sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5fd5a2e6f697c03f3fe4503c267dcbb8795938a717165fd7fb1d4879f723ff7a | Java | 1,068 | 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 umcg.genetica.math.stats;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
impo... |
fb668af98cf271fb72c5ede9dbc92c9e0f8de28fec0b437449776d94d4466dd3 | Java | 1,071 | 43 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.trityper;
import org.molgenis.genotype.Allele;
/**
*
* @author harmjan
*/
public class TriTyperAlleleAnnotation {
private static final byte A = 65;
private static final byte C ... |
a46f061a6ea0408085289d56b7f327d9a60ab1d10344b84d6f458d4d7308bf27 | Java | 1,072 | 48 | /*
* 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;
/**
*
* @author patri
*/
public class BgenixMetadata {
private final String fileName;
priva... |
1b1e0cf573d4f6764d93b348c693e168abc7d9fa6c0aad68d70d9eec2b787708 | Java | 1,073 | 38 | /*
* 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 ConvertToSampleFilterIterator implements Ite... |
cd5b8e051f82353463729b00892ea6c80beab1f497ebfe1112433a1ca0f2bffe | Java | 1,073 | 43 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import java.util.Collection;
import java.util.HashSet;
import org.molgenis.genotype.Sample;
/**
*
* @author Patrick Deelen
*/
public class SampleIdIncludeFilter implements... |
a650a09ea6adc2e32eacf12c6b4521a6446bd1b662fabfe8ad7e42c23d9cb351 | Java | 1,076 | 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 org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class VariantFilterSeq implements VariantFilter {
... |
86a419d9c9dbfa655e8a323fb3efd5c350a41084ceb1eb133e863f32092ac1f2 | Java | 1,077 | 50 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.collections;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public class ChrPosMapTest {
public ChrPosMapTest() {
}
/**
* Test ... |
84f26aaddb94c7a188dc64970226951a8158dce5148ac23ffc2e6d9a773a571e | Java | 1,079 | 49 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.util.HashSet;
import org.molgenis.genotype.util.ChrPos;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class Va... |
07c51f68cfd5a0ce72a1f2e8f4df3d79f9dd396b4ebe9956aba2708306e3df1b | Java | 1,083 | 45 | package nl.systemsgenetics.downstreamer.io;
import java.util.Collection;
import java.util.Collections;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.util.List;
import java.util.Set;
public class DoubleMatrixDatasetBlockDiagonalProvider implements BlockDiagonalDoubleMatrixProvider {
private... |
4e2db51c4f3a6724689db19fa98b7a6c29f177f717df60354c6245435aed1f40 | Java | 1,088 | 31 | package mbqtl.junk;
import mbqtl.stat.RankArray;
public class RankTest {
public static void main(String[] args) {
// double[] data = new double[]{Double.NaN, Double.NaN, Double.NaN};
// RankArray ranker = new RankArray();
// double[] d = ranker.rank(data, true); // does this work with NaNs?
// ... |
d88da0f1bb7beaaaad6378d5a6f99bc4e8409da152134949a85cd353f33ff86f | Java | 1,102 | 55 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
/**
*
* @author Matthieu
*/
public class NarrowPeakElement {
private String chromosome;
private int startPos;
private int stopPos;
private do... |
4376c6189da856db2f7a2c2cf8dbc8cb0e7daa31fc6e248ac11bf64fe3600368 | Java | 1,105 | 52 | package org.molgenis.genotype.annotation;
public enum SexAnnotation {
MALE((byte) 1, "Male"), FEMALE((byte) 2, "Female"), UNKNOWN((byte) 0, "Unknown");
private final byte plinkSex;
private final String gender;
private SexAnnotation(byte plinkSex, String gender) {
this.plinkSex = plinkSex;
this.gender = gende... |
c7a7028d20325af4a73585d68a2058fbb93f918aed8bcf220e66ca77cceaea29 | Java | 1,112 | 44 | /*
* 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.ArrayList;
import java.util.Collection;
import java.util.Iterator;
/**
*
* ... |
41093f6d86164de7cb072b7ac20bbe92337e4b2d4a313b0e1e96118a07b46f24 | Java | 1,113 | 34 | package main.java.decon_eQTL;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.logging.SimpleFormatter;
import java.util.logging.LogRecord;
class CustomRecordFormatter extends SimpleFormatter {
@Override
public String format(final LogRecord r) {
StringBuilder sb = n... |
28419efcb3ee99462bacea811d6174cccf1768209db5aed30189f1c51ea21e3f | Java | 1,115 | 27 | package mbqtl;
public class MbQTLDebug {
public static void main(String[] args) {
String[] args2 = new String[]{
"--mode", "mbqtl",
"--vcf", "/Users/harm-jan/SyncData/TMP/orfeas/transtest/data/genotypes/chrCHR.vcf.gz",
"--gte", "/Users/harm-jan/SyncData/TMP... |
083c4919363eebb7d7e7121da2639ee1d540f5f82250a26f293d8c3c6524aebf | Java | 1,116 | 34 | package edu.cmu.cs.eyetrack.analysis.score.compare;
import java.util.Map;
import edu.cmu.cs.eyetrack.analysis.score.distance.DistanceFunction;
import edu.cmu.cs.eyetrack.analysis.struct.Trajectory;
import edu.cmu.cs.eyetrack.analysis.struct.tobii.TobiiFrame;
import edu.cmu.cs.eyetrack.analysis.struct.trackit.T... |
ed7425bc6b48515a5fad60e4ee2053aa91c10e271d6aada55c38ea01ada43f3a | Java | 1,124 | 35 | package mbqtl.junk;
import umcg.genetica.math.stats.ZScores;
public class ZTest {
public static void main(String[] args) {
// double p = 3.679676003373988E-33;
// double z = ZScores.pToZ(p);
// double p2 = ZScores.zToP(z);
//
// NormalDist d = new NormalDist();
// double p3 = d... |
9183bc506be739a3a71724adcadf5f7a9e31b2f28b627b9f08f4578b9cd48d8c | Java | 1,129 | 42 | package org.molgenis.genotype.util;
import static org.testng.Assert.assertTrue;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URISyntaxException;
import org.molgenis.genotype.GenotypeData;
import org.molgenis.genotype.ResourceTest;
import org.molgenis.genotype... |
c119433fb6726675190b7735a91b1e45caf5e4cd60a12ecbf275364d3c1ab49b | Java | 1,129 | 30 | package main.java.decon_eQTL;
import java.io.IOException;
import java.util.List;
import org.apache.commons.cli.ParseException;
public class Main {
/**
* Deconvolute a set of QTLs given the expression levels, genotypes,
* and cell counts. Calculates the p-values for the deconvoluted QTLs
* and writes them to a... |
e0f1acbb9230553a3aa4ebd26b33fc57334bd00442bfdf071f3439ed4fd88825 | Java | 1,131 | 30 | package nl.systemsgenetics.downstreamer.runners.options;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import java.util.ArrayList;
import java.util.List;
/**
* Parser that doesn't crash on un... |
80e0fcf3d6d25dd624d73c97883aa27b58198f5a91c47d85c12a75d28ddc43bc | Java | 1,136 | 53 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.containers;
/**
*
* @author harm-jan
*/
public class TextResult implements Comparable<TextResult> {
public double pvalue;
public int pid;
public String description;
... |
285dd586ddaf6a9b1291d97061f450913e01794e9c01e8a9300b64da041eba5e | Java | 1,137 | 46 | package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.HashMap;
public class QTLFileSplitter {
public void split(String in, String out) throws IOException {
TextFile tf = new TextFile(in, TextFile.R);
Strin... |
facddb876dbd0f60b1e69edb63ee1a4b30bbf8beead6a8ef665ec040a741123f | Java | 1,137 | 55 | package org.molgenis.genotype.util;
import java.util.HashMap;
import org.molgenis.genotype.variant.GeneticVariant;
public class Ld
{
public static double calculateRsquare(GeneticVariant var1, GeneticVariant var2) {
throw new UnsupportedOperationException("Not supported yet."); //To change body of genera... |
005b943b9c3dc9fcc5b2671b6557e60efb974de5f7c037f5db54913e0a9a1d80 | Java | 1,143 | 41 | package eqtlmappingpipeline.ase;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.molgenis.genotype.snpeff.SnpEffAnnotationTranslator;
import org.molgenis.genotype.... |
981f48087583348f61a557f2550e7e39704b3eb0f9248ef3349b3e7d750ba9b9 | Java | 1,144 | 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 eqtlmappingpipeline.transCorrelationQtl;
import cern.jet.random.tdouble.StudentT;
import cern.jet.random.tdouble.engine.DRand;... |
175a4aecec2a85bfd1e488ec2986ec8adeb47ebdf0386be414766a65e36dcdf0 | Java | 1,148 | 55 | package mbqtl.gfx;
import java.util.Objects;
public class ForestPlotEQTL implements Comparable<ForestPlotEQTL> {
public String EA;
public String NONEA;
public String snp;
public boolean isMeta;
String gene;
public String dataset;
public int samplesize;
public double effectsize;
pu... |
8c3a8e29ba879fde11baa050dd3210e64254bc9f1b8f42ccc7ee9da310634b2a | Java | 1,148 | 41 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine2Stimulus extends Stimulus {
private Polygon polygon;
private static double squeezeFrac = 0.25;
public Sabine2Stimulus(String name, Color color... |
410e70a003c85a13b3bd4717694ff06bf403a8a6025509258ac5dd1621ea52b8 | Java | 1,149 | 43 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.geom.Area;
import java.awt.geom.Ellipse2D;
public class CrescentStimulus extends Stimulus {
public CrescentStimulus(String name, Color color, int width, int height) {
super(name, color, width, height);
makeShape(0,0);
... |
fd9f30e3e25b286441851bca5cf6468f6879407bba5d72df1b680460ad5ecff7 | Java | 1,156 | 33 | package nl.systemsgenetics.downstreamer.summarystatistic;
import nl.systemsgenetics.downstreamer.summarystatistic.filters.SummaryStatisticsRecordFilter;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import java.io.IOException;
import java.util.*;
public class SummaryStatisticRec... |
ce9b8b3ab653689a5871b2a45a95dfcd8cdd718afb44b9ca8390f122c534368f | Java | 1,160 | 41 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine3Stimulus extends Stimulus {
private Polygon polygon;
private static double squeezeFrac = 0.25;
private static double indentFrac = 0.40;
public... |
85fef00e0c0194f3c156a4a7d0aceaee6f5fa060d241060f8bfcf64ceb42140a | Java | 1,168 | 41 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import java.util.concurrent.Callable;
import umcg.genetica.containers.Pair;
import umcg.genetica.math.stats.Descriptives;
/**
*
* @author harmjan
*/
public class Concurre... |
5aa74ac7d082582127fe266bbf5c5f439ccf00bb15321f8f102f431a56440e6f | Java | 1,171 | 41 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import java.util.concurrent.Callable;
import umcg.genetica.containers.Pair;
import umcg.genetica.math.stats.Descriptives;
/**
*
* @author harmjan
*/
public class Concurre... |
afda158b0c0c2c69e6d966664cd970c5a1aff5eaa6a4e96965645b645643efaf | Java | 1,171 | 84 | package org.molgenis.genotype.variant.id;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
public class BlankGeneticVariantId extends GeneticVariantId
{
protected BlankGeneticVariantId()
{
}
@Override
public Iterator<String> iterator()
{
return this.getVariantIds().iterator();... |
352e17828699c1b78e8a293a0f01a3da9094dce8e75eff9e46ee6b281411c6e7 | Java | 1,175 | 46 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.ld;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.io.IOException;
import java.util.ArrayList;
public class BinaryLDMatrixConverter {
public void run(String ldmatrixin, Strin... |
b519472d476d8eebe2cd739d39a66f8053e952a09eb12e2ecd798e76b2490376 | Java | 1,183 | 51 | package mbqtl.stat;
public class WeightedCorrelation {
private static double partialCov(double xi, double mwx, double yi, double mwy, double wi) {
double xminxw = xi - mwx;
double yminyw = yi - mwy;
return xminxw * yminyw * wi;
}
public static double correlate(double[] x, double[... |
7d3c49e35bbb93bac390b8dc03cb790ace1db3e57ae812ad303f2bbe7f2a7f8c | Java | 1,184 | 45 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.math.stats.ZScores;
import umcg.genetica.text.Strings;
import java.io.IOException;
public class EQTLFileR2Calculator {
public void run(String ein, String eout) throws IOExce... |
f688097e87e5972680a8a6f9590aa84199540f8f09d88890a6290a6af7ddb824 | Java | 1,189 | 59 | package umcg.genetica.enums;
/**
* Created by hwestra on 5/27/16.
*/
public enum DiseaseStatus {
CONTROL(0, "Control", 1),
CASE(1, "Case", 2),
UNKNOWN(-1, "Unknown", -1);
private final int number;
private final String name;
private final int famnumber;
private DiseaseStatus(int num, String name, int famnum... |
5c13dc36ce9724a29d3746cd559690467cc17649899fff9adfba77e48258ec46 | Java | 1,190 | 69 | package umcg.genetica.collections.intervaltree;
/**
*
* @author Patrick Deelen
*/
public class StringRange implements Range{
private final int start;
private final int end;
private final String value;
public StringRange(int start, int end, String value) {
this.start = start;
this.end = end;
this.value =... |
9a509c777984db4f28b902b37d83364baa6536757ba5c5cd4036ba5e275c9f64 | Java | 1,195 | 66 | package umcg.genetica.io.bed;
import umcg.genetica.variantAnnotator.GenomicRange;
/**
*
* @author Patrick Deelen
*/
public class BedEntry implements GenomicRange {
private final String chr;
private final int startPosition;
private final int stopPositions;
private final String name;
private final double score... |
c38f7eca5d8f6fa16eb187f45d53688c9950a850c016343f6641e8b0728c525b | Java | 1,199 | 47 | package nl.systemsgenetics.geneticriskscorecalculator;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
/**
*
* @author Patrick Deelen
*/
public class RiskScoreMatrix {
private final DoubleMatrixDataset<Stri... |
421856c52c487b25cb6ea3264e32def6c2c8f0f9a8c7bc1860ba99b8df411c78 | Java | 1,201 | 47 | package eqtlmappingpipeline.metaqtl4;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
* An awesome MetaQTL4
*
*/
public class MetaQTL4ConsoleUI {
private static final Logger logger = LogManager.getLogger(MetaQTL4ConsoleUI.class);
public MetaQTL4ConsoleUI(String[] a... |
3951a6c2d97505a4cc360fea039a9c41e39cb22982a939608ff48f7ff1c01f32 | Java | 1,203 | 53 | package edu.cmu.cs.eyetrack.io;
import java.io.IOException;
import au.com.bytecode.opencsv.CSVWriter;
import edu.cmu.cs.eyetrack.state.GameState;
public class TestRecord {
private static TestRecord instance = null;
private TestRecord() {
}
public static synchronized TestRecord getInstance(... |
59f3723f7185473e6bb0f72a1380ee916ad33cd16ce16bc3953fab7766f530ef | Java | 1,212 | 51 | /*
* 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.math;
import java.io.File;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeClass;
import ... |
705d1bffa397a056ad538ff36e945215d245ee555ed2b7c55e5c3c410228356a | Java | 1,212 | 46 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.containers;
import java.util.HashMap;
import java.util.ArrayList;
/**
*
* @author harmjan
*/
public class Family {
public String id;
public ArrayList<Individual> indi... |
1092379883507b84b9f4a1b0a5c5a5485a8a00723a0c031d429c8aa8865225f9 | Java | 1,220 | 59 | /*
* 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.runners;
import org.apache.commons.math3.stat.descriptive.moment.Kurtosis;
import org.apache.c... |
c287494b781d324baab47a618b47a1ffcdacbb9855fb34cda3e71925599efc1e | Java | 1,224 | 58 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.methylation;
import java.util.LinkedHashMap;
/**
*
* @author Marc Jan
*/
public class SoftfileAnnotation {
private String title = null;
private String accession = null;
private String meshT... |
876c48e762f612c2f57dcb4b8f9a6097dcbbaea2e5f5fd3eae027fcf6b8f2af4 | Java | 1,231 | 53 | package transeqtlcrossmap;
import umcg.genetica.features.FeatureComparator;
import umcg.genetica.features.Gene;
import umcg.genetica.features.Transcript;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.TreeSet;
/**
* Created by hwestra on 11/14/16.
*/
public clas... |
ff7c484e8bfa6f152612431cb989a08df98d89269be4d4d571bf36e958f474bd | Java | 1,234 | 42 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine8Stimulus extends Stimulus {
private Polygon polygon;
private static double squeezeFrac = 0.2;
public Sabine8Stimulus(String name, Color color, ... |
859caa34e107a269bb2d15e733700b2bbd3b8baa6de235dad595644ffb105464 | Java | 1,238 | 41 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew4Stimulus extends Stimulus {
private Polygon polygon;
public SabineNew4Stimulus(String name, Color color, int width, int height) {
super(na... |
d1198d94588fdf42abde79274415128a25e097af323270b442d46708e633da76 | Java | 1,243 | 43 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine9Stimulus extends Stimulus {
private Polygon polygon;
private static double bevelFrac = 0.2;
public Sabine9Stimulus(String name, Color color, in... |
25efa20877ba2595ca69287e5b49e6c8e5ae2d055887a0ba587264947eeec0c1 | Java | 1,245 | 59 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
/**
*
* @author harmjan
*/
public class Result {
int snp;
Double[] finalzscores;
Double[] finalpvalues;
Integer[][] numSamples; // [ds][probe]
boolean... |
b06a2336b5219ee73a336a3459bd8add55d4dc911e6b68f54c0892c972d55ad6 | Java | 1,246 | 47 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.stat;
/**
*
* @author harm-jan
*/
public class PCA {
Jama.EigenvalueDecomposition eig;
public void eigenValueDecomposition(double[][] data) {
Jama.Matrix... |
b6e87389bd1b94a22e090139684a2a27fd49fffcea9aa0ab99ba9ce052987175 | Java | 1,250 | 49 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.geom.GeneralPath;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine4Stimulus extends Stimulus {
private static double sideCurveFrac = 0.6;
private static double middlePointFrac = 0.4;
public Sabine4Stimu... |
f19efdc658f01c67b7f3b05ef23e2124d0f7c95dd8315139d75922179b66aced | Java | 1,251 | 43 | /*
* 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.pathway;
import nl.systemsgenetics.downstreamer.pathway.NaturalRankingTieFighter;
import java.... |
b160414c2de623b2a7f0939f70f124522b58b4a906ae9b3d0774dab56a61db49 | Java | 1,262 | 53 | package ebi.spot.neo4j2owl.importer;
import org.semanticweb.owlapi.expression.OWLEntityChecker;
import org.semanticweb.owlapi.model.*;
import java.util.Map;
public class N2OEntityChecker implements OWLEntityChecker {
private final Map<String, OWLEntity> entities;
N2OEntityChecker(Map<String, OWLEntity> ent... |
5cc8a0a3db49390473a6fa95a542f909675b3b9343605c6d9569782c52647a3e | Java | 1,267 | 50 | package edu.cmu.cs.eyetrack.gui;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import javax.swing.JPanel;
import edu.cmu.cs.eyetrack.helper.Util.PanelID;
@SuppressWarnings("serial")
public abstract class Screen extends JPanel {
protected final EyeTrack owner;
protected PanelI... |
3081fceb542f6a968cbed4897f48fdbc35459bbfc627c5057c090ed0d9cd037e | Java | 1,269 | 41 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew5Stimulus extends Stimulus {
private Polygon polygon;
public SabineNew5Stimulus(String name, Color color, int width, int height) {
super(na... |
06ce8c9f338678e146ef932dda468327f73ee67dea0de921f94930bd409588dd | Java | 1,275 | 62 | package eqtlmappingpipeline.ase;
import java.util.ArrayList;
import java.util.TreeMap;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class FindM... |
bf6fa8582b2be0a2eabdbeb5dd6a6f0a0803e644b0332c943221e63b91cda424 | Java | 1,279 | 73 | package umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
/**
* Created by hwestra on 8/31/15.
*/
public class PeakFeature extends Feature {
// abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name
int summit;
double pileup;
double pval;
double foldenrich;
double qval;
public... |
b8c02ee5b0283d2e65dd095825b2603cd29f768de73df644f818151377f286c5 | Java | 1,282 | 73 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gtf;
import java.io.IOException;
import java.util.Iterator;
import java.util.NoSuchElementException;
/**
*
* @author Patrick Deelen
*/
public class GffElementIterator implements Iterator<Gff... |
32a09ed7be091b6fceb576bc6b4a91dc09c7bc686589175a72596f5733aaeda4 | Java | 1,283 | 41 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew2Stimulus extends Stimulus {
private Polygon polygon;
public SabineNew2Stimulus(String name, Color color, int width, int height) {
super(na... |
11533996e5f8d56a45e2cc2d901ba33a1a896c38f3ffe98a22941b20060f6ab8 | Java | 1,287 | 37 | package nl.systemsgenetics.datg;
public enum DatgConvertModes {
TXT_2_DATG("Convert tab separated .txt or .txt.gz files to a .datg file. The first row is expected to be header information and the first column should contain row names"),
DATG_2_TXT("Convert a datg file to a txt"),
DAT_2_DATG("Special mode ... |
bf3f658c84a9c547f7b55f08be6661c01b76856770f5707dbd5287dab6ead360 | Java | 1,299 | 58 | package eqtlmappingpipeline.trans;
import java.util.BitSet;
public class TransQTLEncoder {
private static byte[] convertShortMatrixToByteArrat(short[][] matrix) {
int len = matrix.length * matrix[0].length * 2; // 2 bytes per short
byte[] concate = new byte[len];
int pos = 0;
for (int i = 0; i < matrix.len... |
ca2979ed8946d5a0b770b0d857c4fc9d1c8de4f49577cf607c4a3f63187f7804 | Java | 1,300 | 42 | package edu.cmu.cs.eyetrack.helper;
import java.io.File;
public abstract class Util {
public static enum PanelID { START_MENU, GAME, BUFFER1, DISTRACTOR_LINEUP, BUFFER2 };
public static String getTrackItVersion() {
return "2.0.5";
}
// Debug settings, debug utilities
public static boolean ... |
fa992db8952ec70098d118d877b5641861372dff23cf6095c6a84396c95458ef | Java | 1,302 | 30 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
64ab72fcbcb8e5a4dced7cec41b9dcafa6a7f2b5156b6b7671eb33f5620f825a | Java | 1,303 | 43 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine6Stimulus extends Stimulus {
private Polygon polygon;
public Sabine6Stimulus(String name, Color color, int width, int height) {
super(name, c... |
ba9af2c9c654a89f95c13b7798f7ae2659f7442c7c72298095d3349651d20144 | Java | 1,303 | 58 | package mbqtl.vcf.filter.genotypefilters;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import mbqtl.vcf.VCFVariant;
/**
* Created by hwestra on 2/8/16.
*/
public class ReadDepthFilter implements VCFGenotypeFilter {
private int minimalReadDepth = 10;
public ReadDepthFilter() {
}
public ReadDepthFil... |
c6cfedcbfdbcd71f3f434335abb7f673d41e6801b4e3188fce0db6769a93a50d | Java | 1,303 | 42 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine5Stimulus extends Stimulus {
private Polygon polygon;
private static double steepnessYFrac = 0.15;
private static double steepnessXFrac = 0.6;
... |
04410dbd3039dab183a3d75a8c0cb0b35513227e4a42e96b1f8500cf7cc56995 | Java | 1,304 | 30 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
d1a5e5665004c58974c6c3a5d9761521a6308386e99970377c5a4303600b34b0 | Java | 1,304 | 81 | package org.molgenis.genotype.util;
import java.io.Serializable;
import java.util.Comparator;
public class ChromosomeComparator implements Comparator<String>, Serializable
{
public static final ChromosomeComparator comparator = new ChromosomeComparator();
public static boolean chrASmallerChrB(String chrA, Strin... |
e6a832e27edf379b034bd501893d34c83b5db318c8da05b7f09c021f9690912a | Java | 1,304 | 47 | package org.molgenis.genotype.plink.drivers;
import static org.testng.AssertJUnit.assertEquals;
import java.io.IOException;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class MapFileDriverTest extends AbstractResourceTest
{
private ... |
0456796418fd6985d5b339a600dc63513fc6586868b2ccb41a6778aa86895ae4 | Java | 1,308 | 43 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import java.util.concurrent.Callable;
import umcg.genetica.containers.Pair;
import umcg.genetica.math.stats.Correlation;
/**
*
* @author harmjan
*/
public class Concurren... |
5489a672b773a788ee994fa9abbcc8a58137bc8863b1f9f3cf22ca122ccd4443 | Java | 1,308 | 59 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
/**
*
* @author harmjan
*/
public class Triple<L, M, R> {
private final L left;
private final M middle;
private final R right;
public Triple(L left, M middle, R rig... |
bddf64180227f4366dd3f68a9f70477f615ad99c24d1bc5272204234d11c12c7 | Java | 1,308 | 30 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
1bd5ae5798a8a749add98fa32fec3b290efa3801f9232835fc386557e29d891c | Java | 1,309 | 43 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import java.util.concurrent.Callable;
import umcg.genetica.containers.Pair;
import umcg.genetica.math.stats.Correlation;
/**
*
* @author marc jan
*/
public class Concurre... |
8d536834808bc1edb072db436256a19f7e8538765da24ae958051d70c21171d6 | Java | 1,310 | 30 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
c7b6b07822614aa7c207240abf7ff96685e4b47dc7f3ffcf0ef151f40ae97a9c | Java | 1,320 | 40 | /*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you ma... |
2a3462f99e81c8bebe0c657b9de77dfdb291733ef2a6809985e99dcb74a3723e | Java | 1,323 | 56 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
/**
*
* @author lude
*/
public class RankIntArray {
public int[] x = null;
public int[] y = null;
public cern.colt.Swapper swapper = null;
public cern.colt.function.tint.I... |
cec2e382213002a312331f08861095fdeac879a1b6e8605a01e29e563cda55c8 | Java | 1,331 | 42 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew1Stimulus extends Stimulus {
private Polygon polygon;
public SabineNew1Stimulus(String name, Color color, int width, int height) {
super(na... |
7af566754e93577210dfdbc1ffe161540a1417212fb542ab6e725cb9fa9bb9c8 | Java | 1,332 | 50 | /*
* 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.math.stats;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import org.testng.ann... |
c22ccdca902d6cea9b671adf836193e0b810f51df6fec603ed40558618da4cc6 | Java | 1,332 | 42 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.Polygon;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew3Stimulus extends Stimulus {
private Polygon polygon;
public SabineNew3Stimulus(String name, Color color, int width, int height) {
super(na... |
505d54925b16b0846101f0835119e081e3067db670216f4d0049448cd2e87f0e | Java | 1,336 | 44 | package network_code_v5.proc;
import network_code_v5.func.*;
import network_code_v5.beans.*;
import java.io.*;
import java.util.*;
public class UCSCbrowserDataProc
{
public UCSCbrowserDataProc(){}
//
public void printUCSCGeneExpressionBedFiles(ConfigBeans configBean)
{
UCSCbrowserData handler = new UCSCbrows... |
9f4936450691849c90f89d69cbeb02612e3fc618b65be7362335c19bf2dc29a4 | Java | 1,339 | 32 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
94ead50733099cbb1898c7f226e864be91e762ba5a2bdc9eb4b555b17696074f | Java | 1,341 | 63 | /*
* 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;
import java.util.ArrayList;
import nl.syste... |
89292ee354f95c643a4b03f939614a951a4bc9d5e3fb89db7c1a5bffbbe585fd | Java | 1,343 | 53 | /*
* 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.math.stats;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeClass;
import org.testng.anno... |
a42ca86d4518bd90da87317972b68cf01d2cc80c370e07fb4da2df7554c6416b | Java | 1,343 | 30 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
5b035317598f74b1cd3e2dc4c48447b311d886b7f7a9bc8bf396c17b13059931 | Java | 1,344 | 35 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
767d7808ab30adfddd2ffd5cc7673b68ef8b6064119eee658906dcb4297e0bb7 | Java | 1,344 | 33 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
4574a6bb12028f0a7fb433f0b9cf53353f8386befe6f2e0a8672303ad899af32 | Java | 1,345 | 31 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
65a75665151b219a2667d5b64dce548fa782955c598cf65fa996a330b3e997f6 | Java | 1,347 | 56 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
/**
*
* @author lude
*/
public class RankDoubleArray {
public double[] x = null;
public int[] y = null;
public cern.colt.Swapper swapper = null;
public cern.colt.function.... |
ccab974d0d1a519a30df8e8e8a6c2d57e7c83944ab18fe91288df7f8eb8ffba3 | Java | 1,349 | 70 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
import java.util.ArrayList;
import java.util.HashMap;
/**
*
* @author harmjan
*/
public class Chromosome {
private String name;
private HashMap<String, Gene> geneHash;
p... |
2a9cfbd96562b53ac136640f45ffcead6411184022a95cfc23ef4b9f2bc4cd95 | Java | 1,354 | 42 | package nl.systemsgenetics.datg;
import org.apache.commons.math3.util.Precision;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.io.IOException;
public class Validator {
public static void compareTwoMatrices(DoubleMatrixDataset<String, String> m1, DoubleMatrixDataset<String, String> m2) throw... |
a422b5d69fa9136c031734e23d3df1413765517d3bfc787e4ec403e6e9752425 | Java | 1,354 | 50 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part1;
import java.awt.Color;
import java.awt.geom.GeneralPath;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class Sabine7Stimulus extends Stimulus {
private static double kappa = 0.5522847498;
private int radius;
public Sabine7Stimulus(String name, Color... |
4cbda4e6d0d249ccda63fcb89b1a6ab1ec8409b4e9afc8167c3cdca6ce5818e7 | Java | 1,355 | 60 | /*
* 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 VariantQcChecker implements VariantFilter {
private double maf;
... |
cdf39efdcf502ac533c7fe6cad1012c56d93e56ba48e093e040e79fcc744493c | Java | 1,355 | 44 | /*
* 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 org.biojava.nb... |
69375d5b2890945ff6b1f754669a8c72e1d3df8aeda1af8d47c9498671cccd8a | Java | 1,357 | 63 | /*
* 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.ejml.simple.SimpleMatrix;
/**
*
* @author adriaan
... |
0b68c6d6b6289772afe2dcefbfe079415edf929e692c7e53bcf2aff91077644e | Java | 1,360 | 65 | /*
* 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 java.util.Comparator;
/**
* @author hwestra
*/
public class FeatureComparator implements Com... |
ea51236b0117f9ef7b7b2a883f36436855f018a38f1bbe6dc9417a778cd0b465 | Java | 1,363 | 64 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline;
import eqtlmappingpipeline.metaqtl3.containers.QTL;
import java.util.Random;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import umcg.genetica.util.SmoothS... |
f862f5f50ec28a81cc5c5ae3356928b8ad31631fcfa53703e62d8bddd95a2d2f | Java | 1,363 | 45 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.Polygon;
public class OctagonStimulus extends Stimulus {
private Polygon polygon;
private double hScale = 1.0/3.0;
private double vScale = 1.0/3.0;
public OctagonStimulus(String name, Color color, int width, int height) {
supe... |
886812ba730bf9a6cb59767d13bc2c63a83f5579b867eb5fb008ff57ebe17bdd | Java | 1,364 | 49 | package edu.cmu.cs.eyetrack.gui.trial;
import java.awt.Color;
import javax.swing.BorderFactory;
import javax.swing.ImageIcon;
import javax.swing.JLabel;
import edu.cmu.cs.eyetrack.io.ResourceLoader;
@SuppressWarnings("serial")
public class Block extends JLabel {
private ImageIcon backgroundImage = nu... |
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