sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
77dac86826092f3db0f543581dc1263e4ebeb11945bc65e32cdb0adb95707bd2 | Java | 614 | 38 | package umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
/**
* Created by hwestra on 11/14/16.
*/
public class UTR extends Feature {
public enum TYPE {
PRIME3,
PRIME5
}
private TYPE type;
private Transcript transcript;
public UTR(Chromosome chromosome, int alignmentStart, int alignmentEnd... |
eff167a8d590fd60a18336611cd2e278a0921bb5f793877d1906bf9e2e790ca4 | Java | 624 | 30 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.deelenp.genotypeharmonizer;
/**
*
* @author Patrick Deelen
*/
public class GenotypeAlignmentException extends Exception {
/**
* Creates a new instance of
* <code>GenotypeAlignmentException</code... |
5d0969e816ad98a85ce05aa8b5de7b852ed3e3dcd3951ee95ee6c270834ff388 | Java | 633 | 34 | package org.molgenis.genotype.tabix;
import java.io.IOException;
import java.io.InputStream;
import java.util.Iterator;
import org.molgenis.genotype.RawLineQueryResult;
public class TabixRawLineQueryResult implements RawLineQueryResult
{
private InputStream inputStream;
private Iterator<String> iterator;
public ... |
b73e261b6c8eafbd1dbfd19c7f8cd9f46e56c520fa2dc2133c8cb21e3e7f15a9 | Java | 643 | 38 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.transCorrelationQtl;
/**
*
* @author patri
*/
public class Qtl {
private final String snp;
private ... |
358769071a894cd6863342ad1e557c3f0659cbcf94c0872c87864c6fad094d45 | Java | 651 | 32 | package org.molgenis.genotype.annotation;
public class SampleAnnotation extends Annotation
{
public enum SampleAnnotationType
{
COVARIATE, PHENOTYPE, OTHER
}
private SampleAnnotationType sampleAnnotationType;
private boolean list;
public SampleAnnotation(String id, String name, String description, Type type,... |
18ed1e552b4f7afa36dd30cc3109dfef70c777dd5708242a22acf523d75b9c98 | Java | 657 | 38 | package org.MetaGenomicDataProcessing;
import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
/**
* Unit test for simple App.
*/
public class AppTest
extends TestCase
{
/**
* Create the test case
*
* @param testName name of the test case
*/
p... |
c3e4126d46a26363ee5559e720f00628f82469e4237cc42ff74e97f355af1a05 | Java | 662 | 34 | package umcg.genetica.io.binInteraction.gene;
import java.util.Arrays;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionGeneStatic extends BinaryInteractionGeneAbstract {
private final int[] variants;
public BinaryInteractionGeneStatic(String name, String chr, int start, int end, int[] variants... |
76318a63381d51a27b82bbc477a2f6fe7527d2b13c590f2152ba457d70d019fd | Java | 666 | 34 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.toolbox;
/**
*
* @author patri
*/
public enum Mode {
OVERLAP_GWAS(true, true);
private final boole... |
e5d1cb4f93cea56fa74da439d4648b941edc9146a073cd78e994d434c1085dba | Java | 670 | 38 | package nl.systemsgenetics.eqtlinteractionanalyser;
import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
/**
* Unit test for simple App.
*/
public class AppTest
extends TestCase
{
/**
* Create the test case
*
* @param testName name of the test case
... |
bd80e39d38ece82238e5281be489373999b0e699a3bab6f5f1e86ec3471b1211 | Java | 672 | 43 | package umcg.genetica.io.binInteraction.gene;
/**
*
* @author Patrick Deelen
*/
public abstract class BinaryInteractionGeneAbstract implements BinaryInteractionGene {
private final String name;
private final String chr;
private final int start;
private final int end;
public BinaryInteractionGeneAbstract(Stri... |
3e4e4643a9c8d7a20cfa78050a03318c783db97f3e070d481462dbf2f1277bae | Java | 677 | 31 | package nl.systemsgenetics.downstreamer.summarystatistic;
public class LdScore extends SNP {
private double centimorgan;
private double ldscore;
public LdScore(String sequence, int pos, String variantId, double ldScore) {
super(sequence, pos, pos);
this.primaryVariantId = variantId;
... |
231b1ffa9837005538dab0045cfa776e4869fdd9720615552a09910a3622a573 | Java | 683 | 25 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.util.regex.Pattern;
/**
*
* @author Matthieu
*/
public class eQtlsInEncodePseudogenes {
private static final Pattern TAB_PATTERN = ... |
9db321fedd5820b26c81b459865d4b6285474159a38e0d381b5d258c19371cbf | Java | 683 | 30 | package umcg.genetica.graphics.themes;
import java.awt.*;
/**
* Created by hwestra on 7/16/15.
*/
public interface Theme {
abstract Color getColor(int i);
abstract Color getLightGrey();
abstract Color getDarkGrey();
abstract Font getLargeFont();
abstract Font getMediumFont();
abstract Font getLargeFontBold(... |
e645a6f76bea94593199d659bedb997aaf4ebfaa74ec767c3b7962540f497e1c | Java | 688 | 40 | package org.molgenis.genotype.plink.datatypes;
/**
* See: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#map
*
*/
public class MapEntry {
private String chromosome;
private String SNP;
private double cM;
private long bpPos;
public MapEntry(String chromosome, String SNP, double cM, long bpPos) {
this... |
566cc511c1f5b1a449cd0751eaf6e3cb342990ccb29ff9ebf25303618c2037a2 | Java | 689 | 43 | package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
/**
*
* @author Patrick Deelen
*/
public class GeneAnnotation {
private final String ensg;
private final String huho;
private final String chr;
private final int start;
private final int end;
public GeneAnnotation(String ensg, Strin... |
4511849709ed102d0adbcf14cb85844a6aed3060671c4869d8ab0dd56d43a0f5 | Java | 697 | 35 | package nl.systemsgenetics.downstreamer.gene;
// TODO: Move this to IO package?
public class IndexedDouble implements Comparable<IndexedDouble> {
private Double value;
private int index;
public IndexedDouble(double value, int index) {
this.value = value;
this.index = index;
}
pub... |
6e3ef53984cbaed27c99a381b6f39e2fc7f8d4fa1682fef34e23c0747171b505 | Java | 701 | 28 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
/**
*
* @author Harm-Jan
*/
public class Probe extends Feat... |
826d928cc6dba71ae4cca3205f8880c09e7fbf1f047876c907aac991711cbc03 | Java | 701 | 32 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variant;
import java.util.Comparator;
import org.molgenis.genotype.util.ChromosomeComparator;
/**
*
* @author Patrick Deelen
*/
public class GeneticVariantChrPosComparator implements Co... |
e2299355077018149a3c7e9bfd1359c5077fd268f20a7e46a7f77f2f4bdefd44 | Java | 701 | 35 | package mbqtl.vcf.filter.variantfilters;
import mbqtl.vcf.VCFVariant;
import umcg.genetica.features.Feature;
import java.util.ArrayList;
/**
* Created by hwestra on 4/26/17.
*/
public class VCFVariantRegionFilter implements VCFVariantFilter {
private final ArrayList<Feature> regions;
public VCFVariantRegionFil... |
4e3ca2fc5365da42d20abfd476e64f52b23cd044c861b9f24b141b3d09c20f4a | Java | 707 | 34 | package org.molgenis.genotype.tabix;
import java.io.IOException;
import java.io.InputStream;
import java.util.Iterator;
import org.molgenis.genotype.VariantQueryResult;
import org.molgenis.genotype.variant.GeneticVariant;
public class TabixQueryResult implements VariantQueryResult
{
private final InputStream inputS... |
b16f80dc63b7aba9741b6439786731bf7a3e061d27b842e89f133a754025742c | Java | 735 | 42 | package umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
/**
* Created by hwestra on 12/3/15.
*/
public class BedGraphFeature extends Feature {
private double value;
private double pos = Double.NaN;
private double neg = Double.NaN;
public BedGraphFeature(Chromosome chr, Integer pos, int i) {
s... |
4e7dad0ec6b080771759d1686f904ee7fe138ab6f7f52725223977fc2bd2621f | Java | 739 | 32 | package ebi.spot.neo4j2owl.importer;
import java.util.Map;
import java.util.Set;
class N2ORelationship {
private final N2OEntity start;
private final N2OEntity end;
private final String relation;
private final Map<String, Set<Object>> props;
N2ORelationship(N2OEntity iri_start, N2OEntity iri_end,... |
d3c98037092f78c0cc610b869cfd015e7f3e5206e7e1cae9e891e71f01256b55 | Java | 745 | 40 | package org.molgenis.genotype;
import java.io.IOException;
public interface VariantQuery
{
/**
* Get a subset of the data in the index
*
* @param sequence
* @param startPos
* , exclusive
* @param stopPos
* , inclusive
*
* @return VariantQueryResult
*
* @throws IOExcepti... |
8f650d46a9d16c66490162fc941de0a32885c1e9342a4823ffcac84c42de363f | Java | 747 | 17 | package org.molgenis.genotype.variant.sampleProvider;
import org.molgenis.genotype.variant.ReadOnlyGeneticVariantBgen;
public class CachedSampleVariantProviderBgen extends CachedSampleVariantProvider implements SampleVariantProviderBgen {
protected final SampleVariantProviderBgen sampleVariantProvider;
publi... |
b26c9b51a79e206d7b468187735c3ee7ba41f94c783e583eee006571395b9ddb | Java | 748 | 30 | package mbqtl.junk;
import umontreal.iro.lecuyer.probdist.BetaDist;
public class BetaDistTest {
public static void main(String[] args) {
// ENSG00000096746.17
// 5650
// 1.05381
// 330.113
// 464.888 10:68246902:rs61854799:T_C -84273 0.0060772 0.223284 0.973735 0.977862
... |
4c59fa3c565e0122316971dc5a5e2fce34936b4b7d3096d4447667ff91eb7e96 | Java | 755 | 42 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
/**
*
* @author patri
*/
public class PredictionInfo {
final String hpo;
final doub... |
26c6e679c125e65e77662efaf46314d8800397dc24e96f4d613e7fd82466787d | Java | 762 | 42 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
/**
*
* @author patri
*/
public class PredictionInfo {
final String hpo;
fin... |
134fe86f20ec04db46f2f85f355a59f563d1da70d3b8b0e4cf64027a3b7f3b84 | Java | 764 | 35 | package umcg.genetica.io.binInteraction.variant;
import java.util.Arrays;
import org.molgenis.genotype.Allele;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionVariantStatic extends BinaryInteractionVariantAbstract {
private final int[] genePointers;
public BinaryInteractionVariantStatic(String... |
ecb628a3e63931c5b128d6917ea656ee29f71325776c7894c78c5219101fc9d8 | Java | 768 | 43 | package umcg.genetica.individuals;
import java.util.ArrayList;
/**
* Created by hwestra on 6/28/16.
*/
public class Family {
String name;
ArrayList<Individual> individuals = new ArrayList<>();
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public Array... |
dd58589ecf45bcbbc4b2d915b63470e92c054cc62e6557a4d9cc726cb2e4a89c | Java | 778 | 32 | package nl.systemsgenetics.downstreamer;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import nl.systemsgenetics.downstreamer.containers.GwasLocus;
public class DownstreamerStep3Results {
private Map<String, List<GwasLocus>> lociPerTrait;
public DownstreamerStep3Results() {
... |
f169c924df2489c3caa721a44e8039dd74138560ec5e11692c407df7b01489a0 | Java | 786 | 34 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.geom.Ellipse2D;
public class CircleStimulus extends Stimulus {
private Ellipse2D.Float circle;
public CircleStimulus(String name, Color color, int diameter) {
super(name, color, diameter, diameter);
circle = ne... |
44245033618e8aa58a124c1afee8bc796c67bde5aafd40a6346deb990c9de40b | Java | 789 | 36 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
*
* @author juha
*/
@Deprecated
public abstract class DoubleMatrixDatasetAC<T, U> {
public enum Load... |
8d364e1737864e3124ade20aaf4fa0661ca49d65745b9ddcc24c4bd29fded0e8 | Java | 790 | 36 | package org.molgenis.genotype.variant;
import org.molgenis.genotype.GenotypeDataException;
public class NotASnpException extends GenotypeDataException
{
/**
*
*/
private static final long serialVersionUID = 1L;
private final GeneticVariant geneticVariant;
@SuppressWarnings("unused")
private NotASnpExcept... |
f4d686625a784f799194e10bf76cc7962d1bd2824054b381a4d2d3bf715a6c18 | Java | 798 | 33 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline;
import eqtlmappingpipeline.gui.EQTLMappingPipelineConsole;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ResourceBundle;
/**
* @author harmjan
*/
publi... |
9027f7c5df68c5c6a676258ab6e282446e60f555a7e02490ea0905ccee4c7672 | Java | 800 | 25 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.probeannotation;
import java.util.ArrayList;
import java.util.HashMap;
/**
*
* @author harm-jan
*/
public class ProbeAnnotation {
HashMap<Integer, Integer> probeTranslation = ne... |
6a707d2cb553b3cee3a480503bcadbb2a53b00f2039569e590515730c771798f | Java | 806 | 29 | /*
* GeneLocationObjectSorter.java
*
* Created on 23 December 2003, 17:14
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
/**
*
* @author Like
*/
public class DoubleArrayIntegerObjectSorter extends VectorSorter {
/** Creates a new instance of GeneLocationObjectSorter */... |
21d3d83b8134b9884bb0e09abf4865c387818df2c1bed5ece751a3d08358eaaf | Java | 819 | 36 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
import org.apache.commons.math3.analysis.MultivariateFunction;
im... |
3e16b20431e370dca4924dd7eba1624ddce94e03c9f56fecf3de2d766abf9566 | Java | 821 | 28 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import java.util.Iterator;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class ConvertToSampleFilterIterable implements Ite... |
29c79d461e85fd99e7b72f59b0a7389efe13819b8dfae355e7642b3aa1726bc3 | Java | 822 | 24 | package umcg.genetica.util;
import umcg.genetica.containers.StringDoubleObject;
public class StringDoubleObjectSorterSortOnDouble extends VectorSorter {
private java.text.Collator collatorUS = null;
/** Creates a new instance of GeneLocationObjectSorter */
public StringDoubleObjectSorterSortOnDouble() {... |
4bd25af0c395522a473f900e3711f8fb5eeecb35d914715bcc82df9914ce1ee8 | Java | 823 | 24 | package umcg.genetica.util;
import umcg.genetica.containers.StringIntegerObject;
public class StringIntegerObjectSorterSortOnInteger extends VectorSorter {
private java.text.Collator collatorUS = null;
/** Creates a new instance of GeneLocationObjectSorter */
public StringIntegerObjectSorterSortOnIntege... |
b86256cf77e23d534f1a22e3ad1f021022b5a4a2c2c9025824fcb5e30023db66 | Java | 825 | 49 | package org.molgenis.genotype;
import static org.testng.AssertJUnit.assertEquals;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AlleleTest
{
@BeforeMethod
public void beforeMethod()
{
}
@Test
public void createString()
{
Allele testAllele = Allele.create("AAA"... |
b0154849057bbcd9675a9bc13cd94d84b73508c4fa08e43b85e275548f06505d | Java | 826 | 42 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class VariantFilterMaf implements VariantFilter {
private double maf;
... |
55712383b3e3efabf5f3901f04d5fc08ee41a4d41fedc854e705d0bab8330110 | Java | 832 | 32 | package umcg.genetica.io.gtf;
import java.io.File;
import java.util.List;
//import org.apache.logging.log4j.BasicConfigurator;
import umcg.genetica.collections.intervaltree.PerChrIntervalTree;
/**
*
* @author Patrick Deelen
*/
public class TestGffIntervalTree {
/**
* @param args the command line argument... |
c9c36bd596e511efbeeb277faf1fa9b4cd99f8838509e5ac8365e9d7ae7a7c63 | Java | 832 | 40 | package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import java.io.IOException;
import java.util.ArrayList;
import java.util.EnumMap;
/**
*
* @author Patrick Deelen
*/
public class SkippedInteractionTracker {
public static enum Reason {
SINGULAR, SHARED_QTL
}
private final String c... |
81ec8b733619fd80d748877d95dd883ad01f89d813a28ecbb0a8d401085b43de | Java | 838 | 50 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variant;
import org.molgenis.genotype.Alleles;
/**
*
* @author Patrick Deelen
*/
public class GenotypeRecordProb implements GenotypeRecord {
private final float[] probs;
public Gen... |
e1e59bacaa47e1422ffbd8eb703760df1e742df0a8c131456989c2f54d9698ff | Java | 841 | 34 | package nl.systemsgenetics.downstreamer.summarystatistic.filters;
import nl.systemsgenetics.downstreamer.summarystatistic.SummaryStatisticRecord;
import java.util.Set;
/**
* The type Variant id filter.
*/
public class VariantIdFilter implements SummaryStatisticsRecordFilter {
private final FilterType filterT... |
699ff6098d7a04e43b59c391d9e7aa2e56e34ac72311464cc61d63c69490271a | Java | 846 | 50 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variant;
import org.molgenis.genotype.Alleles;
/**
*
* @author Patrick Deelen
*/
public class GenotypeRecordGt implements GenotypeRecord {
private final Alleles alleles;
public Geno... |
436b720015f43100a23f4c1e78f568fa6def18a50fcfd7490103ff92f1313394 | Java | 850 | 36 | package mbqtl.vcf.filter.genotypefilters;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import mbqtl.vcf.VCFVariant;
/**
* Created by hwestra on 2/8/16.
*/
public class GenotypeQualityFilter implements VCFGenotypeFilter {
private int minimalGenotypeQual = 30;
public GenotypeQualityFilter() {
}
public Geno... |
862c64eabbbf12ed32a9bb301d145c74f297f364d1d3402b69487e2dc9beaab6 | Java | 850 | 44 | package org.molgenis.genotype.util;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* Least Recently Used (LRU) cache. The items accessed last is removed when
* capacity is reached Code from:
* http://java-planet.blogspot.nl/2005/08/how-to-set
* -up-simple-lru-cache-using.html
*
* @author Patrick Dee... |
5c57b1637415a060b9d88483251065d1f4f64e1b29a2bbaf93991528c836e7cf | Java | 856 | 41 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.summarystatistic;
import static org.testng.Assert.*;
import org.testng.annotations.AfterClass;... |
df26205e19ae75eaf53dc901d5057413b44ecc3e75c0b13a9fac5f6d11f45baf | Java | 868 | 40 | package edu.cmu.cs.eyetrack.analysis.struct.trackit;
import edu.cmu.cs.eyetrack.analysis.struct.Frame;
import edu.cmu.cs.eyetrack.helper.Coordinate;
public class TrackItFrame extends Frame {
private Coordinate<Double> position;
private long timestamp;
public TrackItFrame(Coordinate<Double> position, lo... |
737435697daa3bcee9c64aa65fda7acbc4da2b5a4c30a44624ca8647141240de | Java | 876 | 51 | package org.molgenis.genotype.variant;
import java.util.Collections;
import java.util.Map;
import org.molgenis.genotype.Alleles;
/**
*
* @author Patrick Deelen
*/
public class GenotypeRecordMap implements GenotypeRecord {
private final Map<String, Object> fields;
public GenotypeRecordMap(Map<String, Object> fi... |
b616f701018e7a49b5350b5dbfebf6dc0a4fa195ad4e109b580b84ba33e1f824 | Java | 876 | 33 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import com.itextpdf.text.DocumentException;
import eqtlmappingpipeline.metaqtl3.graphics.EQTLDotPlot;
import java.io.IOException;
import java.util.logging.Level;
import java.util.loggin... |
44ca7c640d72690c9950f4464ae0453d2e7e9e37dfbb04a7361d80a94aa83e92 | Java | 884 | 53 | package eqtlmappingpipeline.ase;
import cern.colt.list.tdouble.DoubleArrayList;
import cern.colt.list.tint.IntArrayList;
import java.util.ArrayList;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.variant.id.GeneticVariantId;
/**
*
* @author Patrick Deelen
*/
public interface AseVariant extends C... |
31e9d3bf70c8380775e8d81cb37a2912fbab4697a12e370d4e4a359e45ca632e | Java | 885 | 50 | package umcg.genetica.io.bedgraph;
import umcg.genetica.variantAnnotator.GenomicRange;
/**
*
* @author Patrick Deelen
*/
public class BedGraphEntry implements GenomicRange {
private final String chr;
private final int startPosition;
private final int stopPositions;
private final double value;
public BedGrap... |
1917b8a00f4282cc2447d571b683856f79e06e3dd9e1336f08934b202e9cde02 | Java | 896 | 39 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Sample;
/**
*
* @author Patrick Deelen
*/
public class SampleCombi... |
9e56935376b74bcdd70eff25654b18054889f73843481a3544f5b63ba75440f1 | Java | 898 | 50 | package umcg.genetica.io.binInteraction.variant;
import org.molgenis.genotype.Allele;
/**
*
* @author Patrick Deelen
*/
public abstract class BinaryInteractionVariantAbstract implements BinaryInteractionVariant{
private final String name;
private final String chr;
private final int pos;
private final Allele r... |
c22dbcc538c9a724e37d526e6cd8f02bcc1fc8f3c617d63c0179cd7e5cedf818 | Java | 898 | 41 | ///*
// * To change this license header, choose License Headers in Project Properties.
// * To change this template file, choose Tools | Templates
// * and open the template in the editor.
// */
//package nl.systemsgenetics.toolbox;
//
//import org.apache.log4j.Layout;
//import org.apache.log4j.Level;
//import org.apac... |
02c48c7200f4a454d8f741f47d31856561eb39a28f3477aba22aab28863909b8 | Java | 904 | 47 | package mbqtl.vcf.filter.variantfilters;
import mbqtl.vcf.VCFVariant;
/**
* Created by hwestra on 3/21/17.
*/
public class VCFVariantHWEPFilter implements VCFVariantFilter {
private double threshold = 1E-4;
public enum MODE {
CASES,
CONTROLS,
OVERALL
}
private MODE m;
public VCFVariantHWEPFilter(doub... |
12f2371cd99b7c403b69d36d814ed600fda8ed79a009f670eb80e888c815f142 | Java | 904 | 52 | package mbqtl.vcf.filter.variantfilters;
import mbqtl.vcf.VCFVariant;
/**
* Created by hwestra on 3/21/17.
*/
public class VCFVariantMAFFilter implements VCFVariantFilter {
private double threshold = 0.01;
public enum MODE {
CASES,
CONTROLS,
OVERALL
}
private MODE m;
public VCFVariantMAFFilter(doubl... |
0a55624e043664104d0a9704f743c43b12f6e07b514db11996f3abcc8229c6e1 | Java | 905 | 52 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.enums;
/**
* @author Harm-Jan
*/
public enum Strand {
POS("+", 0), NEG("-", 1), NA("NA", 2);
public static... |
2fc07dd4c3dcb26d63a5433013f35f8148571b2c046ce3a30fedf6684054c5cb | Java | 906 | 42 | package umcg.genetica.io.binInteraction.variant;
import gnu.trove.list.array.TIntArrayList;
import org.molgenis.genotype.Allele;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionVariantCreator extends BinaryInteractionVariantAbstract {
private TIntArrayList genePointers;
public BinaryInteraction... |
79c1e1ea712b7115fbaeac65a76a05fd94b042d0b0aa803bccefd3a73b45c039 | Java | 906 | 41 | ///*
// * To change this license header, choose License Headers in Project Properties.
// * To change this template file, choose Tools | Templates
// * and open the template in the editor.
// */
//package nl.systemsgenetics.gadocommandline;
//
//import org.apache.log4j.Layout;
//import org.apache.log4j.Level;
//import ... |
8c1cdd75df237207ee4125924385d8c8197ddc293a636796536d429e4a947c08 | Java | 911 | 39 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
import umcg.genetica.io.hpo.HpoOntology;
import java.io.File;
import java.util.List... |
42d4b7a02f70d68c8e6c51b573d467fe2f01779e48f59c6e79d1176b9c9af166 | Java | 913 | 38 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public class CorrelationTest {
public CorrelationTest() {
}
/**
* Te... |
a782950213102c52dcf9a6b5500c9e45a4c8a76ad5d47c707c926b93217e9a98 | Java | 944 | 32 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
import java.io.IOException;
import org.apache.logging.log4j.LogManager;
import org.apache.... |
af5ab36be2b30b997f516ab9291a3b6cb538e7b47def92ce0cccc3cdddf0d5af | Java | 947 | 40 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.variantAnnotator;
import java.util.ArrayList;
import java.util.HashMap;
/**
*
* @author Patrick Deelen
*/
public class VariantAnnotator<E extends GenomicRange> {
HashMap<String, ArrayList<E>>... |
4adb118300866a9d3410d465b4a3f5dd4f42fd627183258fb37f7230e4215d34 | Java | 948 | 41 | package eqtlmappingpipeline.trans;
import eqtlmappingpipeline.metaqtl3.MetaQTL3;
public class TransQTL extends MetaQTL3 {
public void run() {
/* req:
- thread for loading
- thread for lz4+save
- some calculation logic
- predefined chunks per chromosome
- load a chunk of snps in memory
- run as... |
85ae2930207294cdfd2cf59e06018efe5f0d649b2d4d7cff8f5f4bd50c648824 | Java | 950 | 31 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gwascatalog;
import java.util.HashMap;
import java.util.HashSet;
import umcg.genetica.containers.Pair;
/**
*
* @author harmjan
*/
public class GWASPublication {
HashSet<GWASTrait> trait... |
a072f9726920f764f4ac1110fb3c61b09b6b676d56537232fd7cb6cefcab7889 | Java | 951 | 31 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math;
import umcg.genetica.containers.Pair;
/**
*
* @author harmjan
*/
public class Goniometry {
/**
* @param r radius of the circle
* @param originX the origin (center of the cir... |
dac9c040c4ce4afed50aa8aefe08105595f7afec6f26866a84fc67d2d1deddd2 | Java | 953 | 29 | package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
public class HJWTest {
public static void main(String[] args) {
args = new String[]{"-i", "D:\\interactiontest\\databinary2\\",
"-o", "D:\\interactiontest\\output2\\",
"-e", "D:\\interactiontest\\data\\eqtls-filtered.txt",
"-is... |
013260f71ef5b5c0a717f3312f0bcfac32dfc2490f4fd13df81f4d06ebccc500 | Java | 959 | 33 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.chromosomeyexpressionplotter;
import eqtlmappingpipeline.metaqtl3.MetaQTL3;
import eqtlmappingpipeline.metaqtl3.containers.Settings;
import umcg.genetica.io.Gpio;
import java.io.IOException;... |
583717ba9e3084005c5e9bb4780e944bfd7ffbb6afa48a32de9b1c067f38f7cf | Java | 959 | 34 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variant.range;
import java.util.Iterator;
import java.util.List;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class GeneticVariantRangeS... |
70febd3e0759f4e84ac1a60beb35a765162aea74be7b5c20ba2fa6b0e1871dc8 | Java | 959 | 23 | package org.molgenis.genotype.variant.sampleProvider;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import org.molgenis.genotype.variant.GeneticVariant;
import org.testng.annotations.Test;
public class CachedSampleVariantProviderTest
{
@Te... |
b245998b37d4e269e408b2873224e42d44ff5d97089311b06a5b036fd81d2cb3 | Java | 965 | 35 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import java.util.Arrays;
/**
*
* @author juha
*/
public class AUC {
public static double getAUC(double[] a1, double[] a2) {
double[] totalList = new double[a1.length + ... |
e460b413ada8e39f4b13618d9a2d02bc3a8e89ad0a659037442546483df77a6d | Java | 965 | 56 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
/**
*
* @author Matthieu
*/
public class EQtl {
private double pValue;
private String eQtlName;
private String eQtlChr;
private int eQtlChr... |
f65895b059d082ecae40e4e459cf195b944303480e5bb5aa94b56b3d5a16a32d | Java | 968 | 36 | package nl.systemsgenetics.downstreamer.summarystatistic.filters;
import nl.systemsgenetics.downstreamer.summarystatistic.SummaryStatisticRecord;
/**
* The type Pvalue filter larger.
*/
public class PvalueFilterLarger implements SummaryStatisticsRecordFilter {
private static FilterType filterType = FilterType.... |
a4135e88129880fb5a76b701ef859d8d3549affd5212388e5ed3ffc0487f8274 | Java | 970 | 41 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.regulomedb;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Iterator;
/**
*
* @author Patrick Deelen
*/
public class RegulomeDbFile im... |
eea76c166dbf95389057479113b860c619d5bf4ba3543a9a560b4947f180a8fd | Java | 973 | 36 | package nl.systemsgenetics.downstreamer.summarystatistic.filters;
import nl.systemsgenetics.downstreamer.summarystatistic.SummaryStatisticRecord;
/**
* The type Pvalue filter smaller.
*/
public class PvalueFilterSmaller implements SummaryStatisticsRecordFilter {
private static FilterType filterType = FilterTyp... |
a9c9c0b9742f3d008a07e96afc9a619981bb40d22fc60f05dbe00185bf7f771d | Java | 975 | 47 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.util.HashSet;
import java.util.Set;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class VariantIdIncludeFilter... |
c85b078926c4efb14b938847568d45cb6fedbd843f2d6d188972f48288c4a581 | Java | 977 | 57 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.fasta;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public class LargeByteArrayTest {
public LargeByteArrayTest() {
}
/**
... |
dfdd62aaf4e78b7c871bc021340fbbeed30875ae5fdbb7b1ee092bcb2162a790 | Java | 977 | 36 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import java.io.IOException;
import umcg.genetica.io.bin.BinaryFile;
/**
*
* @auth... |
45eede610bccaa73e2fd212ceed5aca6994ec62ce0c32851795676a0583a6d1a | Java | 981 | 48 | package nl.systemsgenetics.genenetworkpathwayenrichment;
/**
* Created by hwestra on 11/10/15.
*/
public class LogisticRegressionResult {
private final double[][] beta; // format: [disease][allele]
private final double[][] stderrs;
// private final double[][] sigprms;
private final double deviance;
// private ... |
8a7f4ebdf4136825a8d957a5a96160d5277184d16dbcd93729a1e7c5149a22d4 | Java | 983 | 37 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.Polygon;
public class TriangleStimulus extends Stimulus {
private Polygon polygon;
public TriangleStimulus(String name, Color color, int height) {
super(name, color, height, height);
polygon = new Polygon();
... |
d9fa52335f773e389afb47521c1f7db34815644c87d2c72999b25194b5e22ff2 | Java | 986 | 46 | package umcg.genetica.io.binInteraction.gene;
import gnu.trove.list.array.TIntArrayList;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionGeneCreator extends BinaryInteractionGeneAbstract {
private TIntArrayList variantPointers;
public BinaryInteractionGeneCreator(String name, String chr, int s... |
7482eefd1bc6054c6b9e16d3287d30aafeec1598ab7b750d0fca98b42a3db37d | Java | 988 | 33 | package nl.systemsgenetics.functionenrichmentoftransqtls;
import java.io.IOException;
import org.apache.commons.lang3.ArrayUtils;
public class FunctionEnrichMain {
public static void main(String[] args) throws IOException, Exception {
if (args.length < 1) {
System.out.println("Usage: (convertchisq|correla... |
1c09b03e7dc0c55d2d9e6b2fcfb0751abc7664f61547db3b9056ffd7c8664e4d | Java | 1,005 | 39 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.Polygon;
public class BoxStimulus extends Stimulus {
private Polygon polygon;
public BoxStimulus(String name, Color color, int width, int height) {
super(name, color, width, height);
polygon = new Polygon();
po... |
fbf933dd46db7c4f22e8487fd0cdff3c3cb090f90349d0f47d0f2ea174d1f198 | Java | 1,006 | 46 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.bgen;
import static org.testng.Assert.*;
import org.testng.annotations.AfterClass;
import org.testng.ann... |
3dc350a814b11e515f625cf7bc8bee98ecc02e2b4776823bb4fdaf5ba799195c | Java | 1,007 | 28 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import java.util.NavigableSet;
import java.util.TreeSet;
/**
*
* @author Patrick Deelen
*/
public class MetaQTL4MetaTraitTreeSet extends TreeSet<MetaQTL4MetaTrait>{
public Na... |
5adf37cd23f09f92eeee924fb56b873bf171cb9d13ff46b70473ab779cb5705e | Java | 1,009 | 57 | package umcg.genetica.enums;
/**
* Created by hwestra on 5/27/16.
*/
public enum Gender {
MALE(0, "Male"),
FEMALE(1, "Female"),
UNKNOWN(-1, "Unknown");
private final int number;
private final String name;
private Gender(int num, String name) {
this.number = num;
this.name = name;
}
public static Gend... |
a2ef881ca49b8baaf830be0cdab5bb77c0926fcbe87ce5edd823d3f5258fde6c | Java | 1,010 | 34 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype;
import java.net.URISyntaxException;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import static org.testng.Assert.assertEquals;
/**
*
* @a... |
685952f78bda2b64bf0d5c6970d26ef7149ce97fb959645f5e1383345fa3542b | Java | 1,016 | 36 | /*
* GeneLocationObjectSorter.java
*
* Created on 23 December 2003, 17:14
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
/**
*
* @author Like
*/
public class StringIntegerObjectSorter extends VectorSorter {
private java.text.Collator collatorUS = null;
/** Creates... |
276387f63b067365abb303fd63d13bfda994ea841920b619dfbb6d55c7c271a9 | Java | 1,019 | 40 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import org.apache.commons.cli.Option;
import org.apache.co... |
da28852fddba60ff9a74dba9257b38bd3fcfe87801c9454aaea0da35fa68c67c | Java | 1,022 | 58 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.containers;
import htsjdk.samtools.util.Locatable;
/**
*
* @author patri
*/
//TODO: integr... |
b44c8a8fa6fb76c3f231a744a1284b195570ee6b473ac67bb58125afe834d1db | Java | 1,025 | 30 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.westrah.binarymetaanalyzer;
import java.util.NavigableSet;
import java.util.TreeSet;
/**
* @author Patrick Deelen
*/
public class MetaQTL4MetaTraitTreeSet extends TreeSet<MetaQTL4MetaTrait> {
publi... |
424b0b29a92fe9e2038b918ba9d92df9654a63dc2330f9b0be65b4347ecbf0aa | Java | 1,036 | 48 | package mbqtl.matrix;
import cern.colt.matrix.AbstractMatrix2D;
/**
* Created by hwestra on 5/16/16.
*/
public class ShortMatrix2D extends AbstractMatrix2D {
private short[] matrix;
public ShortMatrix2D(short[][] matrix) {
rows = matrix.length;
columns = matrix[0].length;
this.matrix = new short[rows * co... |
169907da8fee1e478de080a29ac8ee7426e2230222a12b141c26ed9979c98523 | Java | 1,043 | 39 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.Polygon;
public class DiamondStimulus extends Stimulus {
private Polygon polygon;
public DiamondStimulus(String name, Color color, int width, int height) {
super(name, color, width, height);
polygon = new Polygon(... |
2524af249a0d680b8d730299ab7201d808200a4b9e4d6ec9cd49e836d54fb6d0 | Java | 1,046 | 42 | package org.molgenis.genotype.tabix;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.List;
import org.molgenis.genotype.ResourceTest;
import org.molgenis.genotype.variant.GeneticVariant;
impo... |
78f8a57fd4f2f787fd14f14785f126e84073152e522fac460fe70bcc8af6a5d1 | Java | 1,048 | 35 | package ebi.spot.neo4j2owl.importer;
import org.semanticweb.owlapi.model.*;
public class N2OImportResult {
public long classesLoaded = 0;
public long individualsLoaded = 0;
public long objPropsLoaded = 0;
public long annotationPropertiesloaded = 0;
public long dataPropsLoaded = 0;
public Stri... |
ddc6568c9742b11dc80f4f4012f874a2a4d73f142bd1ffe1623c847877e65872 | Java | 1,063 | 43 | package umcg.genetica.io.binInteraction;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionQueryResult {
private final String variantName;
private final String geneName;
private final String covariateName;
private final BinaryInteractionQtlZscores qtlZscores;
private final BinaryInteractionZscor... |
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