out this way //is this what this method should be doing? if (temp1[i] == temp2[i]) { retval=true; break; } } } return(retval); }

boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,num_blocks,block_size,hlist,num_hlist); retval=true; for (i=0; i<num_loci; i++) { if (ambighet[this_trio][i] == 0) { //TODO:ask mark if this if statement should break out this way //is this what this method should be doing? if (temp1[i] == temp2[i]) { retval=true; break; } } } return(retval); }

1,110,829

boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,num_blocks,block_size,hlist,num_hlist); retval=false; for (i=0; i<num_loci; i++) { if (ambighet[this_trio][i] == 0) { //TODO:ask mark if this if statement should break out this way //is this what this method should be doing? if (temp1[i] == temp2[i]) { retval=true; break; } } } return(retval); }

boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,num_blocks,block_size,hlist,num_hlist); retval=false; for (i=0; i<num_loci; i++) { if (ambighet[this_trio][i] !=0) { //TODO:ask mark if this if statement should break out this way //is this what this method should be doing? if (temp1[i] == temp2[i]) { retval=true; break; } } } return(retval); }

1,110,830

boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,num_blocks,block_size,hlist,num_hlist); retval=false; for (i=0; i<num_loci; i++) { if (ambighet[this_trio][i] == 0) { //TODO:ask mark if this if statement should break out this way //is this what this method should be doing? if (temp1[i] == temp2[i]) { retval=true; break; } } } return(retval); }

boolean kid_consistent(int chap1, int chap2, int num_blocks, int[] block_size, int[][] hlist, int[] num_hlist, int this_trio, int num_loci) { int i, val; boolean retval; int[] temp1 = decode_haplo_str(chap1,num_blocks,block_size,hlist,num_hlist); int[] temp2 = decode_haplo_str(chap2,num_blocks,block_size,hlist,num_hlist); retval=false; for (i=0; i<num_loci; i++) { if (ambighet[this_trio][i] == 0) { //TODO:ask mark if this if statement should break out this way //is this what this method should be doing? if (temp1[i] == temp2[i]) { retval=false; break; } } } return(retval); }

1,110,831

public void runFileTests(HaploData theData, Vector inputSNPResults) throws HaploViewException { Vector res = new Vector(); if(tests == null || theData == null) { return; } Vector blocks = new Vector(); Vector names = new Vector(); for(int i=0;i<tests.size();i++) { //first go through and get all the multimarker tests to package up to hand to theData.generateHaplotypes() AssociationTest currentTest = (AssociationTest) tests.get(i); if(currentTest.getNumMarkers() > 1) { blocks.add(currentTest.getFilteredMarkerArray()); names.add(currentTest.getName()); } } Haplotype[][] blockHaps = theData.generateHaplotypes(blocks, true); Vector blockResults = new AssociationTestSet(blockHaps, names).getResults(); Iterator britr = blockResults.iterator(); for (int i = 0; i < tests.size(); i++){ AssociationTest currentTest = (AssociationTest) tests.get(i); if(currentTest.getNumMarkers() > 1) { //grab the next block result from above //check to see if a specific allele was given HaplotypeAssociationResult har = (HaplotypeAssociationResult) britr.next(); //todo: this is borken. needs count of all other alleles. if (currentTest.getAllele() != null){ boolean foundAllele = false; for (int j = 0; j < har.getAlleleCount(); j++){ if (har.getNumericAlleleName(j).equals(currentTest.getAllele())){ Haplotype[] filtHaps = {har.getHaps()[j]}; res.add(new HaplotypeAssociationResult(filtHaps,0,har.getName())); foundAllele = true; break; } } if (!foundAllele){ throw new HaploViewException(currentTest.getAllele() + ": no such allele for test:\n" + har.getName()); } }else{ res.add(har); } }else if (currentTest.getNumMarkers() == 1){ //grab appropriate single marker result. res.add(inputSNPResults.get(currentTest.getMarkerArray()[0])); } } results = res; }

public void runFileTests(HaploData theData, Vector inputSNPResults) throws HaploViewException { Vector res = new Vector(); if(tests == null || theData == null) { return; } Vector blocks = new Vector(); Vector names = new Vector(); for(int i=0;i<tests.size();i++) { //first go through and get all the multimarker tests to package up to hand to theData.generateHaplotypes() AssociationTest currentTest = (AssociationTest) tests.get(i); if(currentTest.getNumMarkers() > 1) { blocks.add(currentTest.getFilteredMarkerArray()); names.add(currentTest.getName()); } } Haplotype[][] blockHaps = theData.generateHaplotypes(blocks, true); Vector blockResults = new AssociationTestSet(blockHaps, names, alleles).getResults(); Iterator britr = blockResults.iterator(); for (int i = 0; i < tests.size(); i++){ AssociationTest currentTest = (AssociationTest) tests.get(i); if(currentTest.getNumMarkers() > 1) { //grab the next block result from above //check to see if a specific allele was given HaplotypeAssociationResult har = (HaplotypeAssociationResult) britr.next(); //todo: this is borken. needs count of all other alleles. if (currentTest.getAllele() != null){ boolean foundAllele = false; for (int j = 0; j < har.getAlleleCount(); j++){ if (har.getNumericAlleleName(j).equals(currentTest.getAllele())){ Haplotype[] filtHaps = {har.getHaps()[j]}; res.add(new HaplotypeAssociationResult(filtHaps,0,har.getName())); foundAllele = true; break; } } if (!foundAllele){ throw new HaploViewException(currentTest.getAllele() + ": no such allele for test:\n" + har.getName()); } }else{ res.add(har); } }else if (currentTest.getNumMarkers() == 1){ //grab appropriate single marker result. res.add(inputSNPResults.get(currentTest.getMarkerArray()[0])); } } results = res; }

1,110,832

public void runFileTests(HaploData theData, Vector inputSNPResults) throws HaploViewException { Vector res = new Vector(); if(tests == null || theData == null) { return; } Vector blocks = new Vector(); Vector names = new Vector(); for(int i=0;i<tests.size();i++) { //first go through and get all the multimarker tests to package up to hand to theData.generateHaplotypes() AssociationTest currentTest = (AssociationTest) tests.get(i); if(currentTest.getNumMarkers() > 1) { blocks.add(currentTest.getFilteredMarkerArray()); names.add(currentTest.getName()); } } Haplotype[][] blockHaps = theData.generateHaplotypes(blocks, true); Vector blockResults = new AssociationTestSet(blockHaps, names).getResults(); Iterator britr = blockResults.iterator(); for (int i = 0; i < tests.size(); i++){ AssociationTest currentTest = (AssociationTest) tests.get(i); if(currentTest.getNumMarkers() > 1) { //grab the next block result from above //check to see if a specific allele was given HaplotypeAssociationResult har = (HaplotypeAssociationResult) britr.next(); //todo: this is borken. needs count of all other alleles. if (currentTest.getAllele() != null){ boolean foundAllele = false; for (int j = 0; j < har.getAlleleCount(); j++){ if (har.getNumericAlleleName(j).equals(currentTest.getAllele())){ Haplotype[] filtHaps = {har.getHaps()[j]}; res.add(new HaplotypeAssociationResult(filtHaps,0,har.getName())); foundAllele = true; break; } } if (!foundAllele){ throw new HaploViewException(currentTest.getAllele() + ": no such allele for test:\n" + har.getName()); } }else{ res.add(har); } }else if (currentTest.getNumMarkers() == 1){ //grab appropriate single marker result. res.add(inputSNPResults.get(currentTest.getMarkerArray()[0])); } } results = res; }

1,110,833

public void doTag(XMLOutput output) throws Exception { }

public void doTag(XMLOutput output) { }

1,110,834

public void refreshTable(){ this.removeAll(); Vector tableData = new Vector(); int numRes = Chromosome.getFilteredSize(); for (int i = 0; i < numRes; i++){ Vector tempVect = new Vector(); TDTResult currentResult = (TDTResult)result.get(Chromosome.realIndex[i]); tempVect.add(new Integer(i+1)); tempVect.add(currentResult.getName()); tempVect.add(currentResult.getOverTransmittedAllele(type)); tempVect.add(currentResult.getTURatio(type)); tempVect.add(new Double(currentResult.getChiSq(type))); tempVect.add(currentResult.getPValue()); tableData.add(tempVect.clone()); } table = new JTable(tableData,tableColumnNames); table.getColumnModel().getColumn(0).setPreferredWidth(50); table.getColumnModel().getColumn(1).setPreferredWidth(100); if (type != 1){ table.getColumnModel().getColumn(3).setPreferredWidth(160); } table.getColumnModel().getColumn(2).setPreferredWidth(100); JScrollPane tableScroller = new JScrollPane(table); add(tableScroller); }

public void refreshTable(){ this.removeAll(); Vector tableData = new Vector(); int numRes = Chromosome.getFilteredSize(); for (int i = 0; i < numRes; i++){ Vector tempVect = new Vector(); TDTResult currentResult = (TDTResult)result.get(Chromosome.realIndex[i]); tempVect.add(new Integer(Chromosome.realIndex[i]+1)); tempVect.add(currentResult.getName()); tempVect.add(currentResult.getOverTransmittedAllele(type)); tempVect.add(currentResult.getTURatio(type)); tempVect.add(new Double(currentResult.getChiSq(type))); tempVect.add(currentResult.getPValue()); tableData.add(tempVect.clone()); } table = new JTable(tableData,tableColumnNames); table.getColumnModel().getColumn(0).setPreferredWidth(50); table.getColumnModel().getColumn(1).setPreferredWidth(100); if (type != 1){ table.getColumnModel().getColumn(3).setPreferredWidth(160); } table.getColumnModel().getColumn(2).setPreferredWidth(100); JScrollPane tableScroller = new JScrollPane(table); add(tableScroller); }

1,110,835

public void setJellyContext(JellyContext context) throws EvalError { this.context = context; // now pass in all the variables for ( Iterator iter = context.getVariableNames(); iter.hasNext(); ) { String name = (String) iter.next(); Object value = context.getVariable(name); set( name, value ); } // lets pass in the Jelly context set( "jellyContext", context ); }

public void setJellyContext(JellyContext context) throws EvalError { this.context = context; // now pass in all the variables for ( Iterator iter = context.getVariableNames(); iter.hasNext(); ) { String name = (String) iter.next(); Object value = context.getVariable(name); name = convertVariableName(name); if (name != null) { set( name, value ); } } // lets pass in the Jelly context set( "jellyContext", context ); }

1,110,836

public void setJellyContext(JellyContext context) throws EvalError { this.context = context; // now pass in all the variables for ( Iterator iter = context.getVariableNames(); iter.hasNext(); ) { String name = (String) iter.next(); Object value = context.getVariable(name); set( name, value ); } // lets pass in the Jelly context set( "jellyContext", context ); }

public void setJellyContext(JellyContext context) throws EvalError { this.context = context; // now pass in all the variables for ( Iterator iter = context.getVariableNames(); iter.hasNext(); ) { String name = (String) iter.next(); Object value = context.getVariable(name); set( name, value ); } // lets pass in the Jelly context set( "context", context ); }

1,110,837

private void prepareUserForm(ActionForm form, User user){ UserForm userForm = (UserForm)form; userForm.setUsername(user.getUsername()); userForm.setPassword(UserForm.FORM_PASSWORD); userForm.setConfirmPassword(UserForm.FORM_PASSWORD); //TODO Need to handle multiple role scenario if(!AuthConstants.USER_ADMIN.equals(user.getUsername())) userForm.setRole(((Role)user.getRoles().get(0)).getName()); userForm.setStatus(user.getStatus()); }

1,110,838

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } if (inputOptions[1] == null && Options.getAssocTest() != ASSOC_NONE){ throw new HaploViewException("A marker information file is required for association tests."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } if(theData.getPedFile().isHaploidHets()) { JOptionPane.showMessageDialog(this, "One or more males in the file is heterozygous.\nThese genotypes have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } if (type == HAPS_FILE){ readMarkers(markerFile, null); HashSet emptyHashSet = new HashSet(); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; theData.getPedFile().setWhiteList(emptyHashSet); checkPanel = new CheckDataPanel(this); }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.getPedFile().setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ Container contents = getContentPane(); contents.removeAll(); contents.repaint(); defaultLayout = contents.getLayout(); contents.setLayout(new GridBagLayout()); haploProgress = new JProgressBar(0,2); haploProgress.setValue(0); haploProgress.setStringPainted(true); haploProgress.setForeground(new Color(40,40,255)); haploProgress.setPreferredSize(new Dimension(250,20)); progressPanel.setLayout(new BoxLayout(progressPanel,BoxLayout.Y_AXIS)); JLabel progressLabel = new JLabel("Loading data..."); progressPanel.add(progressLabel); progressLabel.setAlignmentX(CENTER_ALIGNMENT); progressPanel.add(haploProgress); contents.add(progressPanel); progressPanel.revalidate(); for (int i = 0; i < viewMenuItems.length; i++){ viewMenuItems[i].setEnabled(false); } dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; contents = getContentPane(); contents.removeAll(); tabs = new HaploviewTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); HaploviewTab ldTab = new HaploviewTab(dPrimeDisplay); ldTab.add(dPrimeScroller); tabs.addTab(VIEW_DPRIME, ldTab); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); HaploviewTab hapsTab = new HaploviewTab(hapDisplay); hapsTab.add(hapScroller); hapsTab.add(hdc); tabs.addTab(VIEW_HAPLOTYPES, hapsTab); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel HaploviewTab checkTab = new HaploviewTab(checkPanel); checkTab.add(checkPanel); CheckDataController cdc = new CheckDataController(checkPanel); checkTab.add(cdc); tabs.addTab(VIEW_CHECK_PANEL, checkTab); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); tabs.setSelectedComponent(checkTab); //only show tagger if we have a .info file if (theData.infoKnown){ //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); HaploviewTabbedPane tagTabs = new HaploviewTabbedPane(); tagTabs.add("Configuration",taggerConfigPanel); taggerResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(taggerResultsPanel); tagTabs.addTab("Results",taggerResultsPanel); HaploviewTab taggerTab = new HaploviewTab(tagTabs); taggerTab.add(tagTabs); tabs.addTab(VIEW_TAGGER,taggerTab); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); } //Association panel if(Options.getAssocTest() != ASSOC_NONE) { HaploviewTabbedPane metaAssoc = new HaploviewTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null,null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); if (!Chromosome.getDataChrom().equalsIgnoreCase("chrx")){ hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); }else{ hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(null,null)); } metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet custPermSet = null; if (custAssocPanel != null){ custPermSet = custAssocPanel.getTestSet(); } AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel = new PermutationTestPanel( new PermutationTestSet(0,theData.getPedFile(),custPermSet, permSet)); metaAssoc.add(permutationPanel,"Permutation Tests"); HaploviewTab associationTab = new HaploviewTab(metaAssoc); associationTab.add(metaAssoc); tabs.addTab(VIEW_ASSOC, associationTab); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } contents.remove(progressPanel); contents.setLayout(defaultLayout); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (isMaxSet == true){ haploProgress.setValue(theData.dPrimeCount); } if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); progressPanel.removeAll(); isMaxSet = false; theData.dPrimeCount = 0; theData.dPrimeTotalCount = -1; setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } if (theData.dPrimeTotalCount != -1 && isMaxSet == false){ haploProgress.setMaximum(theData.dPrimeTotalCount); isMaxSet = true; } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

void readGenotypes(String[] inputOptions, int type){ //input is a 2 element array with //inputOptions[0] = ped file //inputOptions[1] = info file (null if none) //inputOptions[2] = custom association test list file (null if none) //type is either 3 or 4 for ped and hapmap files respectively final File inFile = new File(inputOptions[0]); final AssociationTestSet customAssocSet; try { if (inputOptions[2] != null && inputOptions[1] == null){ throw new HaploViewException("A marker information file is required if a tests file is specified."); } if (inputOptions[1] == null && Options.getAssocTest() != ASSOC_NONE){ throw new HaploViewException("A marker information file is required for association tests."); } this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (inFile.length() < 1){ throw new HaploViewException("Genotype file is empty or nonexistent: " + inFile.getName()); } if (type == HAPS_FILE){ //these are not available for non ped files viewMenuItems[VIEW_CHECK_NUM].setEnabled(false); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(false); Options.setAssocTest(ASSOC_NONE); } theData = new HaploData(); if (type == HAPS_FILE){ theData.prepareHapsInput(new File(inputOptions[0])); }else{ theData.linkageToChrom(inFile, type); } if(theData.getPedFile().isBogusParents()) { JOptionPane.showMessageDialog(this, "One or more individuals in the file reference non-existent parents.\nThese references have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } if(theData.getPedFile().isHaploidHets()) { JOptionPane.showMessageDialog(this, "At least one male in the file is heterozygous.\nThese genotypes have been ignored.", "File Error", JOptionPane.ERROR_MESSAGE); } //deal with marker information theData.infoKnown = false; File markerFile; if (inputOptions[1] == null){ markerFile = null; }else{ markerFile = new File(inputOptions[1]); } //turn on/off gbrowse menu if (Options.isGBrowseShown()){ gbEditItem.setEnabled(true); }else{ gbEditItem.setEnabled(false); } if (type == HAPS_FILE){ readMarkers(markerFile, null); HashSet emptyHashSet = new HashSet(); //initialize realIndex Chromosome.doFilter(Chromosome.getUnfilteredSize()); customAssocSet = null; theData.getPedFile().setWhiteList(emptyHashSet); checkPanel = new CheckDataPanel(this); }else{ readMarkers(markerFile, theData.getPedFile().getHMInfo()); //we read the file in first, so we can whitelist all the markers in the custom test set HashSet whiteListedCustomMarkers = new HashSet(); if (inputOptions[2] != null){ customAssocSet = new AssociationTestSet(inputOptions[2]); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } theData.getPedFile().setWhiteList(whiteListedCustomMarkers); checkPanel = new CheckDataPanel(this); checkPanel.setAlignmentX(Component.CENTER_ALIGNMENT); //set up the indexing to take into account skipped markers. Chromosome.doFilter(checkPanel.getMarkerResults()); } //let's start the math final SwingWorker worker = new SwingWorker(){ public Object construct(){ Container contents = getContentPane(); contents.removeAll(); contents.repaint(); defaultLayout = contents.getLayout(); contents.setLayout(new GridBagLayout()); haploProgress = new JProgressBar(0,2); haploProgress.setValue(0); haploProgress.setStringPainted(true); haploProgress.setForeground(new Color(40,40,255)); haploProgress.setPreferredSize(new Dimension(250,20)); progressPanel.setLayout(new BoxLayout(progressPanel,BoxLayout.Y_AXIS)); JLabel progressLabel = new JLabel("Loading data..."); progressPanel.add(progressLabel); progressLabel.setAlignmentX(CENTER_ALIGNMENT); progressPanel.add(haploProgress); contents.add(progressPanel); progressPanel.revalidate(); for (int i = 0; i < viewMenuItems.length; i++){ viewMenuItems[i].setEnabled(false); } dPrimeDisplay=null; changeKey(); theData.generateDPrimeTable(); theData.guessBlocks(BLOX_GABRIEL); //theData.guessBlocks(BLOX_NONE); //for debugging, doesn't call blocks at first blockMenuItems[0].setSelected(true); zoomMenuItems[0].setSelected(true); theData.blocksChanged = false; contents = getContentPane(); contents.removeAll(); tabs = new HaploviewTabbedPane(); tabs.addChangeListener(new TabChangeListener()); //first, draw the D' picture dPrimeDisplay = new DPrimeDisplay(window); JScrollPane dPrimeScroller = new JScrollPane(dPrimeDisplay); dPrimeScroller.getViewport().setScrollMode(JViewport.BLIT_SCROLL_MODE); dPrimeScroller.getVerticalScrollBar().setUnitIncrement(60); dPrimeScroller.getHorizontalScrollBar().setUnitIncrement(60); HaploviewTab ldTab = new HaploviewTab(dPrimeDisplay); ldTab.add(dPrimeScroller); tabs.addTab(VIEW_DPRIME, ldTab); viewMenuItems[VIEW_D_NUM].setEnabled(true); //compute and show haps on next tab try { hapDisplay = new HaplotypeDisplay(theData); } catch(HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } HaplotypeDisplayController hdc = new HaplotypeDisplayController(hapDisplay); hapScroller = new JScrollPane(hapDisplay); hapScroller.getVerticalScrollBar().setUnitIncrement(60); hapScroller.getHorizontalScrollBar().setUnitIncrement(60); HaploviewTab hapsTab = new HaploviewTab(hapDisplay); hapsTab.add(hapScroller); hapsTab.add(hdc); tabs.addTab(VIEW_HAPLOTYPES, hapsTab); viewMenuItems[VIEW_HAP_NUM].setEnabled(true); displayMenu.setEnabled(true); analysisMenu.setEnabled(true); //check data panel HaploviewTab checkTab = new HaploviewTab(checkPanel); checkTab.add(checkPanel); CheckDataController cdc = new CheckDataController(checkPanel); checkTab.add(cdc); tabs.addTab(VIEW_CHECK_PANEL, checkTab); viewMenuItems[VIEW_CHECK_NUM].setEnabled(true); tabs.setSelectedComponent(checkTab); //only show tagger if we have a .info file if (theData.infoKnown){ //tagger display taggerConfigPanel = new TaggerConfigPanel(theData); HaploviewTabbedPane tagTabs = new HaploviewTabbedPane(); tagTabs.add("Configuration",taggerConfigPanel); taggerResultsPanel = new TaggerResultsPanel(); taggerConfigPanel.addActionListener(taggerResultsPanel); tagTabs.addTab("Results",taggerResultsPanel); HaploviewTab taggerTab = new HaploviewTab(tagTabs); taggerTab.add(tagTabs); tabs.addTab(VIEW_TAGGER,taggerTab); viewMenuItems[VIEW_TAGGER_NUM].setEnabled(true); } //Association panel if(Options.getAssocTest() != ASSOC_NONE) { HaploviewTabbedPane metaAssoc = new HaploviewTabbedPane(); try{ tdtPanel = new TDTPanel(new AssociationTestSet(theData.getPedFile(), null,null, Chromosome.getAllMarkers())); } catch(PedFileException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } metaAssoc.add("Single Marker", tdtPanel); if (!Chromosome.getDataChrom().equalsIgnoreCase("chrx")){ hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(theData.getHaplotypes(), null)); }else{ hapAssocPanel = new HaploAssocPanel(new AssociationTestSet(null,null)); } metaAssoc.add("Haplotypes", hapAssocPanel); //custom association tests custAssocPanel = null; if(customAssocSet != null) { try { customAssocSet.runFileTests(theData, tdtPanel.getTestSet().getMarkerAssociationResults()); custAssocPanel = new CustomAssocPanel(customAssocSet); metaAssoc.addTab("Custom",custAssocPanel); metaAssoc.setSelectedComponent(custAssocPanel); } catch (HaploViewException e) { JOptionPane.showMessageDialog(window, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } AssociationTestSet custPermSet = null; if (custAssocPanel != null){ custPermSet = custAssocPanel.getTestSet(); } AssociationTestSet permSet = new AssociationTestSet(); permSet.cat(tdtPanel.getTestSet()); permSet.cat(hapAssocPanel.getTestSet()); permutationPanel = new PermutationTestPanel( new PermutationTestSet(0,theData.getPedFile(),custPermSet, permSet)); metaAssoc.add(permutationPanel,"Permutation Tests"); HaploviewTab associationTab = new HaploviewTab(metaAssoc); associationTab.add(metaAssoc); tabs.addTab(VIEW_ASSOC, associationTab); viewMenuItems[VIEW_ASSOC_NUM].setEnabled(true); } contents.remove(progressPanel); contents.setLayout(defaultLayout); contents.add(tabs); repaint(); setVisible(true); theData.finished = true; setTitle(TITLE_STRING + " -- " + inFile.getName()); return null; } }; timer = new javax.swing.Timer(50, new ActionListener(){ public void actionPerformed(ActionEvent evt){ if (isMaxSet == true){ haploProgress.setValue(theData.dPrimeCount); } if (theData.finished){ timer.stop(); for (int i = 0; i < blockMenuItems.length; i++){ blockMenuItems[i].setEnabled(true); } clearBlocksItem.setEnabled(true); readMarkerItem.setEnabled(true); blocksItem.setEnabled(true); exportMenuItems[2].setEnabled(true); progressPanel.removeAll(); isMaxSet = false; theData.dPrimeCount = 0; theData.dPrimeTotalCount = -1; setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } if (theData.dPrimeTotalCount != -1 && isMaxSet == false){ haploProgress.setMaximum(theData.dPrimeTotalCount); isMaxSet = true; } } }); worker.start(); timer.start(); }catch(IOException ioexec) { JOptionPane.showMessageDialog(this, ioexec.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch(PedFileException pfe){ JOptionPane.showMessageDialog(this, pfe.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }catch (HaploViewException hve){ JOptionPane.showMessageDialog(this, hve.getMessage(), "File Error", JOptionPane.ERROR_MESSAGE); setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } }

1,110,839

public AntTagLibrary() { this.project = new Project(); BuildLogger logger = new NoBannerLogger(); logger.setMessageOutputLevel( org.apache.tools.ant.Project.MSG_INFO ); logger.setOutputPrintStream( System.out ); logger.setErrorPrintStream( System.err); project.addBuildListener( logger ); project.init(); throw new RuntimeException( "foo" ); }

public AntTagLibrary() { this.project = new Project(); BuildLogger logger = new NoBannerLogger(); logger.setMessageOutputLevel( org.apache.tools.ant.Project.MSG_INFO ); logger.setOutputPrintStream( System.out ); logger.setErrorPrintStream( System.err); project.addBuildListener( logger ); project.init(); }

1,110,840

protected Tag createTag() throws Exception { if ( tagFactory != null) { return tagFactory.createTag(); } return null; }

protected Tag createTag() throws Exception { if ( tagFactory != null) { return tagFactory.createTag(localName, getSaxAttributes()); } return null; }

1,110,841

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } SQLObject p = parent; if (p != null) { p.removeChild(this); } this.primaryKeySeq = argPrimaryKeySeq; if (p != null) { int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } this.primaryKeySeq = argPrimaryKeySeq; fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); SQLObject p = parent; if (p != null) { p.removeChild(this); } this.primaryKeySeq = argPrimaryKeySeq; if (p != null) { int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

1,110,843

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } SQLObject p = parent; if (p != null) { p.removeChild(this); } this.primaryKeySeq = argPrimaryKeySeq; if (p != null) { int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

1,110,844

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } SQLObject p = parent; if (p != null) { p.removeChild(this); } this.primaryKeySeq = argPrimaryKeySeq; if (p != null) { int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

1,110,845

public FontRenderContext getFontRenderContext() { Graphics2D g2 = (Graphics2D) getGraphics(); g2.scale(zoom, zoom); FontRenderContext frc = g2.getFontRenderContext(); if (logger.isDebugEnabled()) logger.debug("Returning frc="+frc); return frc; }

1,110,848

static Vector doSFS(PairwiseLinkage[][] dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[dPrime.length]; for (int x = 0; x < dPrime.length; x++){ if (Chromosome.getFilteredMarker(x).getMAF() < mafThresh){ skipMarker[x]=true; }else{ skipMarker[x]=false; } } //next make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime.length-1; x++){ for (int y = x+1; y < dPrime.length; y++){ PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (skipMarker[x] || skipMarker[y]) continue; if (lod < -90) continue; //missing data if (highCI < cutHighCI || lowCI < cutLowCI) continue; //must pass "strong LD" test Vector addMe = new Vector(); //a vector of x, y, separation long sep; //compute actual separation sep = Chromosome.getFilteredMarker(y).getPosition() - Chromosome.getFilteredMarker(x).getPosition(); addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ //put first pair first strongPairs.add(addMe); }else{ //sort by descending separation of markers in each pair boolean unplaced = true; for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongPairs.insertElementAt(addMe, v); unplaced = false; break; } } if (unplaced){strongPairs.add(addMe);} } } } //now take this list of pairs with "strong LD" and construct blocks boolean[] usedInBlock = new boolean[dPrime.length + 1]; Vector thisBlock; int[] blockArray; for (int v = 0; v < strongPairs.size(); v++){ numStrong = 0; numRec = 0; numInGroup = 0; thisBlock = new Vector(); int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); int sep = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2)); //first see if this block overlaps with another: if (usedInBlock[first] || usedInBlock[last]) continue; //next, count the number of markers in the block. for (int x = first; x <=last ; x++){ if(!skipMarker[x]) numInGroup++; } //skip it if it is too long in bases for it's size in markers if (numInGroup < 4 && sep > maxDist[numInGroup]) continue; thisBlock.add(new Integer(first)); //test this block. requires 95% of informative markers to be "strong" for (int y = first+1; y <= last; y++){ if (skipMarker[y]) continue; thisBlock.add(new Integer(y)); //loop over columns in row y for (int x = first; x < y; x++){ if (skipMarker[x]) continue; PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //monomorphic marker error if (lod == 0 && lowCI == 0 && highCI == 0) continue; //skip bad markers //for small blocks use different CI cutoffs if (numInGroup < 5){ if (lowCI > cutLowCIVar[numInGroup] && highCI >= cutHighCI) numStrong++; }else{ if (lowCI > cutLowCI && highCI >= cutHighCI) numStrong++; //strong LD } if (highCI < recHighCI) numRec++; //recombination } } //change the definition somewhat for small blocks if (numInGroup > 3){ if (numStrong + numRec < 6) continue; }else if (numInGroup > 2){ if (numStrong + numRec < 3) continue; }else{ if (numStrong + numRec < 1) continue; } blockArray = new int[thisBlock.size()]; for (int z = 0; z < thisBlock.size(); z++){ blockArray[z] = ((Integer)thisBlock.elementAt(z)).intValue(); } // System.out.println(first + " " + last + " " + numStrong + " " + numRec); if ((double)numStrong/(double)(numStrong + numRec) > informFrac){ //this qualifies as a block //add to the block list, but in order by first marker number: if (blocks.size() == 0){ //put first block first blocks.add(blockArray); }else{ //sort by ascending separation of markers in each pair boolean placed = false; for (int b = 0; b < blocks.size(); b ++){ if (first < ((int[])blocks.elementAt(b))[0]){ blocks.insertElementAt(blockArray, b); placed = true; break; } } //make sure to put in blocks which fall on the tail end if (!placed) blocks.add(blockArray); } for (int used = first; used <= last; used++){ usedInBlock[used] = true; } } } return blocks; }

static Vector doSFS(PairwiseLinkage[][] dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[dPrime.length]; for (int x = 0; x < dPrime.length; x++){ if (Chromosome.getFilteredMarker(x).getMAF() < mafThresh){ skipMarker[x]=true; }else{ skipMarker[x]=false; } } //next make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime.length-1; x++){ for (int y = x+1; y < dPrime.length; y++){ PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (skipMarker[x] || skipMarker[y]) continue; if (lod < -90) continue; //missing data if (highCI < cutHighCI || lowCI < cutLowCI) continue; //must pass "strong LD" test Vector addMe = new Vector(); //a vector of x, y, separation long sep; //compute actual separation sep = Math.abs(Chromosome.getFilteredMarker(y).getPosition() - Chromosome.getFilteredMarker(x).getPosition()); addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ //put first pair first strongPairs.add(addMe); }else{ //sort by descending separation of markers in each pair boolean unplaced = true; for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongPairs.insertElementAt(addMe, v); unplaced = false; break; } } if (unplaced){strongPairs.add(addMe);} } } } //now take this list of pairs with "strong LD" and construct blocks boolean[] usedInBlock = new boolean[dPrime.length + 1]; Vector thisBlock; int[] blockArray; for (int v = 0; v < strongPairs.size(); v++){ numStrong = 0; numRec = 0; numInGroup = 0; thisBlock = new Vector(); int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); int sep = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2)); //first see if this block overlaps with another: if (usedInBlock[first] || usedInBlock[last]) continue; //next, count the number of markers in the block. for (int x = first; x <=last ; x++){ if(!skipMarker[x]) numInGroup++; } //skip it if it is too long in bases for it's size in markers if (numInGroup < 4 && sep > maxDist[numInGroup]) continue; thisBlock.add(new Integer(first)); //test this block. requires 95% of informative markers to be "strong" for (int y = first+1; y <= last; y++){ if (skipMarker[y]) continue; thisBlock.add(new Integer(y)); //loop over columns in row y for (int x = first; x < y; x++){ if (skipMarker[x]) continue; PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //monomorphic marker error if (lod == 0 && lowCI == 0 && highCI == 0) continue; //skip bad markers //for small blocks use different CI cutoffs if (numInGroup < 5){ if (lowCI > cutLowCIVar[numInGroup] && highCI >= cutHighCI) numStrong++; }else{ if (lowCI > cutLowCI && highCI >= cutHighCI) numStrong++; //strong LD } if (highCI < recHighCI) numRec++; //recombination } } //change the definition somewhat for small blocks if (numInGroup > 3){ if (numStrong + numRec < 6) continue; }else if (numInGroup > 2){ if (numStrong + numRec < 3) continue; }else{ if (numStrong + numRec < 1) continue; } blockArray = new int[thisBlock.size()]; for (int z = 0; z < thisBlock.size(); z++){ blockArray[z] = ((Integer)thisBlock.elementAt(z)).intValue(); } // System.out.println(first + " " + last + " " + numStrong + " " + numRec); if ((double)numStrong/(double)(numStrong + numRec) > informFrac){ //this qualifies as a block //add to the block list, but in order by first marker number: if (blocks.size() == 0){ //put first block first blocks.add(blockArray); }else{ //sort by ascending separation of markers in each pair boolean placed = false; for (int b = 0; b < blocks.size(); b ++){ if (first < ((int[])blocks.elementAt(b))[0]){ blocks.insertElementAt(blockArray, b); placed = true; break; } } //make sure to put in blocks which fall on the tail end if (!placed) blocks.add(blockArray); } for (int used = first; used <= last; used++){ usedInBlock[used] = true; } } } return blocks; }

1,110,849

static Vector doSFS(PairwiseLinkage[][] dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[dPrime.length]; for (int x = 0; x < dPrime.length; x++){ if (Chromosome.getFilteredMarker(x).getMAF() < mafThresh){ skipMarker[x]=true; }else{ skipMarker[x]=false; } } //next make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime.length-1; x++){ for (int y = x+1; y < dPrime.length; y++){ PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (skipMarker[x] || skipMarker[y]) continue; if (lod < -90) continue; //missing data if (highCI < cutHighCI || lowCI < cutLowCI) continue; //must pass "strong LD" test Vector addMe = new Vector(); //a vector of x, y, separation long sep; //compute actual separation sep = Chromosome.getFilteredMarker(y).getPosition() - Chromosome.getFilteredMarker(x).getPosition(); addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ //put first pair first strongPairs.add(addMe); }else{ //sort by descending separation of markers in each pair boolean unplaced = true; for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongPairs.insertElementAt(addMe, v); unplaced = false; break; } } if (unplaced){strongPairs.add(addMe);} } } } //now take this list of pairs with "strong LD" and construct blocks boolean[] usedInBlock = new boolean[dPrime.length + 1]; Vector thisBlock; int[] blockArray; for (int v = 0; v < strongPairs.size(); v++){ numStrong = 0; numRec = 0; numInGroup = 0; thisBlock = new Vector(); int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); int sep = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2)); //first see if this block overlaps with another: if (usedInBlock[first] || usedInBlock[last]) continue; //next, count the number of markers in the block. for (int x = first; x <=last ; x++){ if(!skipMarker[x]) numInGroup++; } //skip it if it is too long in bases for it's size in markers if (numInGroup < 4 && sep > maxDist[numInGroup]) continue; thisBlock.add(new Integer(first)); //test this block. requires 95% of informative markers to be "strong" for (int y = first+1; y <= last; y++){ if (skipMarker[y]) continue; thisBlock.add(new Integer(y)); //loop over columns in row y for (int x = first; x < y; x++){ if (skipMarker[x]) continue; PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //monomorphic marker error if (lod == 0 && lowCI == 0 && highCI == 0) continue; //skip bad markers //for small blocks use different CI cutoffs if (numInGroup < 5){ if (lowCI > cutLowCIVar[numInGroup] && highCI >= cutHighCI) numStrong++; }else{ if (lowCI > cutLowCI && highCI >= cutHighCI) numStrong++; //strong LD } if (highCI < recHighCI) numRec++; //recombination } } //change the definition somewhat for small blocks if (numInGroup > 3){ if (numStrong + numRec < 6) continue; }else if (numInGroup > 2){ if (numStrong + numRec < 3) continue; }else{ if (numStrong + numRec < 1) continue; } blockArray = new int[thisBlock.size()]; for (int z = 0; z < thisBlock.size(); z++){ blockArray[z] = ((Integer)thisBlock.elementAt(z)).intValue(); } // System.out.println(first + " " + last + " " + numStrong + " " + numRec); if ((double)numStrong/(double)(numStrong + numRec) > informFrac){ //this qualifies as a block //add to the block list, but in order by first marker number: if (blocks.size() == 0){ //put first block first blocks.add(blockArray); }else{ //sort by ascending separation of markers in each pair boolean placed = false; for (int b = 0; b < blocks.size(); b ++){ if (first < ((int[])blocks.elementAt(b))[0]){ blocks.insertElementAt(blockArray, b); placed = true; break; } } //make sure to put in blocks which fall on the tail end if (!placed) blocks.add(blockArray); } for (int used = first; used <= last; used++){ usedInBlock[used] = true; } } } return blocks; }

static Vector doSFS(PairwiseLinkage[][] dPrime){ int numStrong = 0; int numRec = 0; int numInGroup = 0; Vector blocks = new Vector(); Vector strongPairs = new Vector(); //first set up a filter of markers which fail the MAF threshhold boolean[] skipMarker = new boolean[dPrime.length]; for (int x = 0; x < dPrime.length; x++){ if (Chromosome.getFilteredMarker(x).getMAF() < mafThresh){ skipMarker[x]=true; }else{ skipMarker[x]=false; } } //next make a list of marker pairs in "strong LD", sorted by distance apart for (int x = 0; x < dPrime.length-1; x++){ for (int y = x+1; y < dPrime.length; y++){ PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (skipMarker[x] || skipMarker[y]) continue; if (lod < -90) continue; //missing data if (highCI < cutHighCI || lowCI < cutLowCI) continue; //must pass "strong LD" test Vector addMe = new Vector(); //a vector of x, y, separation long sep; //compute actual separation sep = Chromosome.getFilteredMarker(y).getPosition() - Chromosome.getFilteredMarker(x).getPosition(); addMe.add(String.valueOf(x)); addMe.add(String.valueOf(y)); addMe.add(String.valueOf(sep)); if (strongPairs.size() == 0){ //put first pair first strongPairs.add(addMe); }else{ //sort by descending separation of markers in each pair boolean unplaced = true; for (int v = 0; v < strongPairs.size(); v ++){ if (sep >= Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))){ strongPairs.insertElementAt(addMe, v); unplaced = false; break; } } if (unplaced){strongPairs.add(addMe);} } } } //now take this list of pairs with "strong LD" and construct blocks boolean[] usedInBlock = new boolean[dPrime.length + 1]; Vector thisBlock; int[] blockArray; for (int v = 0; v < strongPairs.size(); v++){ numStrong = 0; numRec = 0; numInGroup = 0; thisBlock = new Vector(); int first = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(0)); int last = Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(1)); int sep = Math.abs(Integer.parseInt((String)((Vector)strongPairs.elementAt(v)).elementAt(2))); //first see if this block overlaps with another: if (usedInBlock[first] || usedInBlock[last]) continue; //next, count the number of markers in the block. for (int x = first; x <=last ; x++){ if(!skipMarker[x]) numInGroup++; } //skip it if it is too long in bases for it's size in markers if (numInGroup < 4 && sep > maxDist[numInGroup]) continue; thisBlock.add(new Integer(first)); //test this block. requires 95% of informative markers to be "strong" for (int y = first+1; y <= last; y++){ if (skipMarker[y]) continue; thisBlock.add(new Integer(y)); //loop over columns in row y for (int x = first; x < y; x++){ if (skipMarker[x]) continue; PairwiseLinkage thisPair = dPrime[x][y]; if (thisPair == null){ continue; } //get the right bits double lod = thisPair.getLOD(); double lowCI = thisPair.getConfidenceLow(); double highCI = thisPair.getConfidenceHigh(); if (lod < -90) continue; //monomorphic marker error if (lod == 0 && lowCI == 0 && highCI == 0) continue; //skip bad markers //for small blocks use different CI cutoffs if (numInGroup < 5){ if (lowCI > cutLowCIVar[numInGroup] && highCI >= cutHighCI) numStrong++; }else{ if (lowCI > cutLowCI && highCI >= cutHighCI) numStrong++; //strong LD } if (highCI < recHighCI) numRec++; //recombination } } //change the definition somewhat for small blocks if (numInGroup > 3){ if (numStrong + numRec < 6) continue; }else if (numInGroup > 2){ if (numStrong + numRec < 3) continue; }else{ if (numStrong + numRec < 1) continue; } blockArray = new int[thisBlock.size()]; for (int z = 0; z < thisBlock.size(); z++){ blockArray[z] = ((Integer)thisBlock.elementAt(z)).intValue(); } // System.out.println(first + " " + last + " " + numStrong + " " + numRec); if ((double)numStrong/(double)(numStrong + numRec) > informFrac){ //this qualifies as a block //add to the block list, but in order by first marker number: if (blocks.size() == 0){ //put first block first blocks.add(blockArray); }else{ //sort by ascending separation of markers in each pair boolean placed = false; for (int b = 0; b < blocks.size(); b ++){ if (first < ((int[])blocks.elementAt(b))[0]){ blocks.insertElementAt(blockArray, b); placed = true; break; } } //make sure to put in blocks which fall on the tail end if (!placed) blocks.add(blockArray); } for (int used = first; used <= last; used++){ usedInBlock[used] = true; } } } return blocks; }

1,110,850

public TagScript createTagScript(String name, Attributes attributes) throws Exception { Project project = getProject(); // custom Ant tags if ( name.equals("fileScanner") ) { Tag tag = new FileScannerTag(new FileScanner(project)); return TagScript.newInstance(tag); } // is it an Ant task? Class type = (Class) project.getTaskDefinitions().get(name); if ( type != null ) { Task task = (Task) type.newInstance(); task.setProject(project); task.setTaskName(name); TaskTag tag = new TaskTag( task ); tag.setTrim( true ); return TagScript.newInstance(tag); } // an Ant DataType? Object dataType = null; type = (Class) project.getDataTypeDefinitions().get(name); if ( type != null ) { dataType = type.newInstance(); } else { dataType = project.createDataType(name); } if ( dataType != null ) { DataTypeTag tag = new DataTypeTag( name, dataType ); tag.getDynaBean().set( "project", project ); return TagScript.newInstance(tag); } // assume its an Ant property object (classpath, arg etc). Tag tag = new TaskPropertyTag( name ); return TagScript.newInstance(tag); }

1,110,851

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathContext(); if ( select != null ) { stylesheet.applyTemplates( context, select ); } else { stylesheet.applyTemplates( context ); } // #### should support MODE!!! }

1,110,852

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathContext(); if ( select != null ) { stylesheet.applyTemplates( context, select ); } else { stylesheet.applyTemplates( context ); } // #### should support MODE!!! }

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Stylesheet stylesheet = tag.getStylesheet(); Object source = tag.getXPathSource(); if ( select != null ) { stylesheet.applyTemplates( context, select ); } else { stylesheet.applyTemplates( context ); } // #### should support MODE!!! }

1,110,853

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathContext(); if ( select != null ) { stylesheet.applyTemplates( context, select ); } else { stylesheet.applyTemplates( context ); } // #### should support MODE!!! }

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathContext(); if ( select != null ) { stylesheet.applyTemplates( source, select ); } else { stylesheet.applyTemplates( context ); } // #### should support MODE!!! }

1,110,854

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathContext(); if ( select != null ) { stylesheet.applyTemplates( context, select ); } else { stylesheet.applyTemplates( context ); } // #### should support MODE!!! }

public void doTag(XMLOutput output) throws Exception { Stylesheet stylesheet = getStylesheet(); if ( stylesheet == null ) { throw new JellyException( "<applyTemplates> tag must be inside a <stylesheet> tag" ); } Object context = getXPathContext(); if ( select != null ) { stylesheet.applyTemplates( context, select ); } else { stylesheet.applyTemplates( source ); } // #### should support MODE!!! }

1,110,855

private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThresh = -1; double minimumGenoPercent = -1; double hwCutoff = -1; double missingCutoff = -1; int maxMendel = -1; boolean assocTDT = false; boolean assocCC = false; permutationCount = 0; tagging = Tagger.NONE; maxNumTags = Tagger.DEFAULT_MAXNUMTAGS; findTags = true; double cutHighCI = -1; double cutLowCI = -1; double mafThresh = -1; double recHighCI = -1; double informFrac = -1; double fourGameteCutoff = -1; double spineDP = -1; for(int i =0; i < args.length; i++) { if(args[i].equalsIgnoreCase("-help") || args[i].equalsIgnoreCase("-h")) { System.out.println(HELP_OUTPUT); System.exit(0); } else if(args[i].equalsIgnoreCase("-n") || args[i].equalsIgnoreCase("-nogui")) { nogui = true; } else if(args[i].equalsIgnoreCase("-log")){ i++; if (i >= args.length || args[i].charAt(0) == '-'){ logName = "haploview.log"; i--; }else{ logName = args[i]; } } else if(args[i].equalsIgnoreCase("-p") || args[i].equalsIgnoreCase("-pedfile")) { i++; if( i>=args.length || (args[i].charAt(0) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(pedFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last pedfile listed will be used"); } pedFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-pcloadletter")){ die("PC LOADLETTER?! What the fuck does that mean?!"); } else if (args[i].equalsIgnoreCase("-skipcheck") || args[i].equalsIgnoreCase("--skipcheck")){ skipCheck = true; } else if (args[i].equalsIgnoreCase("-excludeMarkers")){ i++; if(i>=args.length || (args[i].charAt(0) == '-')){ die("-excludeMarkers requires a list of markers"); } else { StringTokenizer str = new StringTokenizer(args[i],","); try { StringBuffer sb = new StringBuffer(); if (!quietMode) sb.append("Excluding markers: "); while(str.hasMoreTokens()) { String token = str.nextToken(); if(token.indexOf("..") != -1) { int lastIndex = token.indexOf(".."); int rangeStart = Integer.parseInt(token.substring(0,lastIndex)); int rangeEnd = Integer.parseInt(token.substring(lastIndex+2,token.length())); for(int j=rangeStart;j<=rangeEnd;j++) { if (!quietMode) sb.append(j+" "); excludedMarkers.add(new Integer(j)); } } else { if (!quietMode) sb.append(token+" "); excludedMarkers.add(new Integer(token)); } } argHandlerMessages.add(sb.toString()); } catch(NumberFormatException nfe) { die("-excludeMarkers argument should be of the format: 1,3,5..8,12"); } } } else if(args[i].equalsIgnoreCase("-ha") || args[i].equalsIgnoreCase("-haps")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(hapsFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last haps file listed will be used"); } hapsFileName = args[i]; } } else if(args[i].equalsIgnoreCase("-i") || args[i].equalsIgnoreCase("-info")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(infoFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last info file listed will be used"); } infoFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-a") || args[i].equalsIgnoreCase("-hapmap")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(hapmapFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last hapmap file listed will be used"); } hapmapFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhmpdata")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(phasedhmpdataFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last phased hapmap data file listed will be used"); } phasedhmpdataFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhmpsample")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(phasedhmpsampleFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last phased hapmap sample file listed will be used"); } phasedhmpsampleFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhmplegend")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(phasedhmplegendFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last phased hapmap legend file listed will be used"); } phasedhmplegendFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhapmapdl")){ phasedhapmapDownload = true; } else if (args[i].equalsIgnoreCase("-plink")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(plinkFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last PLINK file listed will be used"); } plinkFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-map")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(plinkFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last map file listed will be used"); } mapFileName = args[i]; } } else if(args[i].equalsIgnoreCase("-k") || args[i].equalsIgnoreCase("-blocks")) { i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ blockFileName = args[i]; blockOutputType = BLOX_CUSTOM; }else{ die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-png")){ outputPNG = true; } else if (args[i].equalsIgnoreCase("-smallpng") || args[i].equalsIgnoreCase("-compressedPNG")){ outputCompressedPNG = true; } else if (args[i].equalsIgnoreCase("-track")){ i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ trackFileName = args[i]; }else{ die("-track requires a filename"); } } else if(args[i].equalsIgnoreCase("-o") || args[i].equalsIgnoreCase("-output") || args[i].equalsIgnoreCase("-blockoutput")) { i++; if(!(i>=args.length) && !((args[i].charAt(0)) == '-')){ if(blockOutputType != -1){ die("Only one block output type argument is allowed."); } if(args[i].equalsIgnoreCase("SFS") || args[i].equalsIgnoreCase("GAB")){ blockOutputType = BLOX_GABRIEL; } else if(args[i].equalsIgnoreCase("GAM")){ blockOutputType = BLOX_4GAM; } else if(args[i].equalsIgnoreCase("MJD") || args[i].equalsIgnoreCase("SPI")){ blockOutputType = BLOX_SPINE; } else if(args[i].equalsIgnoreCase("ALL")) { blockOutputType = BLOX_ALL; } } else { //defaults to SFS output blockOutputType = BLOX_GABRIEL; i--; } } else if(args[i].equalsIgnoreCase("-d") || args[i].equalsIgnoreCase("--dprime") || args[i].equalsIgnoreCase("-dprime")) { outputDprime = true; } else if (args[i].equalsIgnoreCase("-c") || args[i].equalsIgnoreCase("-check")){ outputCheck = true; } else if (args[i].equalsIgnoreCase("-indcheck")){ individualCheck = true; } else if (args[i].equalsIgnoreCase("-mendel")){ mendel = true; } else if (args[i].equalsIgnoreCase("-malehets")){ malehets = true; } else if(args[i].equalsIgnoreCase("-m") || args[i].equalsIgnoreCase("-maxdistance")) { i++; maxDistance = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-b") || args[i].equalsIgnoreCase("-batch")) { //batch mode i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(batchFileName != null){ argHandlerMessages.add("multiple " + args[i-1] + " arguments found. only last batch file listed will be used"); } batchFileName = args[i]; } } else if(args[i].equalsIgnoreCase("-hapthresh")) { i++; hapThresh = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-spacing")) { i++; spacingThresh = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-minMAF")) { i++; minimumMAF = getDoubleArg(args,i,0,0.5); } else if(args[i].equalsIgnoreCase("-minGeno") || args[i].equalsIgnoreCase("-minGenoPercent")) { i++; minimumGenoPercent = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-hwcutoff")) { i++; hwCutoff = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-maxMendel") ) { i++; maxMendel = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-missingcutoff")) { i++; missingCutoff = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-assoctdt")) { assocTDT = true; } else if(args[i].equalsIgnoreCase("-assoccc")) { assocCC = true; } else if(args[i].equalsIgnoreCase("-randomcc")){ assocCC = true; randomizeAffection = true; } else if(args[i].equalsIgnoreCase("-ldcolorscheme")) { i++; if(!(i>=args.length) && !((args[i].charAt(0)) == '-')){ if(args[i].equalsIgnoreCase("default")){ Options.setLDColorScheme(STD_SCHEME); } else if(args[i].equalsIgnoreCase("RSQ")){ Options.setLDColorScheme(RSQ_SCHEME); } else if(args[i].equalsIgnoreCase("DPALT") ){ Options.setLDColorScheme(WMF_SCHEME); } else if(args[i].equalsIgnoreCase("GAB")) { Options.setLDColorScheme(GAB_SCHEME); } else if(args[i].equalsIgnoreCase("GAM")) { Options.setLDColorScheme(GAM_SCHEME); } else if(args[i].equalsIgnoreCase("GOLD")) { Options.setLDColorScheme(GOLD_SCHEME); } } else { //defaults to STD color scheme Options.setLDColorScheme(STD_SCHEME); i--; } } else if(args[i].equalsIgnoreCase("-blockCutHighCI")) { i++; cutHighCI = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockCutLowCI")) { i++; cutLowCI = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockMafThresh")) { i++; mafThresh = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockRecHighCI")) { i++; recHighCI = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockInformFrac")) { i++; informFrac = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-block4GamCut")) { i++; fourGameteCutoff = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockSpineDP")) { i++; spineDP = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-permtests")) { i++; doPermutationTest = true; permutationCount = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-customassoc")) { i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ customAssocTestsFileName = args[i]; }else{ die(args[i-1] + " requires a filename"); } } else if(args[i].equalsIgnoreCase("-aggressiveTagging")) { tagging = Tagger.AGGRESSIVE_TRIPLE; } else if (args[i].equalsIgnoreCase("-pairwiseTagging")){ tagging = Tagger.PAIRWISE_ONLY; } else if (args[i].equalsIgnoreCase("-printalltags")){ Options.setPrintAllTags(true); } else if(args[i].equalsIgnoreCase("-maxNumTags")){ i++; maxNumTags = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-tagrSqCutoff")) { i++; tagRSquaredCutOff = getDoubleArg(args,i,0,1); } else if (args[i].equalsIgnoreCase("-dontaddtags")){ findTags = false; } else if(args[i].equalsIgnoreCase("-tagLODCutoff")) { i++; Options.setTaggerLODCutoff(getDoubleArg(args,i,0,100000)); } else if(args[i].equalsIgnoreCase("-includeTags")) { i++; if(i>=args.length || args[i].charAt(0) == '-') { die(args[i-1] + " requires a list of marker names."); } StringTokenizer str = new StringTokenizer(args[i],","); forceIncludeTags = new Vector(); while(str.hasMoreTokens()) { forceIncludeTags.add(str.nextToken()); } } else if (args[i].equalsIgnoreCase("-includeTagsFile")) { i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { forceIncludeFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if(args[i].equalsIgnoreCase("-excludeTags")) { i++; if(i>=args.length || args[i].charAt(0) == '-') { die("-excludeTags requires a list of marker names."); } StringTokenizer str = new StringTokenizer(args[i],","); forceExcludeTags = new Vector(); while(str.hasMoreTokens()) { forceExcludeTags.add(str.nextToken()); } } else if (args[i].equalsIgnoreCase("-excludeTagsFile")) { i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { forceExcludeFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-captureAlleles")){ i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { captureAllelesFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-designScores")){ i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { designScoresFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-mintagdistance")){ i++; minTagDistance = args[i]; } else if(args[i].equalsIgnoreCase("-chromosome") || args[i].equalsIgnoreCase("-chr")) { i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { chromosomeArg =args[i]; }else { die(args[i-1] + " requires a chromosome name"); } if(!(chromosomeArg.equalsIgnoreCase("X")) && !(chromosomeArg.equalsIgnoreCase("Y"))){ try{ if (Integer.parseInt(chromosomeArg) > 22){ die("-chromosome requires a chromsome name of 1-22, X, or Y"); } }catch(NumberFormatException nfe){ die("-chromosome requires a chromsome name of 1-22, X, or Y"); } } } else if(args[i].equalsIgnoreCase("-population")){ i++; if(!(i>=args.length) && !(args[i].charAt(0)== '-')) { populationArg = args[i]; }else { die(args[i-1] + "requires a population name"); } } else if(args[i].equalsIgnoreCase("-startpos")){ i++; startPos = args[i]; } else if(args[i].equalsIgnoreCase("-endPos")){ i++; endPos = args[i]; } else if(args[i].equalsIgnoreCase("-release")){ i++; release = args[i]; } else if(args[i].equalsIgnoreCase("-q") || args[i].equalsIgnoreCase("-quiet")) { quietMode = true; } else if(args[i].equalsIgnoreCase("-gzip")){ Options.setGzip(true); } else { die("invalid parameter specified: " + args[i]); } } if (logName != null){ logString = "*****************************************************\n" + TITLE_STRING + "\tJava Version: " + JAVA_VERSION + "\n*****************************************************\n\n\n" + "Arguments:\t"; for (int i = 0; i < args.length; i++){ logString = logString + args[i] + "\t"; } logString = logString + "\n\n"; } int countOptions = 0; if(pedFileName != null) { countOptions++; } if(hapsFileName != null) { countOptions++; } if(hapmapFileName != null) { countOptions++; } if(phasedhmpdataFileName != null) { countOptions++; if(phasedhmpsampleFileName == null){ die("You must specify a sample file for phased hapmap input."); }else if(phasedhmplegendFileName == null){ die("You must specify a legend file for phased hapmap input."); } } if(phasedhapmapDownload) { countOptions++; } if(plinkFileName != null){ countOptions++; if(mapFileName == null){ die("You must specify a map file for plink format input."); } } if(batchFileName != null) { countOptions++; } if(countOptions > 1) { die("Only one genotype input file may be specified on the command line."); } else if(countOptions == 0 && nogui) { die("You must specify a genotype input file."); } //mess with vars, set defaults, etc if(skipCheck) { argHandlerMessages.add("Skipping genotype file check"); } if(maxDistance == -1){ maxDistance = MAXDIST_DEFAULT; }else{ argHandlerMessages.add("Max LD comparison distance = " +maxDistance + "kb"); } Options.setMaxDistance(maxDistance); if(hapThresh != -1) { Options.setHaplotypeDisplayThreshold(hapThresh); argHandlerMessages.add("Haplotype display threshold = " + hapThresh); } if(minimumMAF != -1) { CheckData.mafCut = minimumMAF; argHandlerMessages.add("Minimum MAF = " + minimumMAF); } if(minimumGenoPercent != -1) { CheckData.failedGenoCut = (int)(minimumGenoPercent*100); argHandlerMessages.add("Minimum SNP genotype % = " + minimumGenoPercent); } if(hwCutoff != -1) { CheckData.hwCut = hwCutoff; argHandlerMessages.add("Hardy Weinberg equilibrium p-value cutoff = " + hwCutoff); } if(maxMendel != -1) { CheckData.numMendErrCut = maxMendel; argHandlerMessages.add("Maximum number of Mendel errors = "+maxMendel); } if(spacingThresh != -1) { Options.setSpacingThreshold(spacingThresh); argHandlerMessages.add("LD display spacing value = "+spacingThresh); } if(missingCutoff != -1) { Options.setMissingThreshold(missingCutoff); argHandlerMessages.add("Maximum amount of missing data allowed per individual = "+missingCutoff); } if(cutHighCI != -1) { FindBlocks.cutHighCI = cutHighCI; } if(cutLowCI != -1) { FindBlocks.cutLowCI = cutLowCI; } if(mafThresh != -1) { FindBlocks.mafThresh = mafThresh; } if(recHighCI != -1) { FindBlocks.recHighCI = recHighCI; } if(informFrac != -1) { FindBlocks.informFrac = informFrac; } if(fourGameteCutoff != -1) { FindBlocks.fourGameteCutoff = fourGameteCutoff; } if(spineDP != -1) { FindBlocks.spineDP = spineDP; } if(assocTDT) { Options.setAssocTest(ASSOC_TRIO); }else if(assocCC) { Options.setAssocTest(ASSOC_CC); } if (Options.getAssocTest() != ASSOC_NONE && infoFileName == null && hapmapFileName == null) { die("A marker info file must be specified when performing association tests."); } if(doPermutationTest) { if(!assocCC && !assocTDT) { die("An association test type must be specified for permutation tests to be performed."); } } if(customAssocTestsFileName != null) { if(!assocCC && !assocTDT) { die("An association test type must be specified when using a custom association test file."); } if(infoFileName == null) { die("A marker info file must be specified when using a custom association test file."); } } if(tagging != Tagger.NONE) { if(infoFileName == null && hapmapFileName == null && batchFileName == null && phasedhmpdataFileName == null && !phasedhapmapDownload) { die("A marker info file must be specified when tagging."); } if(forceExcludeTags == null) { forceExcludeTags = new Vector(); } else if (forceExcludeFileName != null) { die("-excludeTags and -excludeTagsFile cannot both be used"); } if(forceExcludeFileName != null) { File excludeFile = new File(forceExcludeFileName); forceExcludeTags = new Vector(); try { BufferedReader br = new BufferedReader(new FileReader(excludeFile)); String line; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ forceExcludeTags.add(line); } } }catch(IOException ioe) { die("An error occured while reading the file specified by -excludeTagsFile."); } } if(forceIncludeTags == null ) { forceIncludeTags = new Vector(); } else if (forceIncludeFileName != null) { die("-includeTags and -includeTagsFile cannot both be used"); } if(forceIncludeFileName != null) { File includeFile = new File(forceIncludeFileName); forceIncludeTags = new Vector(); try { BufferedReader br = new BufferedReader(new FileReader(includeFile)); String line; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ forceIncludeTags.add(line); } } }catch(IOException ioe) { die("An error occured while reading the file specified by -includeTagsFile."); } } if (captureAllelesFileName != null) { File captureFile = new File(captureAllelesFileName); captureAlleleTags = new Vector(); try { BufferedReader br = new BufferedReader(new FileReader(captureFile)); String line; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ line = line.trim(); captureAlleleTags.add(line); } } }catch(IOException ioe) { die("An error occured while reading the file specified by -captureAlleles."); } } if (designScoresFileName != null) { File designFile = new File(designScoresFileName); designScores = new Hashtable(1,1); try { BufferedReader br = new BufferedReader(new FileReader(designFile)); String line; int lines = 0; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ StringTokenizer st = new StringTokenizer(line); int length = st.countTokens(); if (length != 2){ die("Invalid formatting on line " + lines); } String marker = st.nextToken(); Double score = new Double(st.nextToken()); designScores.put(marker,score); } lines++; } }catch(IOException ioe) { die("An error occured while reading the file specified by -captureAlleles."); } } if (minTagDistance != null) { try{ if (Integer.parseInt(minTagDistance) < 0){ die("minimum tag distance cannot be negative"); } }catch(NumberFormatException nfe){ die("minimum tag distance must be a positive integer"); } Options.setTaggerMinDistance(Integer.parseInt(minTagDistance)); } //check that there isn't any overlap between include/exclude lists Vector tempInclude = (Vector) forceIncludeTags.clone(); tempInclude.retainAll(forceExcludeTags); if(tempInclude.size() > 0) { StringBuffer sb = new StringBuffer(); for (int i = 0; i < tempInclude.size(); i++) { String s = (String) tempInclude.elementAt(i); sb.append(s).append(","); } die("The following markers appear in both the include and exclude lists: " + sb.toString()); } if(tagRSquaredCutOff != -1) { Options.setTaggerRsqCutoff(tagRSquaredCutOff); } } else if(forceExcludeTags != null || forceIncludeTags != null || tagRSquaredCutOff != -1) { die("-tagrSqCutoff, -excludeTags, -excludeTagsFile, -includeTags and -includeTagsFile cannot be used without a tagging option"); } if(chromosomeArg != null && hapmapFileName != null) { argHandlerMessages.add("-chromosome flag ignored when loading hapmap file"); chromosomeArg = null; } if(chromosomeArg != null) { Chromosome.setDataChrom("chr" + chromosomeArg); }else{ chromosomeArg = ""; } if (phasedhapmapDownload){ if (chromosomeArg == null){ die("-phasedhapmapdl requires a chromosome specification"); }else if (!(populationArg.equalsIgnoreCase("CEU") || populationArg.equalsIgnoreCase("YRI") || populationArg.equalsIgnoreCase("CHB+JPT"))){ die("-phasedhapmapdl requires a population specification of CEU, YRI, or CHB+JPT"); } if (Integer.parseInt(chromosomeArg) < 1 && Integer.parseInt(chromosomeArg) > 22){ if (!(chromosomeArg.equalsIgnoreCase("X")) && !(chromosomeArg.equalsIgnoreCase("Y"))){ die("-chromosome must be betweeen 1 and 22, X, or Y"); } } try{ if (Integer.parseInt(startPos) > Integer.parseInt(endPos)){ die("-endpos must be greater then -startpos"); } }catch(NumberFormatException nfe){ die("-startpos and -endpos must be integer values"); } if (release == null){ release = "21"; } if (!(release.equals("21")) && !(release.startsWith("16"))){ die("release must be either 16a or 21"); } } }

private void argHandler(String[] args){ argHandlerMessages = new Vector(); int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below blockOutputType = -1; double hapThresh = -1; double minimumMAF=-1; double spacingThresh = -1; double minimumGenoPercent = -1; double hwCutoff = -1; double missingCutoff = -1; int maxMendel = -1; boolean assocTDT = false; boolean assocCC = false; permutationCount = 0; tagging = Tagger.NONE; maxNumTags = Tagger.DEFAULT_MAXNUMTAGS; findTags = true; double cutHighCI = -1; double cutLowCI = -1; double mafThresh = -1; double recHighCI = -1; double informFrac = -1; double fourGameteCutoff = -1; double spineDP = -1; for(int i =0; i < args.length; i++) { if(args[i].equalsIgnoreCase("-help") || args[i].equalsIgnoreCase("-h")) { System.out.println(HELP_OUTPUT); System.exit(0); } else if(args[i].equalsIgnoreCase("-n") || args[i].equalsIgnoreCase("-nogui")) { nogui = true; } else if(args[i].equalsIgnoreCase("-log")){ i++; if (i >= args.length || args[i].charAt(0) == '-'){ logName = "haploview.log"; i--; }else{ logName = args[i]; } } else if(args[i].equalsIgnoreCase("-p") || args[i].equalsIgnoreCase("-pedfile")) { i++; if( i>=args.length || (args[i].charAt(0) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(pedFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last pedfile listed will be used"); } pedFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-pcloadletter")){ die("PC LOADLETTER?! What the fuck does that mean?!"); } else if (args[i].equalsIgnoreCase("-skipcheck") || args[i].equalsIgnoreCase("--skipcheck")){ skipCheck = true; } else if (args[i].equalsIgnoreCase("-excludeMarkers")){ i++; if(i>=args.length || (args[i].charAt(0) == '-')){ die("-excludeMarkers requires a list of markers"); } else { StringTokenizer str = new StringTokenizer(args[i],","); try { StringBuffer sb = new StringBuffer(); if (!quietMode) sb.append("Excluding markers: "); while(str.hasMoreTokens()) { String token = str.nextToken(); if(token.indexOf("..") != -1) { int lastIndex = token.indexOf(".."); int rangeStart = Integer.parseInt(token.substring(0,lastIndex)); int rangeEnd = Integer.parseInt(token.substring(lastIndex+2,token.length())); for(int j=rangeStart;j<=rangeEnd;j++) { if (!quietMode) sb.append(j+" "); excludedMarkers.add(new Integer(j)); } } else { if (!quietMode) sb.append(token+" "); excludedMarkers.add(new Integer(token)); } } argHandlerMessages.add(sb.toString()); } catch(NumberFormatException nfe) { die("-excludeMarkers argument should be of the format: 1,3,5..8,12"); } } } else if(args[i].equalsIgnoreCase("-ha") || args[i].equalsIgnoreCase("-haps")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(hapsFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last haps file listed will be used"); } hapsFileName = args[i]; } } else if(args[i].equalsIgnoreCase("-i") || args[i].equalsIgnoreCase("-info")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(infoFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last info file listed will be used"); } infoFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-a") || args[i].equalsIgnoreCase("-hapmap")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(hapmapFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last hapmap file listed will be used"); } hapmapFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhmpdata")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(phasedhmpdataFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last phased hapmap data file listed will be used"); } phasedhmpdataFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhmpsample")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(phasedhmpsampleFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last phased hapmap sample file listed will be used"); } phasedhmpsampleFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhmplegend")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(phasedhmplegendFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last phased hapmap legend file listed will be used"); } phasedhmplegendFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-phasedhapmapdl")){ phasedhapmapDownload = true; } else if (args[i].equalsIgnoreCase("-plink")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(mapFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last PLINK file listed will be used"); } plinkFileName = args[i]; } } else if (args[i].equalsIgnoreCase("-map")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(mapFileName != null){ argHandlerMessages.add("multiple "+args[i-1] + " arguments found. only last map file listed will be used"); } mapFileName = args[i]; } } else if(args[i].equalsIgnoreCase("-k") || args[i].equalsIgnoreCase("-blocks")) { i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ blockFileName = args[i]; blockOutputType = BLOX_CUSTOM; }else{ die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-png")){ outputPNG = true; } else if (args[i].equalsIgnoreCase("-smallpng") || args[i].equalsIgnoreCase("-compressedPNG")){ outputCompressedPNG = true; } else if (args[i].equalsIgnoreCase("-track")){ i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ trackFileName = args[i]; }else{ die("-track requires a filename"); } } else if(args[i].equalsIgnoreCase("-o") || args[i].equalsIgnoreCase("-output") || args[i].equalsIgnoreCase("-blockoutput")) { i++; if(!(i>=args.length) && !((args[i].charAt(0)) == '-')){ if(blockOutputType != -1){ die("Only one block output type argument is allowed."); } if(args[i].equalsIgnoreCase("SFS") || args[i].equalsIgnoreCase("GAB")){ blockOutputType = BLOX_GABRIEL; } else if(args[i].equalsIgnoreCase("GAM")){ blockOutputType = BLOX_4GAM; } else if(args[i].equalsIgnoreCase("MJD") || args[i].equalsIgnoreCase("SPI")){ blockOutputType = BLOX_SPINE; } else if(args[i].equalsIgnoreCase("ALL")) { blockOutputType = BLOX_ALL; } } else { //defaults to SFS output blockOutputType = BLOX_GABRIEL; i--; } } else if(args[i].equalsIgnoreCase("-d") || args[i].equalsIgnoreCase("--dprime") || args[i].equalsIgnoreCase("-dprime")) { outputDprime = true; } else if (args[i].equalsIgnoreCase("-c") || args[i].equalsIgnoreCase("-check")){ outputCheck = true; } else if (args[i].equalsIgnoreCase("-indcheck")){ individualCheck = true; } else if (args[i].equalsIgnoreCase("-mendel")){ mendel = true; } else if (args[i].equalsIgnoreCase("-malehets")){ malehets = true; } else if(args[i].equalsIgnoreCase("-m") || args[i].equalsIgnoreCase("-maxdistance")) { i++; maxDistance = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-b") || args[i].equalsIgnoreCase("-batch")) { //batch mode i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ die(args[i-1] + " requires a filename"); } else{ if(batchFileName != null){ argHandlerMessages.add("multiple " + args[i-1] + " arguments found. only last batch file listed will be used"); } batchFileName = args[i]; } } else if(args[i].equalsIgnoreCase("-hapthresh")) { i++; hapThresh = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-spacing")) { i++; spacingThresh = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-minMAF")) { i++; minimumMAF = getDoubleArg(args,i,0,0.5); } else if(args[i].equalsIgnoreCase("-minGeno") || args[i].equalsIgnoreCase("-minGenoPercent")) { i++; minimumGenoPercent = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-hwcutoff")) { i++; hwCutoff = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-maxMendel") ) { i++; maxMendel = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-missingcutoff")) { i++; missingCutoff = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-assoctdt")) { assocTDT = true; } else if(args[i].equalsIgnoreCase("-assoccc")) { assocCC = true; } else if(args[i].equalsIgnoreCase("-randomcc")){ assocCC = true; randomizeAffection = true; } else if(args[i].equalsIgnoreCase("-ldcolorscheme")) { i++; if(!(i>=args.length) && !((args[i].charAt(0)) == '-')){ if(args[i].equalsIgnoreCase("default")){ Options.setLDColorScheme(STD_SCHEME); } else if(args[i].equalsIgnoreCase("RSQ")){ Options.setLDColorScheme(RSQ_SCHEME); } else if(args[i].equalsIgnoreCase("DPALT") ){ Options.setLDColorScheme(WMF_SCHEME); } else if(args[i].equalsIgnoreCase("GAB")) { Options.setLDColorScheme(GAB_SCHEME); } else if(args[i].equalsIgnoreCase("GAM")) { Options.setLDColorScheme(GAM_SCHEME); } else if(args[i].equalsIgnoreCase("GOLD")) { Options.setLDColorScheme(GOLD_SCHEME); } } else { //defaults to STD color scheme Options.setLDColorScheme(STD_SCHEME); i--; } } else if(args[i].equalsIgnoreCase("-blockCutHighCI")) { i++; cutHighCI = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockCutLowCI")) { i++; cutLowCI = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockMafThresh")) { i++; mafThresh = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockRecHighCI")) { i++; recHighCI = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockInformFrac")) { i++; informFrac = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-block4GamCut")) { i++; fourGameteCutoff = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-blockSpineDP")) { i++; spineDP = getDoubleArg(args,i,0,1); } else if(args[i].equalsIgnoreCase("-permtests")) { i++; doPermutationTest = true; permutationCount = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-customassoc")) { i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ customAssocTestsFileName = args[i]; }else{ die(args[i-1] + " requires a filename"); } } else if(args[i].equalsIgnoreCase("-aggressiveTagging")) { tagging = Tagger.AGGRESSIVE_TRIPLE; } else if (args[i].equalsIgnoreCase("-pairwiseTagging")){ tagging = Tagger.PAIRWISE_ONLY; } else if (args[i].equalsIgnoreCase("-printalltags")){ Options.setPrintAllTags(true); } else if(args[i].equalsIgnoreCase("-maxNumTags")){ i++; maxNumTags = getIntegerArg(args,i); } else if(args[i].equalsIgnoreCase("-tagrSqCutoff")) { i++; tagRSquaredCutOff = getDoubleArg(args,i,0,1); } else if (args[i].equalsIgnoreCase("-dontaddtags")){ findTags = false; } else if(args[i].equalsIgnoreCase("-tagLODCutoff")) { i++; Options.setTaggerLODCutoff(getDoubleArg(args,i,0,100000)); } else if(args[i].equalsIgnoreCase("-includeTags")) { i++; if(i>=args.length || args[i].charAt(0) == '-') { die(args[i-1] + " requires a list of marker names."); } StringTokenizer str = new StringTokenizer(args[i],","); forceIncludeTags = new Vector(); while(str.hasMoreTokens()) { forceIncludeTags.add(str.nextToken()); } } else if (args[i].equalsIgnoreCase("-includeTagsFile")) { i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { forceIncludeFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if(args[i].equalsIgnoreCase("-excludeTags")) { i++; if(i>=args.length || args[i].charAt(0) == '-') { die("-excludeTags requires a list of marker names."); } StringTokenizer str = new StringTokenizer(args[i],","); forceExcludeTags = new Vector(); while(str.hasMoreTokens()) { forceExcludeTags.add(str.nextToken()); } } else if (args[i].equalsIgnoreCase("-excludeTagsFile")) { i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { forceExcludeFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-captureAlleles")){ i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { captureAllelesFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-designScores")){ i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { designScoresFileName =args[i]; }else { die(args[i-1] + " requires a filename"); } } else if (args[i].equalsIgnoreCase("-mintagdistance")){ i++; minTagDistance = args[i]; } else if(args[i].equalsIgnoreCase("-chromosome") || args[i].equalsIgnoreCase("-chr")) { i++; if(!(i>=args.length) && !(args[i].charAt(0) == '-')) { chromosomeArg =args[i]; }else { die(args[i-1] + " requires a chromosome name"); } if(!(chromosomeArg.equalsIgnoreCase("X")) && !(chromosomeArg.equalsIgnoreCase("Y"))){ try{ if (Integer.parseInt(chromosomeArg) > 22){ die("-chromosome requires a chromsome name of 1-22, X, or Y"); } }catch(NumberFormatException nfe){ die("-chromosome requires a chromsome name of 1-22, X, or Y"); } } } else if(args[i].equalsIgnoreCase("-population")){ i++; if(!(i>=args.length) && !(args[i].charAt(0)== '-')) { populationArg = args[i]; }else { die(args[i-1] + "requires a population name"); } } else if(args[i].equalsIgnoreCase("-startpos")){ i++; startPos = args[i]; } else if(args[i].equalsIgnoreCase("-endPos")){ i++; endPos = args[i]; } else if(args[i].equalsIgnoreCase("-release")){ i++; release = args[i]; } else if(args[i].equalsIgnoreCase("-q") || args[i].equalsIgnoreCase("-quiet")) { quietMode = true; } else if(args[i].equalsIgnoreCase("-gzip")){ Options.setGzip(true); } else { die("invalid parameter specified: " + args[i]); } } if (logName != null){ logString = "*****************************************************\n" + TITLE_STRING + "\tJava Version: " + JAVA_VERSION + "\n*****************************************************\n\n\n" + "Arguments:\t"; for (int i = 0; i < args.length; i++){ logString = logString + args[i] + "\t"; } logString = logString + "\n\n"; } int countOptions = 0; if(pedFileName != null) { countOptions++; } if(hapsFileName != null) { countOptions++; } if(hapmapFileName != null) { countOptions++; } if(phasedhmpdataFileName != null) { countOptions++; if(phasedhmpsampleFileName == null){ die("You must specify a sample file for phased hapmap input."); }else if(phasedhmplegendFileName == null){ die("You must specify a legend file for phased hapmap input."); } } if(phasedhapmapDownload) { countOptions++; } if(mapFileName != null){ countOptions++; if(mapFileName == null){ die("You must specify a map file for plink format input."); } } if(batchFileName != null) { countOptions++; } if(countOptions > 1) { die("Only one genotype input file may be specified on the command line."); } else if(countOptions == 0 && nogui) { die("You must specify a genotype input file."); } //mess with vars, set defaults, etc if(skipCheck) { argHandlerMessages.add("Skipping genotype file check"); } if(maxDistance == -1){ maxDistance = MAXDIST_DEFAULT; }else{ argHandlerMessages.add("Max LD comparison distance = " +maxDistance + "kb"); } Options.setMaxDistance(maxDistance); if(hapThresh != -1) { Options.setHaplotypeDisplayThreshold(hapThresh); argHandlerMessages.add("Haplotype display threshold = " + hapThresh); } if(minimumMAF != -1) { CheckData.mafCut = minimumMAF; argHandlerMessages.add("Minimum MAF = " + minimumMAF); } if(minimumGenoPercent != -1) { CheckData.failedGenoCut = (int)(minimumGenoPercent*100); argHandlerMessages.add("Minimum SNP genotype % = " + minimumGenoPercent); } if(hwCutoff != -1) { CheckData.hwCut = hwCutoff; argHandlerMessages.add("Hardy Weinberg equilibrium p-value cutoff = " + hwCutoff); } if(maxMendel != -1) { CheckData.numMendErrCut = maxMendel; argHandlerMessages.add("Maximum number of Mendel errors = "+maxMendel); } if(spacingThresh != -1) { Options.setSpacingThreshold(spacingThresh); argHandlerMessages.add("LD display spacing value = "+spacingThresh); } if(missingCutoff != -1) { Options.setMissingThreshold(missingCutoff); argHandlerMessages.add("Maximum amount of missing data allowed per individual = "+missingCutoff); } if(cutHighCI != -1) { FindBlocks.cutHighCI = cutHighCI; } if(cutLowCI != -1) { FindBlocks.cutLowCI = cutLowCI; } if(mafThresh != -1) { FindBlocks.mafThresh = mafThresh; } if(recHighCI != -1) { FindBlocks.recHighCI = recHighCI; } if(informFrac != -1) { FindBlocks.informFrac = informFrac; } if(fourGameteCutoff != -1) { FindBlocks.fourGameteCutoff = fourGameteCutoff; } if(spineDP != -1) { FindBlocks.spineDP = spineDP; } if(assocTDT) { Options.setAssocTest(ASSOC_TRIO); }else if(assocCC) { Options.setAssocTest(ASSOC_CC); } if (Options.getAssocTest() != ASSOC_NONE && infoFileName == null && hapmapFileName == null) { die("A marker info file must be specified when performing association tests."); } if(doPermutationTest) { if(!assocCC && !assocTDT) { die("An association test type must be specified for permutation tests to be performed."); } } if(customAssocTestsFileName != null) { if(!assocCC && !assocTDT) { die("An association test type must be specified when using a custom association test file."); } if(infoFileName == null) { die("A marker info file must be specified when using a custom association test file."); } } if(tagging != Tagger.NONE) { if(infoFileName == null && hapmapFileName == null && batchFileName == null && phasedhmpdataFileName == null && !phasedhapmapDownload) { die("A marker info file must be specified when tagging."); } if(forceExcludeTags == null) { forceExcludeTags = new Vector(); } else if (forceExcludeFileName != null) { die("-excludeTags and -excludeTagsFile cannot both be used"); } if(forceExcludeFileName != null) { File excludeFile = new File(forceExcludeFileName); forceExcludeTags = new Vector(); try { BufferedReader br = new BufferedReader(new FileReader(excludeFile)); String line; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ forceExcludeTags.add(line); } } }catch(IOException ioe) { die("An error occured while reading the file specified by -excludeTagsFile."); } } if(forceIncludeTags == null ) { forceIncludeTags = new Vector(); } else if (forceIncludeFileName != null) { die("-includeTags and -includeTagsFile cannot both be used"); } if(forceIncludeFileName != null) { File includeFile = new File(forceIncludeFileName); forceIncludeTags = new Vector(); try { BufferedReader br = new BufferedReader(new FileReader(includeFile)); String line; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ forceIncludeTags.add(line); } } }catch(IOException ioe) { die("An error occured while reading the file specified by -includeTagsFile."); } } if (captureAllelesFileName != null) { File captureFile = new File(captureAllelesFileName); captureAlleleTags = new Vector(); try { BufferedReader br = new BufferedReader(new FileReader(captureFile)); String line; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ line = line.trim(); captureAlleleTags.add(line); } } }catch(IOException ioe) { die("An error occured while reading the file specified by -captureAlleles."); } } if (designScoresFileName != null) { File designFile = new File(designScoresFileName); designScores = new Hashtable(1,1); try { BufferedReader br = new BufferedReader(new FileReader(designFile)); String line; int lines = 0; while((line = br.readLine()) != null) { if(line.length() > 0 && line.charAt(0) != '#'){ StringTokenizer st = new StringTokenizer(line); int length = st.countTokens(); if (length != 2){ die("Invalid formatting on line " + lines); } String marker = st.nextToken(); Double score = new Double(st.nextToken()); designScores.put(marker,score); } lines++; } }catch(IOException ioe) { die("An error occured while reading the file specified by -captureAlleles."); } } if (minTagDistance != null) { try{ if (Integer.parseInt(minTagDistance) < 0){ die("minimum tag distance cannot be negative"); } }catch(NumberFormatException nfe){ die("minimum tag distance must be a positive integer"); } Options.setTaggerMinDistance(Integer.parseInt(minTagDistance)); } //check that there isn't any overlap between include/exclude lists Vector tempInclude = (Vector) forceIncludeTags.clone(); tempInclude.retainAll(forceExcludeTags); if(tempInclude.size() > 0) { StringBuffer sb = new StringBuffer(); for (int i = 0; i < tempInclude.size(); i++) { String s = (String) tempInclude.elementAt(i); sb.append(s).append(","); } die("The following markers appear in both the include and exclude lists: " + sb.toString()); } if(tagRSquaredCutOff != -1) { Options.setTaggerRsqCutoff(tagRSquaredCutOff); } } else if(forceExcludeTags != null || forceIncludeTags != null || tagRSquaredCutOff != -1) { die("-tagrSqCutoff, -excludeTags, -excludeTagsFile, -includeTags and -includeTagsFile cannot be used without a tagging option"); } if(chromosomeArg != null && hapmapFileName != null) { argHandlerMessages.add("-chromosome flag ignored when loading hapmap file"); chromosomeArg = null; } if(chromosomeArg != null) { Chromosome.setDataChrom("chr" + chromosomeArg); }else{ chromosomeArg = ""; } if (phasedhapmapDownload){ if (chromosomeArg == null){ die("-phasedhapmapdl requires a chromosome specification"); }else if (!(populationArg.equalsIgnoreCase("CEU") || populationArg.equalsIgnoreCase("YRI") || populationArg.equalsIgnoreCase("CHB+JPT"))){ die("-phasedhapmapdl requires a population specification of CEU, YRI, or CHB+JPT"); } if (Integer.parseInt(chromosomeArg) < 1 && Integer.parseInt(chromosomeArg) > 22){ if (!(chromosomeArg.equalsIgnoreCase("X")) && !(chromosomeArg.equalsIgnoreCase("Y"))){ die("-chromosome must be betweeen 1 and 22, X, or Y"); } } try{ if (Integer.parseInt(startPos) > Integer.parseInt(endPos)){ die("-endpos must be greater then -startpos"); } }catch(NumberFormatException nfe){ die("-startpos and -endpos must be integer values"); } if (release == null){ release = "21"; } if (!(release.equals("21")) && !(release.startsWith("16"))){ die("release must be either 16a or 21"); } } }

1,110,856

public ApplicationEvent(ApplicationConfig config){ super(config); time = System.currentTimeMillis(); }

1,110,859

public ViewerTag(Class widgetClass) { super(widgetClass); }

1,110,860

public List keysOfColumn(SQLColumn col) throws ArchitectException { LinkedList keys = new LinkedList(); Iterator it = getExportedKeys().iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsPkColumn(col)) { keys.add(r); } } it = getExportedKeys().iterator(); while (it.hasNext()) { SQLRelationship r = (SQLRelationship) it.next(); if (r.containsFkColumn(col)) { keys.add(r); } } return keys; }

1,110,861

private void processFile(String fileName, int fileType, String infoFileName){ try { HaploData textData; File outputFile; File inputFile; AssociationTestSet customAssocSet; if(!quietMode && fileName != null){ System.out.println("Using data file: " + fileName); } inputFile = new File(fileName); if(!inputFile.exists()){ System.out.println("input file: " + fileName + " does not exist"); System.exit(1); } textData = new HaploData(); //Vector result = null; if(fileType == HAPS_FILE){ //read in haps file textData.prepareHapsInput(inputFile); } else if (fileType == PED_FILE) { //read in ped file textData.linkageToChrom(inputFile, PED_FILE); if(textData.getPedFile().isBogusParents()) { System.out.println("Error: One or more individuals in the file reference non-existent parents.\nThese references have been ignored."); } if(textData.getPedFile().isHaploidHets()){ System.out.println("Error: One or more males in the file is heterozygous.\nThese genotypes have been ignored."); } }else{ //read in hapmapfile textData.linkageToChrom(inputFile,HMP_FILE); } File infoFile = null; if (infoFileName != null){ infoFile = new File(infoFileName); } textData.prepareMarkerInput(infoFile,textData.getPedFile().getHMInfo()); HashSet whiteListedCustomMarkers = new HashSet(); if (customAssocTestsFileName != null){ customAssocSet = new AssociationTestSet(customAssocTestsFileName); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } Hashtable snpsByName = new Hashtable(); for(int i=0;i<Chromosome.getUnfilteredSize();i++) { SNP snp = Chromosome.getUnfilteredMarker(i); snpsByName.put(snp.getDisplayName(), snp); } if(forceIncludeTags != null) { for(int i=0;i<forceIncludeTags.size();i++) { if(snpsByName.containsKey(forceIncludeTags.get(i))) { whiteListedCustomMarkers.add(snpsByName.get(forceIncludeTags.get(i))); } } } textData.getPedFile().setWhiteList(whiteListedCustomMarkers); boolean[] markerResults = new boolean[Chromosome.getUnfilteredSize()]; Vector result = null; result = textData.getPedFile().getResults(); //once check has been run we can filter the markers for (int i = 0; i < result.size(); i++){ if (((((MarkerResult)result.get(i)).getRating() > 0 || skipCheck) && Chromosome.getUnfilteredMarker(i).getDupStatus() != 2)){ markerResults[i] = true; }else{ markerResults[i] = false; } } for (int i = 0; i < excludedMarkers.size(); i++){ int cur = ((Integer)excludedMarkers.elementAt(i)).intValue(); if (cur < 1 || cur > markerResults.length){ System.out.println("Excluded marker out of bounds: " + cur + "\nMarkers must be between 1 and N, where N is the total number of markers."); System.exit(1); }else{ markerResults[cur-1] = false; } } for(int i=0;i<Chromosome.getUnfilteredSize();i++) { if(textData.getPedFile().isWhiteListed(Chromosome.getUnfilteredMarker(i))) { markerResults[i] = true; } } Chromosome.doFilter(markerResults); if(!quietMode && infoFile != null){ System.out.println("Using marker information file: " + infoFile.getName()); } if(outputCheck && result != null){ textData.getPedFile().saveCheckDataToText(validateOutputFile(fileName + ".CHECK")); } if(individualCheck && result != null){ IndividualDialog id = new IndividualDialog(textData); id.printTable(validateOutputFile(fileName + ".INDCHECK")); } if(mendel && result != null){ MendelDialog md = new MendelDialog(textData); md.printTable(validateOutputFile(fileName + ".MENDEL" )); } Vector cust = new Vector(); AssociationTestSet blockTestSet = null; if(blockOutputType != -1){ textData.generateDPrimeTable(); Haplotype[][] haplos; Haplotype[][] filtHaplos; switch(blockOutputType){ case BLOX_GABRIEL: outputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; case BLOX_4GAM: outputFile = validateOutputFile(fileName + ".4GAMblocks"); break; case BLOX_SPINE: outputFile = validateOutputFile(fileName + ".SPINEblocks"); break; case BLOX_CUSTOM: outputFile = validateOutputFile(fileName + ".CUSTblocks"); //read in the blocks file File blocksFile = new File(blockFileName); if(!quietMode) { System.out.println("Using custom blocks file " + blockFileName); } cust = textData.readBlocks(blocksFile); break; case BLOX_ALL: //handled below, so we don't do anything here outputFile = null; break; default: outputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; } //this handles output type ALL if(blockOutputType == BLOX_ALL) { outputFile = validateOutputFile(fileName + ".GABRIELblocks"); textData.guessBlocks(BLOX_GABRIEL); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid Gabriel blocks."); } outputFile = validateOutputFile(fileName + ".4GAMblocks"); textData.guessBlocks(BLOX_4GAM); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid 4 Gamete blocks."); } outputFile = validateOutputFile(fileName + ".SPINEblocks"); textData.guessBlocks(BLOX_SPINE); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid LD Spine blocks."); } }else{ //guesses blocks based on output type determined above. textData.guessBlocks(blockOutputType, cust); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid blocks."); } } if(Options.getAssocTest() == ASSOC_TRIO || Options.getAssocTest() == ASSOC_CC) { if (blockOutputType == BLOX_ALL){ System.out.println("Haplotype association results cannot be used with block output \"ALL\""); }else{ if (haplos != null){ blockTestSet = new AssociationTestSet(haplos,null); blockTestSet.saveHapsToText(validateOutputFile(fileName + ".HAPASSOC")); }else if (!quietMode){ System.out.println("Skipping block association output: no valid blocks."); } } } } if(outputDprime) { outputFile = validateOutputFile(fileName + ".LD"); if (textData.dpTable != null){ textData.saveDprimeToText(outputFile, TABLE_TYPE, 0, Chromosome.getSize()); }else{ textData.saveDprimeToText(outputFile, LIVE_TYPE, 0, Chromosome.getSize()); } } if (outputPNG || outputCompressedPNG){ outputFile = validateOutputFile(fileName + ".LD.PNG"); if (textData.dpTable == null){ textData.generateDPrimeTable(); textData.guessBlocks(BLOX_CUSTOM, new Vector()); } if (trackFileName != null){ textData.readAnalysisTrack(new File(trackFileName)); if(!quietMode) { System.out.println("Using analysis track file " + trackFileName); } } DPrimeDisplay dpd = new DPrimeDisplay(textData); BufferedImage i = dpd.export(0,Chromosome.getUnfilteredSize(),outputCompressedPNG); try{ Jimi.putImage("image/png", i, outputFile.getAbsolutePath()); }catch(JimiException je){ System.out.println(je.getMessage()); } } AssociationTestSet markerTestSet =null; if(Options.getAssocTest() == ASSOC_TRIO || Options.getAssocTest() == ASSOC_CC){ if (randomizeAffection){ Vector aff = new Vector(); int j=0, k=0; for (int i = 0; i < textData.getPedFile().getNumIndividuals(); i++){ if (i%2 == 0){ aff.add(new Integer(1)); j++; }else{ aff.add(new Integer(2)); k++; } } Collections.shuffle(aff); markerTestSet = new AssociationTestSet(textData.getPedFile(),aff,null,Chromosome.getAllMarkers()); }else{ markerTestSet = new AssociationTestSet(textData.getPedFile(),null,null,Chromosome.getAllMarkers()); } markerTestSet.saveSNPsToText(validateOutputFile(fileName + ".ASSOC")); } if(customAssocSet != null) { if(!quietMode) { System.out.println("Using custom association test file " + customAssocTestsFileName); } try { customAssocSet.setPermTests(doPermutationTest); customAssocSet.runFileTests(textData,markerTestSet.getMarkerAssociationResults()); customAssocSet.saveResultsToText(validateOutputFile(fileName + ".CUSTASSOC")); }catch(IOException ioe) { System.out.println("An error occured writing the custom association results file."); customAssocSet = null; } } if(doPermutationTest) { AssociationTestSet permTests = new AssociationTestSet(); permTests.cat(markerTestSet); if(blockTestSet != null) { permTests.cat(blockTestSet); } final PermutationTestSet pts = new PermutationTestSet(permutationCount,textData.getPedFile(),customAssocSet,permTests); Thread permThread = new Thread(new Runnable() { public void run() { if (pts.isCustom()){ pts.doPermutations(PermutationTestSet.CUSTOM); }else{ pts.doPermutations(PermutationTestSet.SINGLE_PLUS_BLOCKS); } } }); permThread.start(); if(!quietMode) { System.out.println("Starting " + permutationCount + " permutation tests (each . printed represents 1% of tests completed)"); } int dotsPrinted =0; while(pts.getPermutationCount() - pts.getPermutationsPerformed() > 0) { while(( (double)pts.getPermutationsPerformed() / pts.getPermutationCount())*100 > dotsPrinted) { System.out.print("."); dotsPrinted++; } try{ Thread.sleep(100); }catch(InterruptedException ie) {} } System.out.println(); try { pts.writeResultsToFile(validateOutputFile(fileName + ".PERMUT")); } catch(IOException ioe) { System.out.println("An error occured while writing the permutation test results to file."); } } if(tagging != Tagger.NONE) { if(textData.dpTable == null) { textData.generateDPrimeTable(); } Vector snps = Chromosome.getAllMarkers(); HashSet names = new HashSet(); for (int i = 0; i < snps.size(); i++) { SNP snp = (SNP) snps.elementAt(i); names.add(snp.getDisplayName()); } HashSet filteredNames = new HashSet(); for(int i=0;i<Chromosome.getSize();i++) { filteredNames.add(Chromosome.getMarker(i).getDisplayName()); } Vector sitesToCapture = new Vector(); for(int i=0;i<Chromosome.getSize();i++) { sitesToCapture.add(Chromosome.getMarker(i)); } for (int i = 0; i < forceIncludeTags.size(); i++) { String s = (String) forceIncludeTags.elementAt(i); if(!names.contains(s) && !quietMode) { System.out.println("Warning: skipping marker " + s + " in the list of forced included tags since I don't know about it."); } } for (int i = 0; i < forceExcludeTags.size(); i++) { String s = (String) forceExcludeTags.elementAt(i); if(!names.contains(s) && !quietMode) { System.out.println("Warning: skipping marker " + s + " in the list of forced excluded tags since I don't know about it."); } } //chuck out filtered jazz from excludes, and nonexistent markers from both forceExcludeTags.retainAll(filteredNames); forceIncludeTags.retainAll(names); if(!quietMode) { System.out.println("Starting tagging."); } TaggerController tc = new TaggerController(textData,forceIncludeTags,forceExcludeTags,sitesToCapture, tagging,maxNumTags,findTags); tc.runTagger(); while(!tc.isTaggingCompleted()) { try { Thread.sleep(100); }catch(InterruptedException ie) {} } tc.saveResultsToFile(validateOutputFile(fileName + ".TAGS")); tc.dumpTests(validateOutputFile(fileName + ".TESTS")); //todo: I don't like this at the moment, removed subject to further consideration. //tc.dumpTags(validateOutputFile(fileName + ".TAGSNPS")); } } catch(IOException e){ System.err.println("An error has occured:"); System.err.println(e.getMessage()); } catch(HaploViewException e){ System.err.println(e.getMessage()); } catch(PedFileException pfe) { System.err.println(pfe.getMessage()); } catch(TaggerException te){ System.err.println(te.getMessage()); } }

private void processFile(String fileName, int fileType, String infoFileName){ try { HaploData textData; File outputFile; File inputFile; AssociationTestSet customAssocSet; if(!quietMode && fileName != null){ System.out.println("Using data file: " + fileName); } inputFile = new File(fileName); if(!inputFile.exists()){ System.out.println("input file: " + fileName + " does not exist"); System.exit(1); } textData = new HaploData(); //Vector result = null; if(fileType == HAPS_FILE){ //read in haps file textData.prepareHapsInput(inputFile); } else if (fileType == PED_FILE) { //read in ped file textData.linkageToChrom(inputFile, PED_FILE); if(textData.getPedFile().isBogusParents()) { System.out.println("Error: One or more individuals in the file reference non-existent parents.\nThese references have been ignored."); } if(textData.getPedFile().isHaploidHets()){ System.out.println("Error: At least one male in the file is heterozygous.\nThese genotypes have been ignored."); } }else{ //read in hapmapfile textData.linkageToChrom(inputFile,HMP_FILE); } File infoFile = null; if (infoFileName != null){ infoFile = new File(infoFileName); } textData.prepareMarkerInput(infoFile,textData.getPedFile().getHMInfo()); HashSet whiteListedCustomMarkers = new HashSet(); if (customAssocTestsFileName != null){ customAssocSet = new AssociationTestSet(customAssocTestsFileName); whiteListedCustomMarkers = customAssocSet.getWhitelist(); }else{ customAssocSet = null; } Hashtable snpsByName = new Hashtable(); for(int i=0;i<Chromosome.getUnfilteredSize();i++) { SNP snp = Chromosome.getUnfilteredMarker(i); snpsByName.put(snp.getDisplayName(), snp); } if(forceIncludeTags != null) { for(int i=0;i<forceIncludeTags.size();i++) { if(snpsByName.containsKey(forceIncludeTags.get(i))) { whiteListedCustomMarkers.add(snpsByName.get(forceIncludeTags.get(i))); } } } textData.getPedFile().setWhiteList(whiteListedCustomMarkers); boolean[] markerResults = new boolean[Chromosome.getUnfilteredSize()]; Vector result = null; result = textData.getPedFile().getResults(); //once check has been run we can filter the markers for (int i = 0; i < result.size(); i++){ if (((((MarkerResult)result.get(i)).getRating() > 0 || skipCheck) && Chromosome.getUnfilteredMarker(i).getDupStatus() != 2)){ markerResults[i] = true; }else{ markerResults[i] = false; } } for (int i = 0; i < excludedMarkers.size(); i++){ int cur = ((Integer)excludedMarkers.elementAt(i)).intValue(); if (cur < 1 || cur > markerResults.length){ System.out.println("Excluded marker out of bounds: " + cur + "\nMarkers must be between 1 and N, where N is the total number of markers."); System.exit(1); }else{ markerResults[cur-1] = false; } } for(int i=0;i<Chromosome.getUnfilteredSize();i++) { if(textData.getPedFile().isWhiteListed(Chromosome.getUnfilteredMarker(i))) { markerResults[i] = true; } } Chromosome.doFilter(markerResults); if(!quietMode && infoFile != null){ System.out.println("Using marker information file: " + infoFile.getName()); } if(outputCheck && result != null){ textData.getPedFile().saveCheckDataToText(validateOutputFile(fileName + ".CHECK")); } if(individualCheck && result != null){ IndividualDialog id = new IndividualDialog(textData); id.printTable(validateOutputFile(fileName + ".INDCHECK")); } if(mendel && result != null){ MendelDialog md = new MendelDialog(textData); md.printTable(validateOutputFile(fileName + ".MENDEL" )); } Vector cust = new Vector(); AssociationTestSet blockTestSet = null; if(blockOutputType != -1){ textData.generateDPrimeTable(); Haplotype[][] haplos; Haplotype[][] filtHaplos; switch(blockOutputType){ case BLOX_GABRIEL: outputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; case BLOX_4GAM: outputFile = validateOutputFile(fileName + ".4GAMblocks"); break; case BLOX_SPINE: outputFile = validateOutputFile(fileName + ".SPINEblocks"); break; case BLOX_CUSTOM: outputFile = validateOutputFile(fileName + ".CUSTblocks"); //read in the blocks file File blocksFile = new File(blockFileName); if(!quietMode) { System.out.println("Using custom blocks file " + blockFileName); } cust = textData.readBlocks(blocksFile); break; case BLOX_ALL: //handled below, so we don't do anything here outputFile = null; break; default: outputFile = validateOutputFile(fileName + ".GABRIELblocks"); break; } //this handles output type ALL if(blockOutputType == BLOX_ALL) { outputFile = validateOutputFile(fileName + ".GABRIELblocks"); textData.guessBlocks(BLOX_GABRIEL); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid Gabriel blocks."); } outputFile = validateOutputFile(fileName + ".4GAMblocks"); textData.guessBlocks(BLOX_4GAM); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid 4 Gamete blocks."); } outputFile = validateOutputFile(fileName + ".SPINEblocks"); textData.guessBlocks(BLOX_SPINE); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid LD Spine blocks."); } }else{ //guesses blocks based on output type determined above. textData.guessBlocks(blockOutputType, cust); haplos = textData.generateBlockHaplotypes(textData.blocks); if (haplos != null){ filtHaplos = filterHaplos(haplos); textData.pickTags(filtHaplos); textData.saveHapsToText(haplos, textData.computeMultiDprime(filtHaplos), outputFile); }else if (!quietMode){ System.out.println("Skipping block output: no valid blocks."); } } if(Options.getAssocTest() == ASSOC_TRIO || Options.getAssocTest() == ASSOC_CC) { if (blockOutputType == BLOX_ALL){ System.out.println("Haplotype association results cannot be used with block output \"ALL\""); }else{ if (haplos != null){ blockTestSet = new AssociationTestSet(haplos,null); blockTestSet.saveHapsToText(validateOutputFile(fileName + ".HAPASSOC")); }else if (!quietMode){ System.out.println("Skipping block association output: no valid blocks."); } } } } if(outputDprime) { outputFile = validateOutputFile(fileName + ".LD"); if (textData.dpTable != null){ textData.saveDprimeToText(outputFile, TABLE_TYPE, 0, Chromosome.getSize()); }else{ textData.saveDprimeToText(outputFile, LIVE_TYPE, 0, Chromosome.getSize()); } } if (outputPNG || outputCompressedPNG){ outputFile = validateOutputFile(fileName + ".LD.PNG"); if (textData.dpTable == null){ textData.generateDPrimeTable(); textData.guessBlocks(BLOX_CUSTOM, new Vector()); } if (trackFileName != null){ textData.readAnalysisTrack(new File(trackFileName)); if(!quietMode) { System.out.println("Using analysis track file " + trackFileName); } } DPrimeDisplay dpd = new DPrimeDisplay(textData); BufferedImage i = dpd.export(0,Chromosome.getUnfilteredSize(),outputCompressedPNG); try{ Jimi.putImage("image/png", i, outputFile.getAbsolutePath()); }catch(JimiException je){ System.out.println(je.getMessage()); } } AssociationTestSet markerTestSet =null; if(Options.getAssocTest() == ASSOC_TRIO || Options.getAssocTest() == ASSOC_CC){ if (randomizeAffection){ Vector aff = new Vector(); int j=0, k=0; for (int i = 0; i < textData.getPedFile().getNumIndividuals(); i++){ if (i%2 == 0){ aff.add(new Integer(1)); j++; }else{ aff.add(new Integer(2)); k++; } } Collections.shuffle(aff); markerTestSet = new AssociationTestSet(textData.getPedFile(),aff,null,Chromosome.getAllMarkers()); }else{ markerTestSet = new AssociationTestSet(textData.getPedFile(),null,null,Chromosome.getAllMarkers()); } markerTestSet.saveSNPsToText(validateOutputFile(fileName + ".ASSOC")); } if(customAssocSet != null) { if(!quietMode) { System.out.println("Using custom association test file " + customAssocTestsFileName); } try { customAssocSet.setPermTests(doPermutationTest); customAssocSet.runFileTests(textData,markerTestSet.getMarkerAssociationResults()); customAssocSet.saveResultsToText(validateOutputFile(fileName + ".CUSTASSOC")); }catch(IOException ioe) { System.out.println("An error occured writing the custom association results file."); customAssocSet = null; } } if(doPermutationTest) { AssociationTestSet permTests = new AssociationTestSet(); permTests.cat(markerTestSet); if(blockTestSet != null) { permTests.cat(blockTestSet); } final PermutationTestSet pts = new PermutationTestSet(permutationCount,textData.getPedFile(),customAssocSet,permTests); Thread permThread = new Thread(new Runnable() { public void run() { if (pts.isCustom()){ pts.doPermutations(PermutationTestSet.CUSTOM); }else{ pts.doPermutations(PermutationTestSet.SINGLE_PLUS_BLOCKS); } } }); permThread.start(); if(!quietMode) { System.out.println("Starting " + permutationCount + " permutation tests (each . printed represents 1% of tests completed)"); } int dotsPrinted =0; while(pts.getPermutationCount() - pts.getPermutationsPerformed() > 0) { while(( (double)pts.getPermutationsPerformed() / pts.getPermutationCount())*100 > dotsPrinted) { System.out.print("."); dotsPrinted++; } try{ Thread.sleep(100); }catch(InterruptedException ie) {} } System.out.println(); try { pts.writeResultsToFile(validateOutputFile(fileName + ".PERMUT")); } catch(IOException ioe) { System.out.println("An error occured while writing the permutation test results to file."); } } if(tagging != Tagger.NONE) { if(textData.dpTable == null) { textData.generateDPrimeTable(); } Vector snps = Chromosome.getAllMarkers(); HashSet names = new HashSet(); for (int i = 0; i < snps.size(); i++) { SNP snp = (SNP) snps.elementAt(i); names.add(snp.getDisplayName()); } HashSet filteredNames = new HashSet(); for(int i=0;i<Chromosome.getSize();i++) { filteredNames.add(Chromosome.getMarker(i).getDisplayName()); } Vector sitesToCapture = new Vector(); for(int i=0;i<Chromosome.getSize();i++) { sitesToCapture.add(Chromosome.getMarker(i)); } for (int i = 0; i < forceIncludeTags.size(); i++) { String s = (String) forceIncludeTags.elementAt(i); if(!names.contains(s) && !quietMode) { System.out.println("Warning: skipping marker " + s + " in the list of forced included tags since I don't know about it."); } } for (int i = 0; i < forceExcludeTags.size(); i++) { String s = (String) forceExcludeTags.elementAt(i); if(!names.contains(s) && !quietMode) { System.out.println("Warning: skipping marker " + s + " in the list of forced excluded tags since I don't know about it."); } } //chuck out filtered jazz from excludes, and nonexistent markers from both forceExcludeTags.retainAll(filteredNames); forceIncludeTags.retainAll(names); if(!quietMode) { System.out.println("Starting tagging."); } TaggerController tc = new TaggerController(textData,forceIncludeTags,forceExcludeTags,sitesToCapture, tagging,maxNumTags,findTags); tc.runTagger(); while(!tc.isTaggingCompleted()) { try { Thread.sleep(100); }catch(InterruptedException ie) {} } tc.saveResultsToFile(validateOutputFile(fileName + ".TAGS")); tc.dumpTests(validateOutputFile(fileName + ".TESTS")); //todo: I don't like this at the moment, removed subject to further consideration. //tc.dumpTags(validateOutputFile(fileName + ".TAGSNPS")); } } catch(IOException e){ System.err.println("An error has occured:"); System.err.println(e.getMessage()); } catch(HaploViewException e){ System.err.println(e.getMessage()); } catch(PedFileException pfe) { System.err.println(pfe.getMessage()); } catch(TaggerException te){ System.err.println(te.getMessage()); } }

1,110,862

public HaplotypeAssociationResult(Haplotype[] locusHaplos, int freqCutoff, String n) { nf.setGroupingUsed(false); for (int i = 0; i < locusHaplos.length; i++){ alleles.add(locusHaplos[i]); } setFrequencyCutoff(((double)freqCutoff)/100); name = n; haps = locusHaplos; }

public HaplotypeAssociationResult(Haplotype[] locusHaplos, int freqCutoff, String n) { nf.setGroupingUsed(false); for (int i = 0; i < locusHaplos.length; i++){ alleles.add(locusHaplos[i]); } filterByFrequency(((double)freqCutoff)/100); name = n; haps = locusHaplos; }

1,110,863

public String getCountString(int i){ nf.setMinimumFractionDigits(1); nf.setMaximumFractionDigits(1); Haplotype h = (Haplotype) filteredAlleles.get(i); StringBuffer countSB = new StringBuffer(); if(Options.getAssocTest() == ASSOC_TRIO) { countSB.append(nf.format(h.getTransCount())).append(" : ").append(nf.format(h.getUntransCount())); } else if(Options.getAssocTest() == ASSOC_CC) { double caseSum = 0, controlSum = 0; for (int j = 0; j < alleles.size(); j++){ if (i!=j){ caseSum += ((Haplotype)alleles.get(j)).getCaseCount(); controlSum += ((Haplotype)alleles.get(j)).getControlCount(); } } countSB.append(nf.format(h.getCaseCount())).append(" : ").append(nf.format(caseSum)).append(", "); countSB.append(nf.format(h.getControlCount())).append(" : ").append(nf.format(controlSum)); } return countSB.toString(); }

public String getCountString(int i){ nf.setMinimumFractionDigits(1); nf.setMaximumFractionDigits(1); Haplotype h = (Haplotype) filteredAlleles.get(i); StringBuffer countSB = new StringBuffer(); if(Options.getAssocTest() == ASSOC_TRIO) { countSB.append(nf.format(h.getTransCount())).append(" : ").append(nf.format(h.getUntransCount())); } else if(Options.getAssocTest() == ASSOC_CC) { double caseSum = 0, controlSum = 0; for (int j = 0; j < alleles.size(); j++){ if (h != alleles.get(j)){ caseSum += ((Haplotype)alleles.get(j)).getCaseCount(); controlSum += ((Haplotype)alleles.get(j)).getControlCount(); } } countSB.append(nf.format(h.getCaseCount())).append(" : ").append(nf.format(caseSum)).append(", "); countSB.append(nf.format(h.getControlCount())).append(" : ").append(nf.format(controlSum)); } return countSB.toString(); }

1,110,864

public Context getContext() { return context; }

public JellyContext getContext() { return context; }

1,110,865

private void argHandler(String[] args){ //TODO: -specify values from HaplotypeDisplayController (min hap percentage etc) //TODO: -want to be able to output haps file from pedfile /* boolean nogui = false; String batchMode = ""; String hapsFileName = ""; String pedFileName = ""; String infoFileName = ""; String hapmapFileName = ""; String blockFileName = ""; boolean showCheck = false; boolean skipCheck = false; Vector ignoreMarkers = new Vector(); int outputType = -1; int maxDistance = -1; boolean quietMode = false; boolean outputDprime=false; boolean outputPNG = false; boolean outputSmallPNG = false; boolean outputCheck=false;*/ int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below outputType = -1; for(int i =0; i < args.length; i++) { if(args[i].equals("-help") || args[i].equals("-h")) { System.out.println(HELP_OUTPUT); System.exit(0); } else if(args[i].equals("-n") || args[i].equals("-nogui")) { nogui = true; } else if(args[i].equals("-p") || args[i].equals("-pedfile")) { i++; if( i>=args.length || (args[i].charAt(0) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(pedFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last pedfile listed will be used"); } pedFileName = args[i]; } } else if (args[i].equals("-skipcheck") || args[i].equals("--skipcheck")){ skipCheck = true; } //todo: fix ignoremarkers /* else if (args[i].equals("--ignoremarkers")){ i++; if(i>=args.length || (args[i].charAt(0) == '-')){ System.out.println("--ignoremarkers requires a list of markers"); System.exit(1); } else { StringTokenizer str = new StringTokenizer(args[i],","); while(str.hasMoreTokens()) { ignoreMarkers.add(str.nextToken()); } } } */ else if(args[i].equals("-ha") || args[i].equals("-l") || args[i].equals("-haps")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(hapsFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last haps file listed will be used"); } hapsFileName = args[i]; } } else if(args[i].equals("-i") || args[i].equals("-info")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(infoFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last info file listed will be used"); } infoFileName = args[i]; } } else if (args[i].equals("-a") || args[i].equals("-hapmap")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(hapmapFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last hapmap file listed will be used"); } hapmapFileName = args[i]; } } else if(args[i].equals("-k") || args[i].equals("-blocks")) { i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ blockFileName = args[i]; outputType = BLOX_CUSTOM; }else{ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } } else if (args[i].equalsIgnoreCase("-png")){ outputPNG = true; } else if (args[i].equalsIgnoreCase("-smallpng") || args[i].equalsIgnoreCase("-compressedPNG")){ outputCompressedPNG = true; } else if (args[i].equals("-track")){ i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ trackFileName = args[i]; }else{ System.out.println("-track requires a filename"); System.exit(1); } } else if(args[i].equals("-o") || args[i].equals("-output") || args[i].equalsIgnoreCase("-blockoutput")) { i++; if(!(i>=args.length) && !((args[i].charAt(0)) == '-')){ if(outputType != -1){ System.out.println("only one output argument is allowed"); System.exit(1); } if(args[i].equalsIgnoreCase("SFS") || args[i].equalsIgnoreCase("GAB")){ outputType = BLOX_GABRIEL; } else if(args[i].equalsIgnoreCase("GAM")){ outputType = BLOX_4GAM; } else if(args[i].equalsIgnoreCase("MJD") || args[i].equalsIgnoreCase("SPI")){ outputType = BLOX_SPINE; } else if(args[i].equalsIgnoreCase("ALL")) { outputType = BLOX_ALL; } } else { //defaults to SFS output outputType = BLOX_GABRIEL; i--; } } else if(args[i].equals("-d") || args[i].equals("--dprime") || args[i].equals("-dprime")) { outputDprime = true; } else if (args[i].equals("-c") || args[i].equals("-check")){ outputCheck = true; } else if(args[i].equals("-m") || args[i].equals("-maxdistance")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires an integer argument"); System.exit(1); } else { if(maxDistance != -1){ System.out.println("only one "+args[i-1] + " argument allowed"); System.exit(1); } maxDistance = Integer.parseInt(args[i]); if(maxDistance<0){ System.out.println(args[i-1] + " argument must be a positive integer"); System.exit(1); } } } else if(args[i].equals("-b") || args[i].equals("-batch")) { //batch mode i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(batchFileName != null){ System.out.println("multiple " + args[i-1] + " arguments found. only last batch file listed will be used"); } batchFileName = args[i]; } } else if(args[i].equals("-q") || args[i].equals("-quiet")) { quietMode = true; } else { System.out.println("invalid parameter specified: " + args[i]); } } int countOptions = 0; if(pedFileName != null) { countOptions++; } if(hapsFileName != null) { countOptions++; } if(hapmapFileName != null) { countOptions++; } if(batchFileName != null) { countOptions++; } if(countOptions > 1) { System.out.println("Only one genotype input file may be specified on the command line."); System.exit(1); } else if(countOptions == 0) { System.out.println("You must specify a genotype input file."); System.exit(1); } //mess with vars, set defaults, etc if( outputType == -1 && ( pedFileName != null || hapsFileName != null || batchFileName != null || hapmapFileName != null) && !outputDprime && !outputCheck && !outputPNG && !outputCompressedPNG) { outputType = BLOX_GABRIEL; if(nogui && !quietMode) { System.out.println("No output type specified. Default of Gabriel will be used"); } } if(skipCheck && !quietMode) { System.out.println("Skipping genotype file check"); } if(maxDistance == -1){ maxDistance = 500; } Options.setMaxDistance(maxDistance); }

private void argHandler(String[] args){ //TODO: -specify values from HaplotypeDisplayController (min hap percentage etc) //TODO: -want to be able to output haps file from pedfile /* boolean nogui = false; String batchMode = ""; String hapsFileName = ""; String pedFileName = ""; String infoFileName = ""; String hapmapFileName = ""; String blockFileName = ""; boolean showCheck = false; boolean skipCheck = false; Vector ignoreMarkers = new Vector(); int outputType = -1; int maxDistance = -1; boolean quietMode = false; boolean outputDprime=false; boolean outputPNG = false; boolean outputSmallPNG = false; boolean outputCheck=false;*/ int maxDistance = -1; //this means that user didn't specify any output type if it doesn't get changed below outputType = -1; for(int i =0; i < args.length; i++) { if(args[i].equals("-help") || args[i].equals("-h")) { System.out.println(HELP_OUTPUT); System.exit(0); } else if(args[i].equals("-n") || args[i].equals("-nogui")) { nogui = true; } else if(args[i].equals("-p") || args[i].equals("-pedfile")) { i++; if( i>=args.length || (args[i].charAt(0) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(pedFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last pedfile listed will be used"); } pedFileName = args[i]; } } else if (args[i].equals("-skipcheck") || args[i].equals("--skipcheck")){ skipCheck = true; } //todo: fix ignoremarkers /* else if (args[i].equals("--ignoremarkers")){ i++; if(i>=args.length || (args[i].charAt(0) == '-')){ System.out.println("--ignoremarkers requires a list of markers"); System.exit(1); } else { StringTokenizer str = new StringTokenizer(args[i],","); while(str.hasMoreTokens()) { ignoreMarkers.add(str.nextToken()); } } } */ else if(args[i].equals("-ha") || args[i].equals("-l") || args[i].equals("-haps")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(hapsFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last haps file listed will be used"); } hapsFileName = args[i]; } } else if(args[i].equals("-i") || args[i].equals("-info")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(infoFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last info file listed will be used"); } infoFileName = args[i]; } } else if (args[i].equals("-a") || args[i].equals("-hapmap")){ i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(hapmapFileName != null){ System.out.println("multiple "+args[i-1] + " arguments found. only last hapmap file listed will be used"); } hapmapFileName = args[i]; } } else if(args[i].equals("-k") || args[i].equals("-blocks")) { i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ blockFileName = args[i]; outputType = BLOX_CUSTOM; }else{ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } } else if (args[i].equalsIgnoreCase("-png")){ outputPNG = true; } else if (args[i].equalsIgnoreCase("-smallpng") || args[i].equalsIgnoreCase("-compressedPNG")){ outputCompressedPNG = true; } else if (args[i].equals("-track")){ i++; if (!(i>=args.length) && !((args[i].charAt(0)) == '-')){ trackFileName = args[i]; }else{ System.out.println("-track requires a filename"); System.exit(1); } } else if(args[i].equals("-o") || args[i].equals("-output") || args[i].equalsIgnoreCase("-blockoutput")) { i++; if(!(i>=args.length) && !((args[i].charAt(0)) == '-')){ if(outputType != -1){ System.out.println("only one output argument is allowed"); System.exit(1); } if(args[i].equalsIgnoreCase("SFS") || args[i].equalsIgnoreCase("GAB")){ outputType = BLOX_GABRIEL; } else if(args[i].equalsIgnoreCase("GAM")){ outputType = BLOX_4GAM; } else if(args[i].equalsIgnoreCase("MJD") || args[i].equalsIgnoreCase("SPI")){ outputType = BLOX_SPINE; } else if(args[i].equalsIgnoreCase("ALL")) { outputType = BLOX_ALL; } } else { //defaults to SFS output outputType = BLOX_GABRIEL; i--; } } else if(args[i].equals("-d") || args[i].equals("--dprime") || args[i].equals("-dprime")) { outputDprime = true; } else if (args[i].equals("-c") || args[i].equals("-check")){ outputCheck = true; } else if(args[i].equals("-m") || args[i].equals("-maxdistance")) { i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires an integer argument"); System.exit(1); } else { if(maxDistance != -1){ System.out.println("only one "+args[i-1] + " argument allowed"); System.exit(1); } maxDistance = Integer.parseInt(args[i]); if(maxDistance<0){ System.out.println(args[i-1] + " argument must be a positive integer"); System.exit(1); } } } else if(args[i].equals("-b") || args[i].equals("-batch")) { //batch mode i++; if(i>=args.length || ((args[i].charAt(0)) == '-')){ System.out.println(args[i-1] + " requires a filename"); System.exit(1); } else{ if(batchFileName != null){ System.out.println("multiple " + args[i-1] + " arguments found. only last batch file listed will be used"); } batchFileName = args[i]; } } else if(args[i].equals("-q") || args[i].equals("-quiet")) { quietMode = true; } else { System.out.println("invalid parameter specified: " + args[i]); } } int countOptions = 0; if(pedFileName != null) { countOptions++; } if(hapsFileName != null) { countOptions++; } if(hapmapFileName != null) { countOptions++; } if(batchFileName != null) { countOptions++; } if(countOptions > 1) { System.out.println("Only one genotype input file may be specified on the command line."); System.exit(1); } else if(countOptions == 0 && nogui) { System.out.println("You must specify a genotype input file."); System.exit(1); } //mess with vars, set defaults, etc if( outputType == -1 && ( pedFileName != null || hapsFileName != null || batchFileName != null || hapmapFileName != null) && !outputDprime && !outputCheck && !outputPNG && !outputCompressedPNG) { outputType = BLOX_GABRIEL; if(nogui && !quietMode) { System.out.println("No output type specified. Default of Gabriel will be used"); } } if(skipCheck && !quietMode) { System.out.println("Skipping genotype file check"); } if(maxDistance == -1){ maxDistance = 500; } Options.setMaxDistance(maxDistance); }

1,110,866

protected String getBodyText( Context context ) throws Exception { // XXX: could maybe optimise this later on by having a pool of buffers StringWriter writer = new StringWriter(); body.run( context, XMLOutput.createXMLOutput( writer ) ); return writer.toString(); }

1,110,868

public void run(Context context, XMLOutput output) throws Exception { getBody().run(context, output); }

1,110,869

public void clear() { getThreadScriptDataMap().clear(); variables.clear(); }

1,110,870

public void clearScriptData() { threadLocalScriptData = new ThreadLocal(); }

public void clearScriptData() { threadLocalScriptData.clear(); }

1,110,871

public Map getThreadScriptDataMap() { Map rv; Map data = (Map) threadLocalScriptData.get(); if (data == null) { rv = new HashMap(); threadLocalScriptData.set(rv); } else { rv = data; } return rv; }

public Map getThreadScriptDataMap() { Map rv; Thread t = Thread.currentThread(); Map data = (Map) threadLocalScriptData.get(t); if (data == null) { rv = new HashMap(); threadLocalScriptData.set(rv); } else { rv = data; } return rv; }

1,110,872

public Map getThreadScriptDataMap() { Map rv; Map data = (Map) threadLocalScriptData.get(); if (data == null) { rv = new HashMap(); threadLocalScriptData.set(rv); } else { rv = data; } return rv; }

public Map getThreadScriptDataMap() { Map rv; Map data = (Map) threadLocalScriptData.get(); if (data == null) { rv = new HashMap(); threadLocalScriptData.put(t, rv); } else { rv = data; } return rv; }

1,110,873

public void setNullable(int argNullable) { int oldNullable = this.nullable; logger.debug("Changing nullable "+oldNullable+" -> "+argNullable); if (this.nullable != argNullable) { this.nullable = argNullable; fireDbObjectChanged("nullable",oldNullable,argNullable); } }

1,110,879

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } this.primaryKeySeq = argPrimaryKeySeq; fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); SQLObject p = parent; if (p != null) { p.removeChild(this); int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } Integer oldPrimaryKeySeq = primaryKeySeq; if (!isMagicEnabled()) { this.primaryKeySeq = argPrimaryKeySeq; fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); } else try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } this.primaryKeySeq = argPrimaryKeySeq; fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); SQLObject p = parent; if (p != null) { p.removeChild(this); int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

1,110,880

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); Integer oldPrimaryKeySeq = primaryKeySeq; if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } this.primaryKeySeq = argPrimaryKeySeq; fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); SQLObject p = parent; if (p != null) { p.removeChild(this); int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

public void setPrimaryKeySeq(Integer argPrimaryKeySeq) { // do nothing if there's no change if ( (primaryKeySeq == null && argPrimaryKeySeq == null) || (primaryKeySeq != null && primaryKeySeq.equals(argPrimaryKeySeq)) ) { return; } try { startCompoundEdit("Starting PrimaryKeySeq compound edit"); if (argPrimaryKeySeq != null && !this.autoIncrement) { setNullable(DatabaseMetaData.columnNoNulls); } this.primaryKeySeq = argPrimaryKeySeq; fireDbObjectChanged("primaryKeySeq",oldPrimaryKeySeq,argPrimaryKeySeq); SQLObject p = parent; if (p != null) { p.removeChild(this); int idx = 0; int targetPKS = primaryKeySeq == null ? Integer.MAX_VALUE : primaryKeySeq.intValue(); logger.debug("Parent = "+p); logger.debug("Parent.children = "+p.children); for (SQLColumn col : (List<SQLColumn>) p.children) { if (col.getPrimaryKeySeq() == null || col.getPrimaryKeySeq() > targetPKS) { logger.debug("idx is " + idx); break; } idx++; } p.addChild(idx, this); getParentTable().normalizePrimaryKey(); } } catch (ArchitectException e) { throw new ArchitectRuntimeException(e); } finally { endCompoundEdit("Ending PrimaryKeySeq compound edit"); } }

1,110,881

public void setType(int argType) { int oldType = type; if (type != argType) { setSourceDataTypeName(null); this.type = argType; fireDbObjectChanged("type",oldType,argType); } }

1,110,882

public void mouseClicked(MouseEvent evt) { Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if ( c instanceof Relationship) { if (evt.getClickCount() == 2) { ArchitectFrame.getMainInstance().editRelationshipAction.actionPerformed (new ActionEvent(evt.getSource(), ActionEvent.ACTION_PERFORMED, ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)); } else if(evt.getClickCount()==1){ if (c.isSelected()&& componentPreviouslySelected)c.setSelected(false); } } else if ( c instanceof TablePane ) { TablePane tp = (TablePane) c; if ((evt.getModifiers() & MouseEvent.BUTTON1_MASK) != 0) { try { int selectedColIndex = tp.pointToColumnIndex(p); if (evt.getClickCount() == 2) { // double click if (tp.isSelected()) { ArchitectFrame af = ArchitectFrame.getMainInstance(); if (selectedColIndex == TablePane.COLUMN_INDEX_TITLE) { af.editTableAction.actionPerformed (new ActionEvent(tp, ActionEvent.ACTION_PERFORMED, ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)); } else if (selectedColIndex >= 0) { af.editColumnAction.actionPerformed (new ActionEvent(tp, ActionEvent.ACTION_PERFORMED, ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)); } } } else if(evt.getClickCount()==1) { System.out.println("Col index "+selectedColIndex); if (selectedColIndex > TablePane.COLUMN_INDEX_TITLE && componentPreviouslySelected){ ((TablePane)c).deselectColumn(selectedColIndex); } else if (c.isSelected()&& componentPreviouslySelected) { c.setSelected(false); } } } catch (ArchitectException e) { logger.error("Exception converting point to column", e); } } } else { maybeShowPopup(evt); } }

public void mouseClicked(MouseEvent evt) { Point p = evt.getPoint(); unzoomPoint(p); PlayPenComponent c = contentPane.getComponentAt(p); if (c != null) p.translate(-c.getX(), -c.getY()); if ( c instanceof Relationship) { if (evt.getClickCount() == 2) { ArchitectFrame.getMainInstance().editRelationshipAction.actionPerformed (new ActionEvent(evt.getSource(), ActionEvent.ACTION_PERFORMED, ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)); } else if(evt.getClickCount()==1){ if (c.isSelected()&& componentPreviouslySelected)c.setSelected(false); } } else if ( c instanceof TablePane ) { TablePane tp = (TablePane) c; if ((evt.getModifiers() & MouseEvent.BUTTON1_MASK) != 0) { try { int selectedColIndex = tp.pointToColumnIndex(p); if (evt.getClickCount() == 2) { // double click if (tp.isSelected()) { ArchitectFrame af = ArchitectFrame.getMainInstance(); if (selectedColIndex == TablePane.COLUMN_INDEX_TITLE) { af.editTableAction.actionPerformed (new ActionEvent(tp, ActionEvent.ACTION_PERFORMED, ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)); } else if (selectedColIndex >= 0) { af.editColumnAction.actionPerformed (new ActionEvent(tp, ActionEvent.ACTION_PERFORMED, ArchitectSwingConstants.ACTION_COMMAND_SRC_PLAYPEN)); } } } else if(evt.getClickCount()==1) { logger.debug("Col index "+selectedColIndex); if (selectedColIndex > TablePane.COLUMN_INDEX_TITLE && componentPreviouslySelected){ ((TablePane)c).deselectColumn(selectedColIndex); } else if (c.isSelected()&& componentPreviouslySelected) { c.setSelected(false); } } } catch (ArchitectException e) { logger.error("Exception converting point to column", e); } } } else { maybeShowPopup(evt); } }

1,110,883

private void addDependantsFromKeys(ResultSet rs) throws SQLException { Conflict prev = null; while (rs.next()) { Conflict c = new Conflict("FOREIGN KEY", rs.getString("FKTABLE_CAT"), rs.getString("FKTABLE_SCHEM"), rs.getString("FK_NAME")); // multi-column keys get multiple rows in this result set. We need to skip 'em. if (c.equals(prev)) continue; prev = c; c.setSqlDropStatement( ddlg.makeDropForeignKeySQL(c.getCatalog(), c.getSchema(), rs.getString("FKTABLE_NAME"), c.getName())); dependants.add(c); } }

1,110,884

public void findConflicting() throws SQLException, ArchitectException { doingFindConflicting = true; Connection con = null; try { conflicts = new ArrayList(); monitorableProgress = 0; if (logger.isDebugEnabled()) { logger.debug("About to find conflicting objects for DDL Script: "+ddlStatements); } con = targetDatabase.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); Iterator it = ddlStatements.iterator(); while (it.hasNext()) { DDLStatement ddlStmt = (DDLStatement) it.next(); monitorableProgress += 1; if (ddlStmt.getType() != DDLStatement.StatementType.CREATE) continue; SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; String cat = ddlStmt.getTargetCatalog(); String sch = ddlStmt.getTargetSchema(); if (logger.isDebugEnabled()) { logger.debug("Finding conflicts for TABLE '" + cat + "'.'" + sch + "'.'" + t.getPhysicalName() + "'"); } ResultSet rs = dbmd.getTables( ddlg.toIdentifier(cat), ddlg.toIdentifier(sch), ddlg.toIdentifier(t.getPhysicalName()), null); while (rs.next()) { Conflict c = new Conflict( rs.getString("TABLE_TYPE"), rs.getString("TABLE_CAT"), rs.getString("TABLE_SCHEM"), rs.getString("TABLE_NAME")); c.setSqlDropStatement(ddlg.makeDropTableSQL(c.getCatalog(), c.getSchema(), c.getName())); c.addTableDependants(dbmd); conflicts.add(c); } rs.close(); } else if (clazz.equals(SQLRelationship.class)) { logger.error("Relationship conflicts are not supported yet!"); } else { throw new IllegalArgumentException( "Unknown subclass of SQLObject: " + clazz.getName()); } } if (logger.isDebugEnabled()) { logger.debug("Found conflicts: " + conflicts); } } finally { findConflictingFinished = true; doingFindConflicting = false; try { if (con != null) con.close(); } catch (SQLException ex) { logger.error("Couldn't close connection"); } } }

public void findConflicting() throws SQLException, ArchitectException { doingFindConflicting = true; Connection con = null; try { conflicts = new ArrayList(); monitorableProgress = 0; if (logger.isDebugEnabled()) { logger.debug("About to find conflicting objects for DDL Script: "+ddlStatements); } con = targetDatabase.getConnection(); DatabaseMetaData dbmd = con.getMetaData(); Iterator it = ddlStatements.iterator(); while (it.hasNext()) { DDLStatement ddlStmt = (DDLStatement) it.next(); monitorableProgress += 1; if (ddlStmt.getType() != DDLStatement.StatementType.CREATE) continue; SQLObject so = ddlStmt.getObject(); Class clazz = so.getClass(); if (clazz.equals(SQLTable.class)) { SQLTable t = (SQLTable) so; String cat = ddlStmt.getTargetCatalog(); String sch = ddlStmt.getTargetSchema(); if (logger.isDebugEnabled()) { logger.debug("Finding conflicts for TABLE '" + cat + "'.'" + sch + "'.'" + t.getPhysicalName() + "'"); } ResultSet rs = dbmd.getTables( ddlg.toIdentifier(cat), ddlg.toIdentifier(sch), ddlg.toIdentifier(t.getPhysicalName()), null); while (rs.next()) { Conflict c = new Conflict( rs.getString("TABLE_TYPE"), rs.getString("TABLE_CAT"), rs.getString("TABLE_SCHEM"), rs.getString("TABLE_NAME")); ddlg.setTargetCatalog(c.getCatalog()); ddlg.setTargetSchema(c.getSchema()); c.setSqlDropStatement(ddlg.makeDropTableSQL(c.getName())); c.addTableDependants(dbmd); conflicts.add(c); } rs.close(); } else if (clazz.equals(SQLRelationship.class)) { logger.error("Relationship conflicts are not supported yet!"); } else { throw new IllegalArgumentException( "Unknown subclass of SQLObject: " + clazz.getName()); } } if (logger.isDebugEnabled()) { logger.debug("Found conflicts: " + conflicts); } } finally { findConflictingFinished = true; doingFindConflicting = false; try { if (con != null) con.close(); } catch (SQLException ex) { logger.error("Couldn't close connection"); } } }

1,110,885

public Tag getTagOfTagScript(TagScript script) { if( script == null ) return null; return (Tag) tagHolderMap.get(script); }

public Tag getTagOfTagScript(TagScript script) { if( script == null ) return null; Tag tag = (Tag) tagHolderMap.get(script); if( tag == null && getParent() != null) { return getParent().getTagOfTagScript(script); } else { return tag; } }

1,110,886

public void run(Context context, XMLOutput output) throws Exception { tagLibrary = new DynamicTagLibrary( getUri() ); context.registerTagLibrary( getUri(), tagLibrary ); getBody().run(context, output); tagLibrary = null; }

public void run(JellyContext context, XMLOutput output) throws Exception { tagLibrary = new DynamicTagLibrary( getUri() ); context.registerTagLibrary( getUri(), tagLibrary ); getBody().run(context, output); tagLibrary = null; }

1,110,887

public DynamicTagLibrary(String uri) { this.uri = uri; }

1,110,888

public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ this.results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); TDTResult curRes = (TDTResult)results.get(j); //System.out.println("marker "+ j + ":\t " + allele1T + "\t" + allele1U + "\t" + allele2T + "\t" + allele2U); curRes.tallyInd(allele1T,allele1U); curRes.tallyInd(allele2T,allele2U); } } for(int i=0;i<this.results.size();i++){ TDTResult tempRes = (TDTResult)this.results.get(i); int[][] counts = tempRes.counts; //System.out.println( counts[0][0] + "\t" + counts[1][1] + "\t" + counts[0][1] + "\t" + counts[1][0]); } return this.results; }

1,110,889

public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ this.results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); TDTResult curRes = (TDTResult)results.get(j); //System.out.println("marker "+ j + ":\t " + allele1T + "\t" + allele1U + "\t" + allele2T + "\t" + allele2U); curRes.tallyInd(allele1T,allele1U); curRes.tallyInd(allele2T,allele2U); } } for(int i=0;i<this.results.size();i++){ TDTResult tempRes = (TDTResult)this.results.get(i); int[][] counts = tempRes.counts; //System.out.println( counts[0][0] + "\t" + counts[1][1] + "\t" + counts[0][1] + "\t" + counts[1][0]); } return this.results; }

public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); TDTResult curRes = (TDTResult)results.get(j); //System.out.println("marker "+ j + ":\t " + allele1T + "\t" + allele1U + "\t" + allele2T + "\t" + allele2U); curRes.tallyInd(allele1T,allele1U); curRes.tallyInd(allele2T,allele2U); } } for(int i=0;i<this.results.size();i++){ TDTResult tempRes = (TDTResult)this.results.get(i); int[][] counts = tempRes.counts; //System.out.println( counts[0][0] + "\t" + counts[1][1] + "\t" + counts[0][1] + "\t" + counts[1][0]); } return this.results; }

1,110,890

public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ this.results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); TDTResult curRes = (TDTResult)results.get(j); //System.out.println("marker "+ j + ":\t " + allele1T + "\t" + allele1U + "\t" + allele2T + "\t" + allele2U); curRes.tallyInd(allele1T,allele1U); curRes.tallyInd(allele2T,allele2U); } } for(int i=0;i<this.results.size();i++){ TDTResult tempRes = (TDTResult)this.results.get(i); int[][] counts = tempRes.counts; //System.out.println( counts[0][0] + "\t" + counts[1][1] + "\t" + counts[0][1] + "\t" + counts[1][0]); } return this.results; }

1,110,891

public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ this.results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); TDTResult curRes = (TDTResult)results.get(j); //System.out.println("marker "+ j + ":\t " + allele1T + "\t" + allele1U + "\t" + allele2T + "\t" + allele2U); curRes.tallyInd(allele1T,allele1U); curRes.tallyInd(allele2T,allele2U); } } for(int i=0;i<this.results.size();i++){ TDTResult tempRes = (TDTResult)this.results.get(i); int[][] counts = tempRes.counts; //System.out.println( counts[0][0] + "\t" + counts[1][1] + "\t" + counts[0][1] + "\t" + counts[1][0]); } return this.results; }

public Vector calcTDT(Vector chromosomes) { int numChroms; Chromosome chromT, chromU,chromTemp; String ped,ind; Vector temp; numChroms = chromosomes.size(); temp = (Vector)chromosomes.clone(); chromosomes = temp; int numMarkers = Chromosome.getSize(); for(int k=0;k<numMarkers;k++){ this.results.add(new TDTResult(Chromosome.getMarker(k))); } for(int i=0;i<chromosomes.size()-3;i++){ Chromosome chrom1T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom1U = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2T = (Chromosome)chromosomes.get(i); i++; Chromosome chrom2U = (Chromosome)chromosomes.get(i); //System.out.println("ind1T: " + chrom1T.getPed() + "\t" + chrom1T.getIndividual() ); //System.out.println("ind1U: " + chrom1U.getPed() + "\t" + chrom1U.getIndividual() ); //System.out.println("ind2T: " + chrom2T.getPed() + "\t" + chrom2T.getIndividual() ); //System.out.println("ind2U: " + chrom2U.getPed() + "\t" + chrom2U.getIndividual() ); for(int j=0;j<numMarkers;j++){ byte allele1T = chrom1T.getGenotype(j); byte allele1U = chrom1U.getGenotype(j); byte allele2T = chrom2T.getGenotype(j); byte allele2U = chrom2U.getGenotype(j); TDTResult curRes = (TDTResult)results.get(j); //System.out.println("marker "+ j + ":\t " + allele1T + "\t" + allele1U + "\t" + allele2T + "\t" + allele2U); curRes.tallyInd(allele1T,allele1U); curRes.tallyInd(allele2T,allele2U); } } for(int i=0;i<this.results.size();i++){ TDTResult tempRes = (TDTResult)this.results.get(i); int[][] counts = tempRes.counts; //System.out.println( counts[0][0] + "\t" + counts[1][1] + "\t" + counts[0][1] + "\t" + counts[1][0]); } return results; }

1,110,892

public void doTag(XMLOutput output) throws Exception { Object obj = getObject(); if ( this.task != null ) { Method method = MethodUtils.getAccessibleMethod( this.task.getClass(), "addText", addTaskParamTypes ); if (method != null) { String text = getBodyText(); Object[] args = { text }; method.invoke(this.task, args); } else { getBody().run(context, output); } this.task.perform(); } else { getBody().run( context, output ); AntTagSupport parent = (AntTagSupport) findAncestorWithClass(AntTagSupport.class); if ( parent != null ) { // otherwise it -must- be a top-level, non-parented datatype. Object parentObj = parent.getObject(); if ( parentObj != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( parentObj.getClass() ); try { ih.storeElement( getAntProject(), parentObj, getObject(), getTagName() ); } catch (Exception e) { } } } } }

public void doTag(XMLOutput output) throws Exception { Object obj = getObject(); if ( this.task != null ) { Method method = MethodUtils.getAccessibleMethod( this.task.getClass(), "addText", addTaskParamTypes ); if (method != null) { String text = getBodyText(); Object[] args = { text }; method.invoke(this.task, args); } else { invokeBody(output); } this.task.perform(); } else { getBody().run( context, output ); AntTagSupport parent = (AntTagSupport) findAncestorWithClass(AntTagSupport.class); if ( parent != null ) { // otherwise it -must- be a top-level, non-parented datatype. Object parentObj = parent.getObject(); if ( parentObj != null ) { IntrospectionHelper ih = IntrospectionHelper.getHelper( parentObj.getClass() ); try { ih.storeElement( getAntProject(), parentObj, getObject(), getTagName() ); } catch (Exception e) { } } } } }

1,110,893

public void actionPerformed( ActionEvent evt ) { if ( evt.getActionCommand().equals( "save" ) ) { try { ctrl.save(); } catch ( Exception e ) { log.warn( "exception while saving" + e.getMessage() ); e.printStackTrace(); } } else if ( evt.getActionCommand().equals( "discard" ) ) { log.debug( "Discarding data" ); ctrl.discard(); } else if ( evt.getSource() == qualityField ) { log.debug( "quality changed" ); ctrl.viewChanged( this, PhotoInfoController.QUALITY ); } }

public void actionPerformed( ActionEvent evt ) { if ( evt.getActionCommand().equals( "save" ) ) { try { ctrl.save(); } catch ( Exception e ) { log.warn( "exception while saving" + e.getMessage() ); e.printStackTrace(); } } else if ( evt.getActionCommand().equals( "discard" ) ) { log.debug( "Discarding data" ); ctrl.discard(); } else if ( evt.getSource() == qualityField ) { log.debug( "quality changed" ); if ( getQuality() != null ) { ctrl.viewChanged( this, PhotoInfoController.QUALITY ); } } }

1,110,895

public String getPhotographer( ) { return photographerField.getText( ); }

public String getPhotographer( ) { String str = photographerField.getText( ); return str; }

1,110,897

public Number getQuality() { return new Integer( qualityField.getSelectedIndex() ); }

public Number getQuality() { int q = qualityField.getSelectedIndex(); Integer retval = null; if ( q >= 0 ) { retval = new Integer( q ); } return retval; }

1,110,898

public void insertUpdate( DocumentEvent ev ) { Document changedDoc = ev.getDocument(); String changedField = (String) changedDoc.getProperty( FIELD_NAME ); ctrl.viewChanged( this, changedField );// // Handle fuzzy time// if ( changedDoc == fuzzyDateDoc ) {// log.warn( "Fuzzy date entered" );// String fdStr = fuzzyDateField.getText();// FuzzyDate fd = FuzzyDate.parse( fdStr );// // if ( fd != null ) {// // log.warn( "FuzzyDate parsed succesfully!!!" );// // shootingDayField.setValue( fd.getDate() );// // timeAccuracyField.setValue( new Double( fd.getAccuracy() ) );// // } // } }

public void insertUpdate( DocumentEvent ev ) { Document changedDoc = ev.getDocument(); String changedField = (String) changedDoc.getProperty( FIELD_NAME ); Object fieldValue = ctrl.getField( changedField ); if ( fieldValue != null || changedDoc.getLength() > 0 ) { ctrl.viewChanged( this, changedField ); }// // Handle fuzzy time// if ( changedDoc == fuzzyDateDoc ) {// log.warn( "Fuzzy date entered" );// String fdStr = fuzzyDateField.getText();// FuzzyDate fd = FuzzyDate.parse( fdStr );// // if ( fd != null ) {// // log.warn( "FuzzyDate parsed succesfully!!!" );// // shootingDayField.setValue( fd.getDate() );// // timeAccuracyField.setValue( new Double( fd.getAccuracy() ) );// // } // } }

1,110,899

public void propertyChange( PropertyChangeEvent ev ) { if ( ev.getPropertyName().equals( "value" ) ) { Object src = ev.getSource(); if ( src.getClass() == JFormattedTextField.class ) { Object field = ((JFormattedTextField) src).getClientProperty( FIELD_NAME ); Object value = ((JFormattedTextField) src).getValue(); /* Field value is set to null (as it is when ctrl is controlling multiple photos which have differing value for te field) this is called every time the field is accessed, so we must not notify the controller. After the user has actually set the value it is no longer null. */ if ( value != null ) { log.warn( "Property changed: " + (String) field ); System.out.println( "Property changed: " + (String) field ); ctrl.viewChanged( this, (String) field ); } } } }

1,110,900

public void setQuality( Number quality ) { if ( quality != null ) { qualityField.setSelectedIndex( quality.intValue() ); } else { qualityField.setSelectedIndex( 0 ); } }

public void setQuality( Number quality ) { if ( quality != null ) { qualityField.setSelectedIndex( quality.intValue() ); } else { qualityField.setSelectedIndex( -1 ); } }

1,110,901

public void addSQLObjectListener(SQLObjectListener l) { if (l == null) throw new NullPointerException("You can't add a null listener"); if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } getSQLObjectListeners().add(l); }

1,110,903

public void addSQLObjectListener(SQLObjectListener l) { if (l == null) throw new NullPointerException("You can't add a null listener"); if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } getSQLObjectListeners().add(l); }

public void addSQLObjectListener(SQLObjectListener l) { if (l == null) throw new NullPointerException("You can't add a null listener"); if (getSQLObjectListeners().contains(l)) { if (logger.isDebugEnabled()) { logger.debug("NOT Adding duplicate listener "+l+" to SQLObject "+this); } return; } }

1,110,904

protected void fireDbChildrenInserted(int[] newIndices, List newChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenInserted event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, newIndices, (SQLObject[]) newChildren.toArray(new SQLObject[newChildren.size()]), isSecondaryChangeMode()); Iterator it = getSQLObjectListeners().iterator(); int count = 0; while (it.hasNext()) { count ++; ((SQLObjectListener) it.next()).dbChildrenInserted(e); } logger.debug(getClass().getName()+": notified "+count+" listeners"); }

1,110,905

protected void fireDbChildrenInserted(int[] newIndices, List newChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenInserted event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, newIndices, (SQLObject[]) newChildren.toArray(new SQLObject[newChildren.size()]), isSecondaryChangeMode()); Iterator it = getSQLObjectListeners().iterator(); int count = 0; while (it.hasNext()) { count ++; ((SQLObjectListener) it.next()).dbChildrenInserted(e); } logger.debug(getClass().getName()+": notified "+count+" listeners"); }

protected void fireDbChildrenInserted(int[] newIndices, List newChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenInserted event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, newIndices, (SQLObject[]) newChildren.toArray(new SQLObject[newChildren.size()]), isSecondaryChangeMode()); Iterator it = getSQLObjectListeners().iterator(); int count = 0; while (it.hasNext()) { count ++; ((SQLObjectListener) it.next()).dbChildrenInserted(e); } }

1,110,906

protected void fireDbChildrenRemoved(int[] oldIndices, List oldChildren) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbChildrenRemoved event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent (this, oldIndices, (SQLObject[]) oldChildren.toArray(new SQLObject[oldChildren.size()]), isSecondaryChangeMode()); Iterator it = getSQLObjectListeners().iterator(); while (it.hasNext()) { ((SQLObjectListener) it.next()).dbChildrenRemoved(e); } }

1,110,907

protected void fireDbObjectChanged(String propertyName, Object oldValue, Object newValue) { SQLObjectEvent e = new SQLObjectEvent( this, propertyName, oldValue, newValue, isSecondaryChangeMode()); boolean same = (oldValue == null ? oldValue == newValue : oldValue.equals(newValue)); if (same) { logger.debug("Object changed event aborted, the old value '"+oldValue+"' of " +propertyName+" equals the new value '"+newValue+"'"); return; } if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbObjectChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } int count = 0; Iterator it = getSQLObjectListeners().iterator(); while (it.hasNext()) { count++; ((SQLObjectListener) it.next()).dbObjectChanged(e); } if (logger.isDebugEnabled()) logger.debug("Notified "+count+" listeners."); }

1,110,908

protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSecondaryChangeMode()); int count = 0; Iterator it = getSQLObjectListeners().iterator(); while (it.hasNext()) { count++; ((SQLObjectListener) it.next()).dbStructureChanged(e); } if (logger.isDebugEnabled()) logger.debug("Notified "+count+" listeners."); }

public void fireDbStructureChanged() { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSecondaryChangeMode()); int count = 0; Iterator it = getSQLObjectListeners().iterator(); while (it.hasNext()) { count++; ((SQLObjectListener) it.next()).dbStructureChanged(e); } if (logger.isDebugEnabled()) logger.debug("Notified "+count+" listeners."); }

1,110,909

protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSecondaryChangeMode()); int count = 0; Iterator it = getSQLObjectListeners().iterator(); while (it.hasNext()) { count++; ((SQLObjectListener) it.next()).dbStructureChanged(e); } if (logger.isDebugEnabled()) logger.debug("Notified "+count+" listeners."); }

protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, null, isSecondaryChangeMode()); int count = 0; Iterator it = getSQLObjectListeners().iterator(); while (it.hasNext()) { count++; ((SQLObjectListener) it.next()).dbStructureChanged(e); } if (logger.isDebugEnabled()) logger.debug("Notified "+count+" listeners."); }

1,110,910

protected void fireDbStructureChanged(String propertyName) { if (logger.isDebugEnabled()) { logger.debug(getClass().getName()+" "+toString()+": " + "firing dbStructureChanged event " + "(secondary = "+isSecondaryChangeMode()+")"); } SQLObjectEvent e = new SQLObjectEvent( this, propertyName, isSecondaryChangeMode()); int count = 0; Iterator it = getSQLObjectListeners().iterator(); while (it.hasNext()) { count++; ((SQLObjectListener) it.next()).dbStructureChanged(e); } if (logger.isDebugEnabled()) logger.debug("Notified "+count+" listeners."); }

1,110,911

public List getSQLObjectListeners() { if (sqlObjectListeners == null) { sqlObjectListeners = new LinkedList(); } return sqlObjectListeners; }

1,110,912

public void removeSQLObjectListener(SQLObjectListener l) { getSQLObjectListeners().remove(l); }

public void removeSQLObjectListener(SQLObjectListener l) { synchronized(sqlObjectListeners) { sqlObjectListeners.remove(l); } }

1,110,913

public void invokeBody(XMLOutput output) throws Exception { if ( isTrim() && ! hasTrimmed ) { trimBody(); } getBody().run(context, output); }

1,110,915

protected void trimBody() { // #### should refactor this code into // #### trimWhitespace() methods on the Script objects if ( body instanceof CompositeTextScriptBlock ) { CompositeTextScriptBlock block = (CompositeTextScriptBlock) body; List list = block.getScriptList(); int size = list.size(); if ( size > 0 ) { Script script = (Script) list.get(0); if ( script instanceof TextScript ) { TextScript textScript = (TextScript) script; textScript.trimStartWhitespace(); } if ( size > 1 ) { script = (Script) list.get(size - 1); if ( script instanceof TextScript ) { TextScript textScript = (TextScript) script; textScript.trimEndWhitespace(); } } } } else if ( body instanceof ScriptBlock ) { ScriptBlock block = (ScriptBlock) body; List list = block.getScriptList(); for ( int i = list.size() - 1; i >= 0; i-- ) { Script script = (Script) list.get(i); if ( script instanceof TextScript ) { TextScript textScript = (TextScript) script; String text = textScript.getText(); text = text.trim(); if ( text.length() == 0 ) { list.remove(i); } else { textScript.setText(text); } } } } else if ( body instanceof TextScript ) { TextScript textScript = (TextScript) body; textScript.trimWhitespace(); } this.hasTrimmed = true; }

protected void trimBody() { // #### should refactor this code into // #### trimWhitespace() methods on the Script objects if ( body instanceof CompositeTextScriptBlock ) { CompositeTextScriptBlock block = (CompositeTextScriptBlock) body; List list = block.getScriptList(); int size = list.size(); if ( size > 0 ) { Script script = (Script) list.get(0); if ( script instanceof TextScript ) { TextScript textScript = (TextScript) script; textScript.trimStartWhitespace(); } if ( size > 1 ) { script = (Script) list.get(size - 1); if ( script instanceof TextScript ) { TextScript textScript = (TextScript) script; textScript.trimEndWhitespace(); } } } } else if ( body instanceof ScriptBlock ) { ScriptBlock block = (ScriptBlock) body; List list = block.getScriptList(); for ( int i = list.size() - 1; i >= 0; i-- ) { Script script = (Script) list.get(i); if ( script instanceof TextScript ) { TextScript textScript = (TextScript) script; String text = textScript.getText(); text = text.trim(); if ( text.length() == 0 ) { list.remove(i); } else { textScript.setText(text); } } } } else if ( body instanceof TextScript ) { TextScript textScript = (TextScript) body; textScript.trimWhitespace(); } }

1,110,916

public boolean containsMBean(String objectName) { for(Iterator it=mbeanList.iterator(); it.hasNext();){ MBeanConfig mbeanConfig = (MBeanConfig)it.next(); if(mbeanConfig.getObjectName().equals(objectName)){ return true; } } return false; }

1,110,917

public BaseObject getFirstObject(String fieldname, XWikiContext context) { Collection objectscoll = getxWikiObjects().values(); if (objectscoll == null) return null; for (Iterator itobjs = objectscoll.iterator(); itobjs.hasNext();) { Vector objects = (Vector) itobjs.next(); for (Iterator itobjs2 = objects.iterator(); itobjs2.hasNext();) { BaseObject obj = (BaseObject) itobjs2.next(); if (obj != null) { BaseClass bclass = obj.getxWikiClass(context); if (bclass!=null) { Set set = bclass.getPropertyList(); if ((set != null) && set.contains(fieldname)) return obj; } Set set = obj.getPropertyList(); if ((set != null) && set.contains(fieldname)) return obj; } } } return null; }

1,110,918

public boolean equals(Object o) { if (this == o) return true; if (!(o instanceof DashboardConfig)) return false; final DashboardConfig dashboardConfig = (DashboardConfig) o; if (!dashboardId.equals(dashboardConfig.dashboardId)) return false; return true; }

1,110,919

public static boolean isKnownDataType(Class clazz){ if(clazz.isPrimitive() || clazz.isAssignableFrom(Boolean.class) || clazz.isAssignableFrom(Character.class) || clazz.isAssignableFrom(Byte.class) || clazz.isAssignableFrom(Short.class) || clazz.isAssignableFrom(Integer.class) || clazz.isAssignableFrom(Long.class) || clazz.isAssignableFrom(Float.class) || clazz.isAssignableFrom(Double.class) || clazz.isAssignableFrom(Void.class) || clazz.isAssignableFrom(String.class) || clazz.isAssignableFrom(BigInteger.class) || clazz.isAssignableFrom(BigDecimal.class) || clazz.isAssignableFrom(Date.class)){ return true; } return false; }

1,110,920

public void run(JellyContext context, XMLOutput output) throws Exception { if ( ! context.isCacheTags() ) { clearTag(); } try { Tag tag = getTag(); if ( tag == null ) { return; } tag.setContext(context); if ( tag instanceof DynaTag ) { DynaTag dynaTag = (DynaTag) tag; // ### probably compiling this to 2 arrays might be quicker and smaller for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Expression expression = (Expression) entry.getValue(); Class type = dynaTag.getAttributeType(name); Object value = null; if (type != null && type.isAssignableFrom(Expression.class) && !type.isAssignableFrom(Object.class)) { value = expression; } else { value = expression.evaluate(context); } dynaTag.setAttribute(name, value); } } else { // treat the tag as a bean DynaBean dynaBean = new ConvertingWrapDynaBean( tag ); for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Expression expression = (Expression) entry.getValue(); DynaProperty property = dynaBean.getDynaClass().getDynaProperty(name); if (property == null) { throw new JellyException("This tag does not understand the '" + name + "' attribute" ); } Class type = property.getType(); Object value = null; if (type.isAssignableFrom(Expression.class) && !type.isAssignableFrom(Object.class)) { value = expression; } else { value = expression.evaluate(context); } dynaBean.set(name, value); } } tag.doTag(output); } catch (JellyException e) { handleException(e); } catch (Exception e) { handleException(e); } catch (Error e) { handleException(e); } }

public void run(JellyContext context, XMLOutput output) throws Exception { if ( ! context.isCacheTags() ) { clearTag(); } try { Tag tag = getTag(); if ( tag == null ) { return; } tag.setContext(context); if ( tag instanceof DynaTag ) { DynaTag dynaTag = (DynaTag) tag; // ### probably compiling this to 2 arrays might be quicker and smaller for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Expression expression = (Expression) entry.getValue(); Class type = dynaTag.getAttributeType(name); Object value = null; if (type != null && type.isAssignableFrom(Expression.class) && !type.isAssignableFrom(Object.class)) { value = expression; } else { value = expression.evaluateRecurse(context); } dynaTag.setAttribute(name, value); } } else { // treat the tag as a bean DynaBean dynaBean = new ConvertingWrapDynaBean( tag ); for (Iterator iter = attributes.entrySet().iterator(); iter.hasNext();) { Map.Entry entry = (Map.Entry) iter.next(); String name = (String) entry.getKey(); Expression expression = (Expression) entry.getValue(); DynaProperty property = dynaBean.getDynaClass().getDynaProperty(name); if (property == null) { throw new JellyException("This tag does not understand the '" + name + "' attribute" ); } Class type = property.getType(); Object value = null; if (type.isAssignableFrom(Expression.class) && !type.isAssignableFrom(Object.class)) { value = expression; } else { value = expression.evaluateRecurse(context); } dynaBean.set(name, value); } } tag.doTag(output); } catch (JellyException e) { handleException(e); } catch (Exception e) { handleException(e); } catch (Error e) { handleException(e); } }

1,110,921

private void makeDialog(SQLTable st, int colIdx) throws ArchitectException { if (editDialog != null) { columnEditPanel.setModel(st); columnEditPanel.selectColumn(colIdx); editDialog.setTitle("Column Properties of "+st.getName()); editDialog.setVisible(true); //editDialog.requestFocus(); } else { JPanel panel = new JPanel(); panel.setLayout(new BorderLayout(12,12)); panel.setBorder(BorderFactory.createEmptyBorder(12,12,12,12)); columnEditPanel = new ColumnEditPanel(st, colIdx); panel.add(columnEditPanel, BorderLayout.CENTER); editDialog = ArchitectPanelBuilder.createArchitectPanelDialog( columnEditPanel, ArchitectFrame.getMainInstance(), "Column Properties of "+st.getName(), "OK", new AbstractAction(){ public void actionPerformed(ActionEvent e) { columnEditPanel.applyChanges(); EditColumnAction.this.putValue(SHORT_DESCRIPTION, "Editting "+columnEditPanel.getColName().getText() ); } }, null); panel.setOpaque(true); editDialog.pack(); editDialog.setLocationRelativeTo(ArchitectFrame.getMainInstance()); editDialog.setVisible(true); } }

private void makeDialog(SQLTable st, int colIdx) throws ArchitectException { if (editDialog != null) { columnEditPanel.setModel(st); columnEditPanel.selectColumn(colIdx); editDialog.setTitle("Column Properties of "+st.getName()); editDialog.setVisible(true); //editDialog.requestFocus(); } else { JPanel panel = new JPanel(); panel.setLayout(new BorderLayout(12,12)); panel.setBorder(BorderFactory.createEmptyBorder(12,12,12,12)); columnEditPanel = new ColumnEditPanel(st, colIdx); panel.add(columnEditPanel, BorderLayout.CENTER); editDialog = ArchitectPanelBuilder.createArchitectPanelDialog( columnEditPanel, ArchitectFrame.getMainInstance(), "Column Properties of "+st.getName(), "OK", new AbstractAction(){ public void actionPerformed(ActionEvent e) { columnEditPanel.applyChanges(); EditColumnAction.this.putValue(SHORT_DESCRIPTION, "Editting "+columnEditPanel.getColName().getText() ); } }, new AbstractAction(){ public void actionPerformed(ActionEvent e) { columnEditPanel.discardChanges(); } }); panel.setOpaque(true); editDialog.pack(); editDialog.setLocationRelativeTo(ArchitectFrame.getMainInstance()); editDialog.setVisible(true); } }

1,110,922

public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationConfig config = context.getApplicationConfig(); WeblogicApplicationForm appForm = (WeblogicApplicationForm)actionForm; /* populate the form */ appForm.setApplicationId(config.getApplicationId()); appForm.setName(config.getName()); appForm.setHost(config.getHost()); appForm.setPort(String.valueOf(config.getPort())); appForm.setUsername(config.getUsername()); appForm.setPassword(ApplicationForm.FORM_PASSWORD); return mapping.findForward(Forwards.SUCCESS); }

public ActionForward execute(WebContext context, ActionMapping mapping, ActionForm actionForm, HttpServletRequest request, HttpServletResponse response) { ApplicationConfig config = context.getApplicationConfig(); ApplicationForm appForm = (ApplicationForm)actionForm; ModuleConfig moduleConfig = ModuleRegistry.getModule(config.getType()); MetaApplicationConfig metaAppConfig = moduleConfig.getMetaApplicationConfig(); /* populate the form */ appForm.setApplicationId(config.getApplicationId()); appForm.setName(config.getName()); appForm.setHost(config.getHost()); appForm.setPort(String.valueOf(config.getPort())); appForm.setUsername(config.getUsername()); appForm.setPassword(ApplicationForm.FORM_PASSWORD); return mapping.findForward(Forwards.SUCCESS); }

1,110,923