_id stringlengths 2 7 | title stringlengths 3 140 | partition stringclasses 3
values | text stringlengths 73 34.1k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q26100 | SeqRes2AtomAligner.storeUnAlignedSeqRes | train | public static void storeUnAlignedSeqRes(Structure structure, List<Chain> seqResChains, boolean headerOnly) {
if (headerOnly) {
List<Chain> atomChains = new ArrayList<>();
for (Chain seqRes: seqResChains) {
// In header-only mode skip ATOM records.
// Here we store chains with SEQRES instead of AtomGr... | java | {
"resource": ""
} |
q26101 | AbstractAlignmentJmol.setAtoms | train | public void setAtoms(Atom[] atoms){
Structure s = new StructureImpl();
Chain c = new ChainImpl();
c.setId("A");
for (Atom a: atoms){
c.addGroup(a.getGroup());
}
s.addChain(c);
setStructure(s);
} | java | {
"resource": ""
} |
q26102 | AbstractAlignmentJmol.evalString | train | public void evalString(String rasmolScript){
if ( jmolPanel == null ){
logger.error("please install Jmol first");
return;
}
jmolPanel.evalString(rasmolScript);
} | java | {
"resource": ""
} |
q26103 | AbstractAlignmentJmol.setStructure | train | public void setStructure(Structure s) {
if (jmolPanel == null){
logger.error("please install Jmol first");
return;
}
setTitle(s.getPDBCode());
jmolPanel.setStructure(s);
// actually this is very simple
// just convert the structure to a PDB file
//String pdb = s.toPDB();
//System.out.println(s.... | java | {
"resource": ""
} |
q26104 | StructureInterfaceCluster.getTotalArea | train | public double getTotalArea() {
double area = 0;
for (StructureInterface interf:members) {
area+=interf.getTotalArea();
}
return area/members.size();
} | java | {
"resource": ""
} |
q26105 | MmtfUtils.calculateDsspSecondaryStructure | train | public static void calculateDsspSecondaryStructure(Structure bioJavaStruct) {
SecStrucCalc ssp = new SecStrucCalc();
try{
ssp.calculate(bioJavaStruct, true);
}
catch(StructureException e) {
LOGGER.warn("Could not calculate secondary structure (error {}). Will try to get a DSSP file from the RCSB web serv... | java | {
"resource": ""
} |
q26106 | MmtfUtils.getUnitCellAsArray | train | public static float[] getUnitCellAsArray(PDBCrystallographicInfo xtalInfo) {
CrystalCell xtalCell = xtalInfo.getCrystalCell();
if(xtalCell==null){
return null;
}else{
float[] inputUnitCell = new float[6];
inputUnitCell[0] = (float) xtalCell.getA();
inputUnitCell[1] = (float) xtalCell.getB();
inputU... | java | {
"resource": ""
} |
q26107 | MmtfUtils.techniquesToStringArray | train | public static String[] techniquesToStringArray(Set<ExperimentalTechnique> experimentalTechniques) {
if(experimentalTechniques==null){
return new String[0];
}
String[] outArray = new String[experimentalTechniques.size()];
int index = 0;
for (ExperimentalTechnique experimentalTechnique : experimentalTechniqu... | java | {
"resource": ""
} |
q26108 | MmtfUtils.dateToIsoString | train | public static String dateToIsoString(Date inputDate) {
DateFormat dateStringFormat = new SimpleDateFormat("yyyy-MM-dd");
return dateStringFormat.format(inputDate);
} | java | {
"resource": ""
} |
q26109 | MmtfUtils.getTransformMap | train | public static Map<double[], int[]> getTransformMap(BioAssemblyInfo bioassemblyInfo, Map<String, Integer> chainIdToIndexMap) {
Map<Matrix4d, List<Integer>> matMap = new LinkedHashMap<>();
List<BiologicalAssemblyTransformation> transforms = bioassemblyInfo.getTransforms();
for (BiologicalAssemblyTransformation t... | java | {
"resource": ""
} |
q26110 | MmtfUtils.convertToDoubleArray | train | public static double[] convertToDoubleArray(Matrix4d transformationMatrix) {
// Initialise the output array
double[] outArray = new double[16];
// Iterate over the matrix
for(int i=0; i<4; i++){
for(int j=0; j<4; j++){
// Now set this element
outArray[i*4+j] = transformationMatrix.getElement(i,j);
... | java | {
"resource": ""
} |
q26111 | MmtfUtils.getNumGroups | train | public static int getNumGroups(Structure structure) {
int count = 0;
for(int i=0; i<structure.nrModels(); i++) {
for(Chain chain : structure.getChains(i)){
count+= chain.getAtomGroups().size();
}
}
return count;
} | java | {
"resource": ""
} |
q26112 | MmtfUtils.getAtomsForGroup | train | public static List<Atom> getAtomsForGroup(Group inputGroup) {
Set<Atom> uniqueAtoms = new HashSet<Atom>();
List<Atom> theseAtoms = new ArrayList<Atom>();
for(Atom a: inputGroup.getAtoms()){
theseAtoms.add(a);
uniqueAtoms.add(a);
}
List<Group> altLocs = inputGroup.getAltLocs();
for(Group thisG: altLocs... | java | {
"resource": ""
} |
q26113 | MmtfUtils.getNumBondsInGroup | train | public static int getNumBondsInGroup(List<Atom> atomsInGroup) {
int bondCounter = 0;
for(Atom atom : atomsInGroup) {
if(atom.getBonds()==null){
continue;
}
for(Bond bond : atom.getBonds()) {
// Now set the bonding information.
Atom other = bond.getOther(atom);
// If both atoms are in the gr... | java | {
"resource": ""
} |
q26114 | MmtfUtils.getSecStructTypeFromDsspIndex | train | public static SecStrucType getSecStructTypeFromDsspIndex(int dsspIndex) {
String dsspType = DsspType.dsspTypeFromInt(dsspIndex).getDsspType();
for(SecStrucType secStrucType : SecStrucType.values())
{
if(dsspType==secStrucType.name)
{
return secStrucType;
}
}
// Return a null entry.
return null;... | java | {
"resource": ""
} |
q26115 | MmtfUtils.getStructureInfo | train | public static MmtfSummaryDataBean getStructureInfo(Structure structure) {
MmtfSummaryDataBean mmtfSummaryDataBean = new MmtfSummaryDataBean();
// Get all the atoms
List<Atom> theseAtoms = new ArrayList<>();
List<Chain> allChains = new ArrayList<>();
Map<String, Integer> chainIdToIndexMap = new LinkedHashMap<>... | java | {
"resource": ""
} |
q26116 | MmtfUtils.insertSeqResGroup | train | public static void insertSeqResGroup(Chain chain, Group group, int sequenceIndexId) {
List<Group> seqResGroups = chain.getSeqResGroups();
addGroupAtId(seqResGroups, group, sequenceIndexId);
} | java | {
"resource": ""
} |
q26117 | MmtfUtils.addSeqRes | train | public static void addSeqRes(Chain modelChain, String sequence) {
List<Group> seqResGroups = modelChain.getSeqResGroups();
GroupType chainType = getChainType(modelChain.getAtomGroups());
for(int i=0; i<sequence.length(); i++){
char singleLetterCode = sequence.charAt(i);
Group group = null;
if(seqResGroup... | java | {
"resource": ""
} |
q26118 | GenericInsdcHeaderFormat._write_feature | train | protected String _write_feature(FeatureInterface<AbstractSequence<C>, C> feature, int record_length) {
String location = _insdc_feature_location_string(feature, record_length);
String f_type = feature.getType().replace(" ", "_");
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb,Loc... | java | {
"resource": ""
} |
q26119 | GenericInsdcHeaderFormat._split_multi_line | train | protected ArrayList<String> _split_multi_line(String text, int max_len) {
// TODO Auto-generated method stub
ArrayList<String> output = new ArrayList<String>();
text = text.trim();
if(text.length() <= max_len) {
output.add(text);
return output;
}
ArrayList<String> words = new ArrayList<String>();
C... | java | {
"resource": ""
} |
q26120 | SimpleGapPenalty.setType | train | private void setType() {
type = (gop == 0) ? GapPenalty.Type.LINEAR : ((gep == 0) ? GapPenalty.Type.CONSTANT : GapPenalty.Type.AFFINE);
} | java | {
"resource": ""
} |
q26121 | ProteinModificationXmlReader.getChildNodes | train | private static Map<String,List<Node>> getChildNodes(Node parent) {
if (parent==null)
return Collections.emptyMap();
Map<String,List<Node>> children = new HashMap<String,List<Node>>();
NodeList nodes = parent.getChildNodes();
int nNodes = nodes.getLength();
for (int i=0; i<nNodes; i++) {
Node node = no... | java | {
"resource": ""
} |
q26122 | RNAToAminoAcidTranslator.postProcessCompoundLists | train | @Override
protected void postProcessCompoundLists(
List<List<AminoAcidCompound>> compoundLists) {
for (List<AminoAcidCompound> compounds : compoundLists) {
if (trimStops) {
trimStop(compounds);
}
}
} | java | {
"resource": ""
} |
q26123 | RNAToAminoAcidTranslator.trimStop | train | protected void trimStop(List<AminoAcidCompound> sequence) {
AminoAcidCompound stop = sequence.get(sequence.size() - 1);
boolean isStop = false;
if (aminoAcidToCodon.containsKey(stop)) {
for (Codon c : aminoAcidToCodon.get(stop)) {
if (c.isStop()) {
isStop = true;
break;
}
}
}
if (isSt... | java | {
"resource": ""
} |
q26124 | ResidueGroup.combineWith | train | public void combineWith(List<List<Integer>> alignRes) {
for (int i = 0; i < order(); i++)
alignRes.get(i).add(residues.get(i));
} | java | {
"resource": ""
} |
q26125 | AllChemCompProvider.downloadFile | train | public static void downloadFile() throws IOException {
initPath();
initServerName();
String localName = getLocalFileName();
String u = serverName + "/" + COMPONENTS_FILE_LOCATION;
downloadFileFromRemote(new URL(u), new File(localName));
} | java | {
"resource": ""
} |
q26126 | AllChemCompProvider.run | train | @Override
public void run() {
long timeS = System.currentTimeMillis();
initPath();
ensureFileExists();
try {
loadAllChemComps();
long timeE = System.currentTimeMillis();
logger.debug("Time to init chem comp dictionary: " + (timeE - timeS) / 1000 + " sec.");
} catch (IOException e) {
logger.... | java | {
"resource": ""
} |
q26127 | SequenceFileProxyLoader.init | train | private boolean init() throws IOException, CompoundNotFoundException {
BufferedReader br = new BufferedReader(new FileReader(file));
br.skip(sequenceStartIndex);
String sequence = sequenceParser.getSequence(br, sequenceLength);
setContents(sequence);
br.close(); // close file to prevent too many being open
... | java | {
"resource": ""
} |
q26128 | StructurePairAligner.main | train | public static void main(String[] args) throws Exception {
// UPDATE THE FOLLOWING LINES TO MATCH YOUR SETUP
PDBFileReader pdbr = new PDBFileReader();
pdbr.setPath("/Users/andreas/WORK/PDB/");
// String pdb1 = "1crl";
// String pdb2 = "1ede";
String pdb1 = "1buz";
String pdb2 = "1ali";
String outputfi... | java | {
"resource": ""
} |
q26129 | StructurePairAligner.align | train | public void align(Structure s1, Structure s2) throws StructureException {
align(s1, s2, params);
} | java | {
"resource": ""
} |
q26130 | StructurePairAligner.align | train | public void align(Structure s1, Structure s2, StrucAligParameters params)
throws StructureException {
// step 1 convert the structures to Atom Arrays
Atom[] ca1 = getAlignmentAtoms(s1);
Atom[] ca2 = getAlignmentAtoms(s2);
notifyStartingAlignment(s1.getName(), ca1, s2.getName(), ca2);
align(ca1, ca2, para... | java | {
"resource": ""
} |
q26131 | StructurePairAligner.align | train | public void align(Structure s1, String chainId1, Structure s2,
String chainId2) throws StructureException {
align(s1, chainId1, s2, chainId2, params);
} | java | {
"resource": ""
} |
q26132 | StructurePairAligner.align | train | public void align(Structure s1, String chainId1, Structure s2,
String chainId2, StrucAligParameters params)
throws StructureException {
reset();
this.params = params;
Chain c1 = s1.getPolyChainByPDB(chainId1);
Chain c2 = s2.getPolyChainByPDB(chainId2);
Structure s3 = new StructureImpl();
s3.addChain... | java | {
"resource": ""
} |
q26133 | JmolPanel.jmolColorByChain | train | public void jmolColorByChain(){
String script =
"function color_by_chain(objtype, color_list) {"+ String.format("%n") +
""+ String.format("%n") +
" if (color_list) {"+ String.format("%n") +
" if (color_list.type == \"string\") {"+ String.format("%n") +
" color_list = color_list.split(\... | java | {
"resource": ""
} |
q26134 | AminoAcidCompoundSet.addAmbiguousEquivalents | train | private void addAmbiguousEquivalents(String one, String two, String either) {
Set<AminoAcidCompound> equivalents;
AminoAcidCompound cOne, cTwo, cEither;
equivalents = new HashSet<AminoAcidCompound>();
equivalents.add(cOne = aminoAcidCompoundCache.get(one));
equivalents.add(cTwo = aminoAcidCompoundCache.get(t... | java | {
"resource": ""
} |
q26135 | SimpleMMcifConsumer.getNewGroup | train | private Group getNewGroup(String recordName,Character aminoCode1, long seq_id,String groupCode3) {
Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(groupCode3);
if ( g != null && !g.getChemComp().isEmpty()) {
if ( g instanceof AminoAcidImpl) {
AminoAcidImpl aa = (AminoAcidImpl) g;
aa.setId(... | java | {
"resource": ""
} |
q26136 | SimpleMMcifConsumer.isKnownChain | train | private static Chain isKnownChain(String asymId, List<Chain> chains){
for (int i = 0; i< chains.size();i++){
Chain testchain = chains.get(i);
//System.out.println("comparing chainID >"+chainID+"< against testchain " + i+" >" +testchain.getName()+"<");
if (asymId.equals(testchain.getId())) {
//System.ou... | java | {
"resource": ""
} |
q26137 | SimpleMMcifConsumer.convertAtom | train | private Atom convertAtom(AtomSite atom){
Atom a = new AtomImpl();
a.setPDBserial(Integer.parseInt(atom.getId()));
a.setName(atom.getLabel_atom_id());
double x = Double.parseDouble (atom.getCartn_x());
double y = Double.parseDouble (atom.getCartn_y());
double z = Double.parseDouble (atom.getCartn_z());
... | java | {
"resource": ""
} |
q26138 | SimpleMMcifConsumer.documentStart | train | @Override
public void documentStart() {
structure = new StructureImpl();
currentChain = null;
currentGroup = null;
currentNmrModelNumber = null;
//atomCount = 0;
allModels = new ArrayList<List<Chain>>();
currentModel = new ArrayList<Chain>();
entities = new ArrayList<Entity>... | java | {
"resource": ""
} |
q26139 | SimpleMMcifConsumer.addAncilliaryEntityData | train | private void addAncilliaryEntityData(StructAsym asym, int entityId, Entity entity, EntityInfo entityInfo) {
// Loop through each of the entity types and add the corresponding data
// We're assuming if data is duplicated between sources it is consistent
// This is a potentially huge assumption...
for (EntitySr... | java | {
"resource": ""
} |
q26140 | SimpleMMcifConsumer.addInformationFromESG | train | private void addInformationFromESG(EntitySrcGen entitySrcInfo, int entityId, EntityInfo c) {
c.setAtcc(entitySrcInfo.getPdbx_gene_src_atcc());
c.setCell(entitySrcInfo.getPdbx_gene_src_cell());
c.setOrganismCommon(entitySrcInfo.getGene_src_common_name());
c.setOrganismScientific(entitySrcInfo.getPdbx_gene_src_sc... | java | {
"resource": ""
} |
q26141 | SimpleMMcifConsumer.addInformationFromESN | train | private void addInformationFromESN(EntitySrcNat esn, int eId, EntityInfo c) {
c.setAtcc(esn.getPdbx_atcc());
c.setCell(esn.getPdbx_cell());
c.setOrganismCommon(esn.getCommon_name());
c.setOrganismScientific(esn.getPdbx_organism_scientific());
c.setOrganismTaxId(esn.getPdbx_ncbi_taxonomy_id());
} | java | {
"resource": ""
} |
q26142 | SimpleMMcifConsumer.addInfoFromESS | train | private void addInfoFromESS(EntitySrcSyn ess, int eId, EntityInfo c) {
c.setOrganismCommon(ess.getOrganism_common_name());
c.setOrganismScientific(ess.getOrganism_scientific());
c.setOrganismTaxId(ess.getNcbi_taxonomy_id());
} | java | {
"resource": ""
} |
q26143 | SimpleMMcifConsumer.addSites | train | private void addSites() {
List<Site> sites = structure.getSites();
if (sites == null) sites = new ArrayList<Site>();
for (StructSiteGen siteGen : structSiteGens) {
// For each StructSiteGen, find the residues involved, if they exist then
String site_id = siteGen.getSite_id(); // multiple could be in same... | java | {
"resource": ""
} |
q26144 | JMatrixPanel.drawPairs | train | public void drawPairs(Graphics g){
if ( aligs == null)
return;
int nr = aligs.length;
Graphics2D g2D = (Graphics2D)g;
Stroke oldStroke = g2D.getStroke();
g2D.setStroke(stroke);
Color color;
float hue;
int width = Math.round(scale);
int w2 = width / 2 ;
for (int i = 0; i < aligs.length; i++)... | java | {
"resource": ""
} |
q26145 | JMatrixPanel.drawBoxes | train | public void drawBoxes(Graphics g){
if ( fragmentPairs == null )
return;
g.setColor(Color.yellow);
for (int i = 0; i < fragmentPairs.length; i++) {
FragmentPair fp =fragmentPairs[i];
int xp = fp.getPos1();
int yp = fp.getPos2();
int width = Math.round(scale);
g.drawRect(Math.round(xp*scale),... | java | {
"resource": ""
} |
q26146 | JMatrixPanel.drawDistances | train | public void drawDistances(Graphics g1){
Graphics2D g = (Graphics2D)g1;
int c = matrix.getRowDimension();
int d = matrix.getColumnDimension();
float scale = getScale();
int width = Math.round(scale);
for (int i = 0; i < c; i++) {
int ipaint = Math.round(i*scale);
for (int j = 0; j < d; j++) {
d... | java | {
"resource": ""
} |
q26147 | ABITrace.ABITraceInit | train | private void ABITraceInit(BufferedInputStream bis) throws IOException{
byte[] bytes = null;
ByteArrayOutputStream baos = new ByteArrayOutputStream();
int b;
while ((b = bis.read()) >= 0)
{
baos.write(b);
}
bis.close(); baos.close();
bytes = baos.toByteArray();
initData(bytes);
} | java | {
"resource": ""
} |
q26148 | ABITrace.getTrace | train | public int[] getTrace (String base) throws CompoundNotFoundException {
if (base.equals("A")) {
return A;
} else if (base.equals("C")) {
return C;
} else if (base.equals("G")) {
return G;
} else if (base.equals("T")) {
return T;
} else {
throw new CompoundNotFoundException("Don't know base: " + ... | java | {
"resource": ""
} |
q26149 | ABITrace.calculateScale | train | private double calculateScale(int height) {
double newScale = 0.0;
double max = (double) getMaximum();
double ht = (double) height;
newScale = ((ht - 50.0)) / max;
return newScale;
} | java | {
"resource": ""
} |
q26150 | ABITrace.getMaximum | train | private int getMaximum() {
int max = 0;
for (int x = 0; x <= T.length - 1; x++) {
if (T[x] > max) max = T[x];
if (A[x] > max) max = A[x];
if (C[x] > max) max = C[x];
if (G[x] > max) max = G[x];
}
return max;
} | java | {
"resource": ""
} |
q26151 | ABITrace.initData | train | private void initData(byte[] fileData) {
traceData = fileData;
if (isABI()) {
setIndex();
setBasecalls();
setQcalls();
setSeq();
setTraces();
} else throw new IllegalArgumentException("Not a valid ABI file.");
} | java | {
"resource": ""
} |
q26152 | ABITrace.setTraces | train | private void setTraces() {
int pointers[] = new int[4]; //alphabetical, 0=A, 1=C, 2=G, 3=T
int datas[] = new int[4];
char order[] = new char[4];
datas[0] = DATA9;
datas[1] = DATA10;
datas[2] = DATA11;
datas[3] = DATA12;
for (int i = 0; i <= 3; i++) {
order[i] = (char) traceData[FWO + i];
}
for... | java | {
"resource": ""
} |
q26153 | ABITrace.setSeq | train | private void setSeq() {
char tempseq[] = new char[seqLength];
for (int x = 0; x <= seqLength - 1; ++x) {
tempseq[x] = (char) traceData[PBAS2 + x];
}
sequence = new String(tempseq);
} | java | {
"resource": ""
} |
q26154 | ABITrace.setQcalls | train | private void setQcalls() {
qCalls = new int[seqLength];
byte[] qq = new byte[seqLength];
getSubArray(qq, PCON);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int i = 0; i <= seqLength - 1; ++i) {
try {
qCalls[i] = (int) dis.readByte();
} catch (IOException e)//This sh... | java | {
"resource": ""
} |
q26155 | ABITrace.setBasecalls | train | private void setBasecalls() {
baseCalls = new int[seqLength];
byte[] qq = new byte[seqLength * 2];
getSubArray(qq, PLOC);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int i = 0; i <= seqLength - 1; ++i) {
try {
baseCalls[i] = (int) dis.readShort();
} catch (IOExcepti... | java | {
"resource": ""
} |
q26156 | ABITrace.setIndex | train | private void setIndex() {
int DataCounter, PBASCounter, PLOCCounter, PCONCounter, NumRecords, indexBase;
byte[] RecNameArray = new byte[4];
String RecName;
DataCounter = 0;
PBASCounter = 0;
PLOCCounter = 0;
PCONCounter = 0;
indexBase = getIntAt(absIndexBase + macJunk);
NumRecords = getIntAt(absIndex... | java | {
"resource": ""
} |
q26157 | ABITrace.getSubArray | train | private void getSubArray(byte[] b, int traceDataOffset) {
for (int x = 0; x <= b.length - 1; x++) {
b[x] = traceData[traceDataOffset + x];
}
} | java | {
"resource": ""
} |
q26158 | ABITrace.isABI | train | private boolean isABI() {
char ABI[] = new char[4];
for (int i = 0; i <= 2; i++) {
ABI[i] = (char) traceData[i];
}
if (ABI[0] == 'A' && (ABI[1] == 'B' && ABI[2] == 'I')) {
return true;
} else {
for (int i = 128; i <= 130; i++) {
ABI[i-128] = (char) traceData[i];
}
if (ABI[0] == 'A' && (ABI... | java | {
"resource": ""
} |
q26159 | GeneNamesParser.main | train | public static void main(String[] args) {
try {
List<GeneName> geneNames = getGeneNames();
logger.info("got {} gene names", geneNames.size());
for ( GeneName g : geneNames){
if ( g.getApprovedSymbol().equals("FOLH1"))
logger.info("Gene Name: {}", g);
}
// and returns a list of beans that co... | java | {
"resource": ""
} |
q26160 | GeneNamesParser.getGeneNames | train | public static List<GeneName> getGeneNames(InputStream inStream) throws IOException{
ArrayList<GeneName> geneNames = new ArrayList<GeneName>();
BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));
// skip reading first line (it is the legend)
String line = reader.readLine();
while ((... | java | {
"resource": ""
} |
q26161 | GeneSequence.addIntronsUsingExons | train | public void addIntronsUsingExons() throws Exception {
if (intronAdded) { //going to assume introns are correct
return;
}
if (exonSequenceList.size() == 0) {
return;
}
ExonComparator exonComparator = new ExonComparator();
//sort based on start position and sense;
Collections.sort(exonSequenceList, ex... | java | {
"resource": ""
} |
q26162 | GeneSequence.addTranscript | train | public TranscriptSequence addTranscript(AccessionID accession, int begin, int end) throws Exception {
if (transcriptSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
TranscriptSequence transcriptSequence = new TranscriptSequence(this, begin, ... | java | {
"resource": ""
} |
q26163 | GeneSequence.removeIntron | train | public IntronSequence removeIntron(String accession) {
for (IntronSequence intronSequence : intronSequenceList) {
if (intronSequence.getAccession().getID().equals(accession)) {
intronSequenceList.remove(intronSequence);
intronSequenceHashMap.remove(accession);
return intronSequence;
}
}
return n... | java | {
"resource": ""
} |
q26164 | GeneSequence.addIntron | train | public IntronSequence addIntron(AccessionID accession, int begin, int end) throws Exception {
if (intronSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
intronAdded = true;
IntronSequence intronSequence = new IntronSequence(this, begin, en... | java | {
"resource": ""
} |
q26165 | GeneSequence.removeExon | train | public ExonSequence removeExon(String accession) {
for (ExonSequence exonSequence : exonSequenceList) {
if (exonSequence.getAccession().getID().equals(accession)) {
exonSequenceList.remove(exonSequence);
exonSequenceHashMap.remove(accession);
// we now have a new gap which creates an intron
intronS... | java | {
"resource": ""
} |
q26166 | GeneSequence.addExon | train | public ExonSequence addExon(AccessionID accession, int begin, int end) throws Exception {
if (exonSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
ExonSequence exonSequence = new ExonSequence(this, begin, end); //sense should be the same as... | java | {
"resource": ""
} |
q26167 | GeneSequence.getSequence5PrimeTo3Prime | train | public DNASequence getSequence5PrimeTo3Prime() {
String sequence = getSequenceAsString(this.getBioBegin(), this.getBioEnd(), this.getStrand());
if (getStrand() == Strand.NEGATIVE) {
//need to take complement of sequence because it is negative and we are returning the gene sequence from the opposite strand
Str... | java | {
"resource": ""
} |
q26168 | PDBHeader.toPDB | train | @Override
public void toPDB(StringBuffer buf){
// 1 2 3 4 5 6 7
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//HEADER COMPLEX (SERINE PROTEASE/INHIBITORS) 06-FEB-98 1A4W
//TITLE CRYSTAL STRUCTURES OF THRO... | java | {
"resource": ""
} |
q26169 | PDBHeader.setExperimentalTechnique | train | public boolean setExperimentalTechnique(String techniqueStr) {
ExperimentalTechnique et = ExperimentalTechnique.getByName(techniqueStr);
if (et==null) return false;
if (techniques==null) {
techniques = EnumSet.of(et);
return true;
} else {
return techniques.add(et);
}
} | java | {
"resource": ""
} |
q26170 | ChargeAdder.addCharges | train | public static void addCharges(Structure structure) {
// Loop through the models
for(int i=0; i<structure.nrModels(); i++){
for(Chain c: structure.getChains(i)){
for(Group g: c.getAtomGroups()){
ChemComp thisChemComp = ChemCompGroupFactory.getChemComp(g.getPDBName());
List<ChemCompAtom> chemAtoms = ... | java | {
"resource": ""
} |
q26171 | SymmOptimizer.updateMultipleAlignment | train | private void updateMultipleAlignment() throws StructureException,
RefinerFailedException {
msa.clear();
// Override the alignment with the new information
Block b = msa.getBlock(0);
b.setAlignRes(block);
repeatCore = b.getCoreLength();
if (repeatCore < 1)
throw new RefinerFailedException(
"Opti... | java | {
"resource": ""
} |
q26172 | SymmOptimizer.shrinkBlock | train | private boolean shrinkBlock() throws StructureException,
RefinerFailedException {
// Let shrink moves only if the repeat is larger enough
if (repeatCore <= Lmin)
return false;
// Select column by maximum distance
updateMultipleAlignment();
Matrix residueDistances = MultipleAlignmentTools
.getAvera... | java | {
"resource": ""
} |
q26173 | SymmOptimizer.saveHistory | train | private void saveHistory(String folder) throws IOException {
String name = msa.getStructureIdentifier(0).getIdentifier();
FileWriter writer = new FileWriter(folder + name
+ "-symm_opt.csv");
writer.append("Step,Time,RepeatLength,RMSD,TMscore,MCscore\n");
for (int i = 0; i < lengthHistory.size(); i++) {
... | java | {
"resource": ""
} |
q26174 | MmtfStructureWriter.addBonds | train | private void addBonds(Atom atom, List<Atom> atomsInGroup, List<Atom> allAtoms) {
if(atom.getBonds()==null){
return;
}
for(Bond bond : atom.getBonds()) {
// Now set the bonding information.
Atom other = bond.getOther(atom);
// If both atoms are in the group
if (atomsInGroup.indexOf(other)!=-1){
... | java | {
"resource": ""
} |
q26175 | MmtfStructureWriter.storeEntityInformation | train | private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> entityInfos) {
for (EntityInfo entityInfo : entityInfos) {
String description = entityInfo.getDescription();
String type;
if (entityInfo.getType()==null){
type = null;
}
else{
type = entityInfo.getType().getEntityType()... | java | {
"resource": ""
} |
q26176 | MmtfStructureWriter.storeBioassemblyInformation | train | private void storeBioassemblyInformation(Map<String, Integer> chainIdToIndexMap, Map<Integer, BioAssemblyInfo> inputBioAss) {
int bioAssemblyIndex = 0;
for (Entry<Integer, BioAssemblyInfo> entry : inputBioAss.entrySet()) {
Map<double[], int[]> transformMap = MmtfUtils.getTransformMap(entry.getValue(), chainIdToI... | java | {
"resource": ""
} |
q26177 | TranscriptSequence.removeCDS | train | public CDSSequence removeCDS(String accession) {
for (CDSSequence cdsSequence : cdsSequenceList) {
if (cdsSequence.getAccession().getID().equals(accession)) {
cdsSequenceList.remove(cdsSequence);
cdsSequenceHashMap.remove(accession);
return cdsSequence;
}
}
return null;
} | java | {
"resource": ""
} |
q26178 | TranscriptSequence.addCDS | train | public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase) throws Exception {
if (cdsSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
CDSSequence cdsSequence = new CDSSequence(this, begin, end, phase); //sense should be ... | java | {
"resource": ""
} |
q26179 | TranscriptSequence.getDNACodingSequence | train | public DNASequence getDNACodingSequence() {
StringBuilder sb = new StringBuilder();
for (CDSSequence cdsSequence : cdsSequenceList) {
sb.append(cdsSequence.getCodingSequence());
}
DNASequence dnaSequence = null;
try {
dnaSequence = new DNASequence(sb.toString().toUpperCase());
} catch (CompoundNotFou... | java | {
"resource": ""
} |
q26180 | TranscriptSequence.getProteinSequence | train | public ProteinSequence getProteinSequence(TranscriptionEngine engine) {
DNASequence dnaCodingSequence = getDNACodingSequence();
RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine);
ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine);
proteinSequence.setAccession(n... | java | {
"resource": ""
} |
q26181 | SequenceScalePanel.setPaintDefaults | train | protected void setPaintDefaults(Graphics2D g2D){
g2D.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
g2D.setFont(seqFont);
} | java | {
"resource": ""
} |
q26182 | SequenceScalePanel.drawSequence | train | protected int drawSequence(Graphics2D g2D, int y){
//g2D.drawString(panelName,10,10);
g2D.setColor(SEQUENCE_COLOR);
int aminosize = Math.round(1*scale);
if ( aminosize < 1)
aminosize = 1;
// only draw within the ranges of the Clip
Rectangle drawHere = g2D.getClipBounds();
int startpos = coordManager... | java | {
"resource": ""
} |
q26183 | CalcPoint.centroid | train | public static Point3d centroid(Point3d[] x) {
Point3d center = new Point3d();
for (Point3d p : x) {
center.add(p);
}
center.scale(1.0 / x.length);
return center;
} | java | {
"resource": ""
} |
q26184 | CalcPoint.transform | train | public static void transform(Matrix4d rotTrans, Point3d[] x) {
for (Point3d p : x) {
rotTrans.transform(p);
}
} | java | {
"resource": ""
} |
q26185 | CalcPoint.translate | train | public static void translate(Vector3d trans, Point3d[] x) {
for (Point3d p : x) {
p.add(trans);
}
} | java | {
"resource": ""
} |
q26186 | CalcPoint.clonePoint3dArray | train | public static Point3d[] clonePoint3dArray(Point3d[] x) {
Point3d[] clone = new Point3d[x.length];
for (int i = 0; i < x.length; i++) {
clone[i] = new Point3d(x[i]);
}
return clone;
} | java | {
"resource": ""
} |
q26187 | CalcPoint.rmsd | train | public static double rmsd(Point3d[] x, Point3d[] y) {
if (x.length != y.length) {
throw new IllegalArgumentException(
"Point arrays are not of the same length.");
}
double sum = 0.0;
for (int i = 0; i < x.length; i++) {
sum += x[i].distanceSquared(y[i]);
}
return Math.sqrt(sum / x.length);
} | java | {
"resource": ""
} |
q26188 | MenuCreator.initMenu | train | public static JMenuBar initMenu(){
// show a menu
JMenuBar menu = new JMenuBar();
JMenu file= new JMenu("File");
file.getAccessibleContext().setAccessibleDescription("File Menu");
JMenuItem openI = new JMenuItem("Open");
openI.setMnemonic(KeyEvent.VK_O);
openI.addActionListener(new ActionListener(){
... | java | {
"resource": ""
} |
q26189 | MenuCreator.showAboutDialog | train | private static void showAboutDialog(){
JDialog dialog = new JDialog();
dialog.setSize(new Dimension(300,300));
String msg = "This viewer is based on <b>BioJava</b> and <b>Jmol</>. <br>Author: Andreas Prlic <br> ";
msg += "Structure Alignment algorithm based on a variation of the PSC++ algorithm by Peter Lack... | java | {
"resource": ""
} |
q26190 | AnchoredPairwiseSequenceAligner.getAnchors | train | public int[] getAnchors() {
int[] anchor = new int[getScoreMatrixDimensions()[0] - 1];
for (int i = 0; i < anchor.length; i++) {
anchor[i] = -1;
}
for (int i = 0; i < anchors.size(); i++) {
anchor[anchors.get(i).getQueryIndex()] = anchors.get(i).getTargetIndex();
}
return anchor;
} | java | {
"resource": ""
} |
q26191 | AnchoredPairwiseSequenceAligner.setAnchors | train | public void setAnchors(int[] anchors) {
super.anchors = new ArrayList<Anchor>();
if (anchors != null) {
for (int i = 0; i < anchors.length; i++) {
if (anchors[i] >= 0) {
addAnchor(i, anchors[i]);
}
}
}
} | java | {
"resource": ""
} |
q26192 | GenbankReaderHelper.readGenbankProteinSequence | train | public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
File file) throws Exception {
FileInputStream inStream = new FileInputStream(file);
LinkedHashMap<String, ProteinSequence> proteinSequences = readGenbankProteinSequence(inStream);
inStream.close();
return proteinSequences;
} | java | {
"resource": ""
} |
q26193 | GenbankReaderHelper.readGenbankProteinSequence | train | public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
InputStream inStream) throws Exception {
GenbankReader<ProteinSequence, AminoAcidCompound> GenbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
inStream,
new GenericGenbankHeaderParser<ProteinSequence, AminoA... | java | {
"resource": ""
} |
q26194 | GenbankReaderHelper.readGenbankDNASequence | train | public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(
InputStream inStream) throws Exception {
GenbankReader<DNASequence, NucleotideCompound> GenbankReader = new GenbankReader<DNASequence, NucleotideCompound>(
inStream,
new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
... | java | {
"resource": ""
} |
q26195 | GenbankReaderHelper.readGenbankRNASequence | train | public static LinkedHashMap<String, RNASequence> readGenbankRNASequence(
InputStream inStream) throws Exception {
GenbankReader<RNASequence, NucleotideCompound> GenbankReader = new GenbankReader<RNASequence, NucleotideCompound>(
inStream,
new GenericGenbankHeaderParser<RNASequence, NucleotideCompound>(),
... | java | {
"resource": ""
} |
q26196 | CachedRemoteScopInstallation.loadRepresentativeDomains | train | private void loadRepresentativeDomains() throws IOException {
URL u = null;
try {
u = new URL(RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains");
} catch (MalformedURLException e) {
throw new IOException("URL " + RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains" + ... | java | {
"resource": ""
} |
q26197 | Calc.getDistance | train | public static final double getDistance(Atom a, Atom b) {
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
double s = x * x + y * y + z * z;
return Math.sqrt(s);
} | java | {
"resource": ""
} |
q26198 | Calc.angle | train | public static final double angle(Atom a, Atom b){
Vector3d va = new Vector3d(a.getCoordsAsPoint3d());
Vector3d vb = new Vector3d(b.getCoordsAsPoint3d());
return Math.toDegrees(va.angle(vb));
} | java | {
"resource": ""
} |
q26199 | Calc.unitVector | train | public static final Atom unitVector(Atom a) {
double amount = amount(a) ;
double[] coords = new double[3];
coords[0] = a.getX() / amount ;
coords[1] = a.getY() / amount ;
coords[2] = a.getZ() / amount ;
a.setCoords(coords);
return a;
} | java | {
"resource": ""
} |
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