sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
19ee9694e1f86469a1fedd956667d9839124b5a1766a28443973fc1c83c6c057 | Java | 1,367 | 34 | /*-
* #%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... |
e7624a476b030c28d43c015483c2368322c957940ff632be4e11654fc438cfb7 | Java | 1,370 | 61 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
/**
*
* @author Matthieu
*/
public class RepeatElement {
private String chromosome;
private int startPos;
private int stopPos;
private String... |
3b51131042733c5bbe7c52ba76aa7292c5fb8358e29f85a5daa7d9e3f4d106b5 | Java | 1,374 | 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... |
a1ba6b0db221c840938e8689a824d19130c2c333b9eb7e18ca26c1bb5e88e55b | Java | 1,393 | 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 umcg.genetica.math;
import org.apache.commons.math3.special.Erf;
import org.apache.commons.math3.util.FastMath;
/**
* Code a... |
34c9c774860f418e47fc24f38da0a9e7425a36a5373fd8e4d22ab16607e91c6d | Java | 1,397 | 40 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OException;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import java.io.File;
import java.io.IOException;
import java.util.concurrent.ExecutionException;
public class N2OImporterRunner {
public static void main(String[] args) {... |
0af268210665c44b3f569b93d81d4e3ed31b237d358a0a4c7034025917bc9cb1 | Java | 1,404 | 71 | /*
* 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;
import umcg.genetica.enums.Strand;
import java.util.ArrayList;... |
227aedc87e62360f0df3e9d8aa24a331d1b2163bc12186baae2d538d2e75be28 | Java | 1,412 | 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.development.originalLude;
import java.util.concurrent.Callable;
import java.util.concurrent.T... |
63128a1d8ee8e64c3334e9feec62137989e5ace5e8533893a8dca2819b0a7a9e | Java | 1,414 | 60 | /*
* 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.div;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;... |
8d2d069fe3e9e7fbf3e7665e3db61b0b27c8119142489a456bd5200c749a3da9 | Java | 1,415 | 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 nl.systemsgenetics.downstreamer.development;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Set;
imp... |
290e27abfe54eaf3c0b81866e693c1db366671f8423c4df7a4bf576bd8265da3 | Java | 1,419 | 36 | /*-
* #%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... |
a81568f8729ee565876adca54eb89d18f1b56644d3502c00fd1f93749b1ba896 | Java | 1,421 | 81 | package org.molgenis.genotype.annotation;
import org.apache.commons.lang3.builder.ToStringBuilder;
/**
* Generic Annotation class. Describes samples, sequences etc.
*/
public abstract class Annotation
{
public enum Type
{
INTEGER, BOOLEAN, FLOAT, STRING, CHAR, UNKOWN, SEX, CASECONTROL
}
private String id;
p... |
cf5147a13b431356f923c769aaf2c3df1e4a4b44600499978c19384ed2f943b3 | Java | 1,425 | 29 | /*******************************************************************************
* Copyright (c) 2015 David Lamparter, Daniel Marbach
*
* 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 wi... |
c712abf6968898528c8f4b5234e4582b8baa97c39229e096097ba294a5508a0a | Java | 1,426 | 44 | 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 SabineNew6Stimulus extends Stimulus {
private Polygon polygon;
public SabineNew6Stimulus(String name, Color color, int width, int height) {
super(na... |
98ff53b90aeefef5b1ad34aa2c2a0db2eb1a49fecf99c040e24b3f8929f50ebf | Java | 1,427 | 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.io.chrContacts;
/**
*
* @author MaKKie_Admin
*/
public class ChrContact implements Comparable<ChrContact> {
... |
4e9b75fd27bd445c59f7ff447f48e6399b9bb9c3c5e53233013a22825f362928 | Java | 1,428 | 38 | /*-
* #%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... |
4eaafa467fd713bd3c738ca16b90f466c3b75fc8e011eaf04581db1f2e5f25b2 | Java | 1,431 | 69 | package org.molgenis.genotype.plink.datatypes;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.molgenis.genotype.Alleles;
public class PedEntry implements Iterable<Alleles> {
// list iterates SNP's, so 1 list per individual
private final Iterator<Alleles> bialleles;
privat... |
b204c0ac4dbf27aade31d24b73c9b5bc0f99bfe644f1d90ea3d32ea33ff8934f | Java | 1,451 | 37 | /*-
* #%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... |
9e91df760fa6a05d5db164349d23596ddf666b7762b8963ffb1ce10ca87a0ff8 | Java | 1,454 | 50 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.util.Random;
/**
*
* @author MarcJan
*/
public class InplaceArrayQuickSort {
public static final Random RND = new Random();
private static void swap(Object[] arra... |
147ad223887b832b612370aa69e3820afcde2afb78d150243eae7ce38deb9ec9 | Java | 1,459 | 52 | package mbqtl;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Random;
public class Util {
public static HashMap<String, Integer> hash(ArrayList<String> list) {
HashMap<String, Integer> hash = new HashMap<>();
for (int i = 0; i < list.size(); i++) {
hash.put(lis... |
95248d8d23daa5732ab84dd553ce9283c0b74960b668acc6a78e3acbb4a12b92 | Java | 1,465 | 58 | package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
/*
* 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.
*/
/**
*
* @author adriaan
* Used as a class to store all variab... |
be2112a857945163d352b566107c5eef8858358d6e63b536c2bd1868e31d43b8 | Java | 1,468 | 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 nl.systemsgenetics.gadocommandline;
/**
*
* @author patri
*/
public class GenePrioritisationResult implements Comparable<Ge... |
4c3db43b628f996c9a3ae3d5d00af65ef1942f50de49c8ead307ba7b2ab801f3 | Java | 1,471 | 37 | /*-
* #%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... |
7cf2a7e5e05cc437b0f4834003e4fdc8350e2aeae3f469d788f46a9e18cc98c3 | Java | 1,471 | 66 | /*
* 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 Patrick Deelen
*/
public class BgenixVariantData {
private final String chrom... |
bf1a54f43ccff36f776f69dcc9915cf92aa8c196963fdb7b9ab089fc93bf6fe1 | Java | 1,475 | 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 nl.systemsgenetics.genenetworkbackend.hpo;
/**
*
* @author patri
*/
public class GenePrioritisationResult implements Compar... |
01eadb686859016a5754372c1383f0bc2ffc4be3f65e32599e05c2ef8111cba8 | Java | 1,480 | 63 | package umcg.genetica.math.matrix2;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.bin.RandomAccessFile;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.List;
@Deprecated //is now directly availble in datg writer
public class DoubleMatrixDatasetAppendableWriter {
... |
3a107689cb480be813b933dcfcc230b65dd76756e662bdda9d64e1928f7f1d82 | Java | 1,493 | 38 | /*-
* #%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... |
7d0ebe96ea63ff09fd022f9a2b959db45bec424d20ec848807219861864fd163 | Java | 1,502 | 60 | /*
* 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;
/**
*
* @author Harm-Jan
*/
public class BedFileFeature extends Feature {
// private final Trac... |
da11feee8cb05291ab51b3e081099c27ced305c1ae8ed22b32fe8b0952ce096a | Java | 1,502 | 56 | package network_code_v5.proc;
import network_code_v5.func.*;
import network_code_v5.beans.*;
import java.io.*;
import java.util.*;
public class GenerateBioTapestryNetworkProc
{
public GenerateBioTapestryNetworkProc(){}
/*
*
*/
public void integrateInteractionFiles(ConfigBeans configBean)
{
NetworkIntera... |
1b41b92a7cee7a7fabce305d5c689ad24acffd436ced1be2f74f49bb107188ca | Java | 1,504 | 39 | package mbqtl.junk;
import cern.jet.random.tdouble.StudentT;
import cern.jet.random.tdouble.engine.DRand;
import umcg.genetica.math.stats.Correlation;
import umcg.genetica.math.stats.ZScores;
import java.text.DecimalFormat;
public class PTest {
public static void main(String[] args) {
// double spearman =... |
17e66c8c6c6e6e164f54baf53b4982ca0313c92e6e923810396678fde6b9587d | Java | 1,508 | 65 | package edu.cmu.cs.eyetrack.test;
public class SingleRunScore {
private long frameCountOverall = 0;
private long frameCountOnTarget = 0;
private long fixationPointCount = 0;
private long fixationNearDistractorNotTargetCount = 0;
private double score;
public SingleRunScore() {
}
public long... |
e8e6df921ff34f6323ec382d54246e8969e29c36e7a9001ccbb21195c3a10dbf | Java | 1,511 | 46 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.util.stream.IntStream;
/**
* @author harmjan
*/
public class Log2Transform {
public static void log2transform... |
6a42934c65d5d4d1ed50fa5f6967f3acf471e9d83c88fde930b125f07a662a70 | Java | 1,513 | 56 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats;
/**
*
* @author harmjan
*/
public class MetaQTL4DatasetSettings {
private final String name;
private... |
81f6cc50397cf14db9a06317144597865c97a8518a0c15ed6bf7e013780beae2 | Java | 1,519 | 52 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
/**
*
* @author harmjan
*/
public class Regression {
public static double[] getLinearRegressionCoefficients(double[] x, double[] y) {
if (y.length != x.length) {
... |
25df0f387ec078f3dfbf58ee4659be7d03d70df311d2bdc64d6082b85831b5ee | Java | 1,531 | 50 | package org.molgenis.genotype.util;
import org.molgenis.genotype.GenotypeDataException;
/**
*
* @author Patrick Deelen
*/
public class MachR2Calculator {
/**
* Calculate the MACH r2 measure
*
* For formula see: doi:10.1038/nrg2796 S3
*
* @param dosages
* @return
*/
publi... |
77d6cc50f87baed1a7fffbf8e542f912057d6e9c37f722a2cf4e3a87d595d531 | Java | 1,533 | 58 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.annotation;
/**
*
* @author harmjan
*/
public enum CaseControlAnnotation {
CASE((byte) 2), CONTROL((byte) 1), UNKNOWN((byte) 0);
private final byte plinkCase;
private CaseC... |
9386f935a9fa0945a9d333c3076e2bd654fdd1f7036b798eac6db5189d30f950 | Java | 1,534 | 41 | /*-
* #%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... |
c733b87e2568f95fbd578eb0edb00427b7dd5fa764ce35bcc10dbce078498de3 | Java | 1,536 | 63 | package nl.umcg.deelenp.genotypeharmonizer;
import java.io.BufferedWriter;
import java.io.Closeable;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class SnpLogWriter implements Closeable{
p... |
9cd08eb8504bda2046fcc9c6abdfcba4bbccc74262fd8a4dc2dda4f95dd05743 | Java | 1,539 | 73 | /*
* 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 static org.testng.Assert.*;
import org.testng.annotations.AfterClass;
import org.testng.annotations... |
101998879c4d3973bcabbbd2df9da636172f22d248b07351ab6d4d9f37e14e30 | Java | 1,540 | 54 | package nl.systemsgenetics.downstreamer.summarystatistic.filters;
import nl.systemsgenetics.downstreamer.summarystatistic.Locus;
import nl.systemsgenetics.downstreamer.summarystatistic.SummaryStatisticRecord;
/**
* The type Region filter.
*/
public class RegionFilter implements SummaryStatisticsRecordFilter {
... |
fde5c6b0afb871874bd73ae389aa7e599d67dbe5f4e9504aa52691d9d0393a1f | Java | 1,543 | 50 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.geom.GeneralPath;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew10Stimulus extends Stimulus {
private static double kappa = 0.5522847498;
private int radius; // Radius of the little bump circle
p... |
7e9f064818b95b94e33446305e3319908a1a1b09301966314b2cba01a632839c | Java | 1,547 | 84 | /*
* 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.collections.intervaltree;
import java.util.Objects;
import umcg.genetica.variantAnnotator.GenomicRange;
/**
*
... |
13d85358fec2c8cb48c1023e88e0d67897db93292d8037f98df2d2b4aff31485 | Java | 1,551 | 43 | /*-
* #%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... |
8edcae0a5f13d77749e1b97f7c7852492fa8c208bbdfd171e8c5750d09c3e5c3 | Java | 1,551 | 46 | 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 Sabine10Stimulus extends Stimulus {
private Polygon polygon;
private static double bevelFrac = 0.35;
private static double horizontalSqueezeFrac = 0.5... |
2ed656f18cb020b5c36c710df4baad15a8bdf7d9d41bf0721aef24240827c412 | Java | 1,562 | 83 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.ucsc;
import java.util.ArrayList;
import java.util.Collections;
/**
*
* @author harmjan
*/
public class UCSCTrack implements Comparable<UCSCTrack> {
private String name;
private Arr... |
f4ccb3a06ef5c83d8f6ac85be6fce7ff1d2bc4d5a0f6563cc6abf03b7cab81b4 | Java | 1,562 | 60 | /*
* 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.div;
import cern.jet.random.tdouble.StudentT;
import cern.jet.random.tdouble.engine.DRan... |
00899000af16ba1affa3a45bbd8cc94b9242fd0af031f10ae481286b637323c4 | Java | 1,569 | 76 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.stat.dist;
/**
*
* @author harm-jan
*/
public class Bin {
protected double lower, upper;
protected int count;
protected Double frequency;
protecte... |
8ab560b49595410c4ec190b7f405eb88a9976b8489a55e2444b6d107bd46a520 | Java | 1,576 | 51 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.geom.GeneralPath;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew8Stimulus extends Stimulus {
private static double kappa = 0.5522847498;
private int radius; // Radius of the little bump circle
pu... |
4e2ea854e74d22cec7781ea713544784c3920fdd3ce252bc1859c910f4fa917d | Java | 1,578 | 44 | /*-
* #%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... |
787c647250912a0a915c85c79fbc4c56b8c364ebb28deb65a51907f1e9e9f682 | Java | 1,580 | 65 | package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import au.com.bytecode.opencsv.CSVWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
/**
*
* @author Patrick Deelen
*/
public class SkippedInteractionWriter {
private final CS... |
ebb63aeaa9af66d8097b64ee99888a3924be5673b45de38d138f970ed5b06fce | Java | 1,583 | 48 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.Polygon;
public class CrossStimulus extends Stimulus {
private Polygon polygon;
private double hArm = 1.0/3.0;
private double vArm = 1.0/3.0;
public CrossStimulus(String name, Color color, int width, int height) {
super(name, co... |
0b736cd73efab86ad1765bbd182eebd2116fce5ce0d6cb634cf944540be1d25b | Java | 1,584 | 40 | /*-
* #%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... |
058720523415acd234d1f939c59990a6668517e85a83734ffbfda67859d48433 | Java | 1,589 | 48 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.cis;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread;
import java.util.HashMap;
import java.util.concurrent.ArrayBlockingQueue;
import org.apache.logg... |
98d5f840c4b2d63dd6402ad37bf53cf6c7b943e12e2ccfa42d08fa63da43f3ee | Java | 1,594 | 59 | package mbqtl.stat;
import JSci.maths.statistics.NormalDistribution;
import cern.jet.random.tdouble.StudentT;
import cern.jet.random.tdouble.engine.DRand;
import org.apache.commons.math3.distribution.FDistribution;
public class PVal {
private static final NormalDistribution NORM_DIST = new NormalDistribution(0.0D... |
ad89ea0d5fd40e6e3aaf9d8ad510c23e22bd9b73c4c8babff5679e94d96dad09 | Java | 1,595 | 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 nl.systemsgenetics.downstreamer.io;
import java.io.IOException;
import org.apache.commons.math3.util.Precision;
import umcg.g... |
615d0cd4953118c423e1b54fce06490788f9298cb8cdf8455934cb5a8b739087 | Java | 1,596 | 75 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.editable;
import org.molgenis.genotype.Alleles;
/**
*
* @author Patrick Deelen
*/
public class VariantInformation {
private final String variantId;
private final int startPos;
priv... |
70817ccb35c4117e53d16f52f99f22fbbb38cae8d52fb4e7464722db8c6524c9 | Java | 1,596 | 66 | package org.molgenis.genotype;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import static org.molgenis.genotype.GenotypeData.SAMPLE_MISSING_RATE_FLOAT;
import org.molgenis.genotype.annotation.Annotation;
import org.molgenis.genotype.annotation.SampleAnnotation;
import org.molgenis.... |
9a78912491cb299f4697df13417b8cfeb07ea4e4013bc1765bc435d327d64fb3 | Java | 1,596 | 68 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gtf;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
/**
*
* @author Patrick Deelen
*/
public class GffAttributeFilter {
protected ... |
10ed7e25d5230f52b448656b1e79386c0a9cb750e1628fcbc3683d821c4b6d11 | Java | 1,599 | 78 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.util.Iterator;
import java.util.NoSuchElementException;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class Va... |
0d29dfd1282e923ca95d20d97fcf92fb3729138f3f0921e5abbf1af10ad6ee0b | Java | 1,608 | 45 | package nl.systemsgenetics.downstreamer;
import nl.systemsgenetics.downstreamer.pathway.PathwayEnrichments;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.util.List;
public class DownstreamerStep2Results {
private DoubleMatrixDataset<String, String> genePvalues;
private DoubleMatrixData... |
25cc27920e80199cd48564b882e483c63674835b7c75c35be7e589bc41d8f0a0 | Java | 1,620 | 47 | /*
* Copyright @ 2018 Atlassian Pty Ltd
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or ag... |
e059e959648662c7232a6602158354d7faa7bb7544cea6c23bdd03c089e17872 | Java | 1,621 | 62 | /*
* 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.io.chrContacts;
/**
*
* @author MaKKie_Admin
*/
public class DesiredChrContact extends ChrContact {
priv... |
ea2392b3a0941eb23316a68419c3482e9af3d738ae300d7191c4746dc8ad154c | Java | 1,621 | 59 | 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 Sabine1Stimulus extends Stimulus {
private static double topCurveFrac = 0.6;
private static double sideCurveFrac = topCurveFrac;
public Sabin... |
7f1fe8c8529658cd4596fbd15624a7f8d6af021abc9d1b628ecb5a92128dbbf3 | Java | 1,624 | 60 | package mbqtl.vcf.filter.genotypefilters;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import mbqtl.vcf.VCFVariant;
/**
* Created by hwestra on 2/8/16.
*/
public class AllelicDepthFilter implements VCFGenotypeFilter {
private int minimumReadDepth;
private double abCutoff = 0.15;
public AllelicDepthFilter()... |
3d05d75465a708c37e1446d024e1ded51a04fdcc1f25d7a57dbf50178fbd939e | Java | 1,626 | 45 | /*-
* #%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... |
64034337ab558f38958039e67bc35328fd22879908218e06503704e432a51415 | Java | 1,626 | 54 | package deformablemesh.examples;
import ij.IJ;
import ij.ImageJ;
import ij.plugin.PlugIn;
import org.scijava.java3d.*;
import org.scijava.java3d.utils.geometry.Sphere;
import org.scijava.java3d.utils.universe.SimpleUniverse;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3d;
import j... |
1b06d57313bcea1945df06edb34e85193af7ea9376b4ed030395d2450af15f59 | Java | 1,627 | 66 | package umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.enums.Strand;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.ArrayList;
/**
* Created by hwestra on 9/13/16.
*/
public class GFFFile {
public ArrayList<Feature> readGFF(String gff, boo... |
f3bb1694716c13d90b12f33405186807879fe6d2faefb9372b6d2f70c29e3304 | Java | 1,630 | 40 | package org.molgenis.genotype.plink;
import java.util.LinkedHashMap;
import java.util.Map;
import org.molgenis.genotype.GenotypeData;
import org.molgenis.genotype.annotation.Annotation;
import org.molgenis.genotype.annotation.SampleAnnotation;
import org.molgenis.genotype.annotation.SampleAnnotation.SampleAnnotationT... |
cfb4fdc0773f6f47ef0f257118013884e8d5546c935858368da0e7a2b9c5154d | Java | 1,631 | 45 | /*-
* #%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... |
d0f4bf46a309f451377bf1bd4b828a4ea975388e726a9879948440b7c5e5066e | Java | 1,635 | 73 | package eqtlmappingpipeline.ase;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
/**
*
* @author Patrick Deelen
*/
public class AseCalculator implements Runnable {
private final AseVariant[] aseVariants;
private final AtomicInteger counter;
public AseCalcu... |
13df3d9cea0178119f2660769da7b99d2e7d7704bbb8a36ac7cc74eb422303c6 | Java | 1,638 | 66 | package umcg.genetica.collections.intervaltree;
import java.util.ArrayList;
import java.util.Arrays;
/**
*
* @author Patrick Deelen
*/
class IntervalTreeNode<E extends Range> {
private final int centerPoint;
private final IntervalTreeNode left;
private final IntervalTreeNode right;
private final E[] startSort... |
773093cf147a55198b6e9b3754d8e2e4308e24cfcc007511a1939eca73c0dcbb | Java | 1,641 | 56 | /* Copyright (c) 2019 Thomas Braschler <thomas.braschler@unige.ch>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version... |
2686befa1c5c6923f9785ac8c48f7334a31014f0782e44d040fc8d931ad8b979 | Java | 1,654 | 64 | package mbqtl.vcf.filter.variantfilters;
import mbqtl.vcf.VCFVariant;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.features.SNPFeature;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
/**
* Created by hwestra on 4/18/17.
*/
pu... |
c1905fe06f2be1add87319033a9ff409c8e2ed5ea029bd46469cfade037ad0b8 | Java | 1,672 | 51 | package org.molgenis.genotype.util;
import static org.testng.AssertJUnit.assertEquals;
import java.util.ArrayList;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.testng.annotations.Test;
public class MafCalculatorTest
{
@Test
public void calculateMaf()
{
ArrayList<Allel... |
d4bd6a481db269c148f28bc29b9f7b6a3421173cb33d0a1f1bdc771ddec0dcdb | Java | 1,690 | 52 | package main.java.decon_eQTL;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.logging.ConsoleHandler;
import java.util.logging.FileHandler;
import java.util.logging.Level;
import java.ut... |
1068935f2d48ba24fb000889e9bddcbaf71ede58be326ba0c9ce83ee9b619fcb | Java | 1,691 | 37 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
3022cc11e681feaa1c4b7b2457608f07dcd34b27bf05db2ee78be3f7557d3564 | Java | 1,691 | 37 | /*-
* #%L
* Ops created for BoneJ2
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the abov... |
505a6258ecb23737534c3c691348e2af98ffbc257170cdf650cd60aca10ef8dc | Java | 1,694 | 48 | /*-
* #%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... |
6b9a27484fe3d9bca91983403780632d3c92e51d7d338439c74ee8afef3e8567 | Java | 1,696 | 68 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binaryInteraction;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public class BinaryI... |
45bd4208707d80d5f299bbac9a420ba4f0e23419fd4d679136964094b3c01939 | Java | 1,699 | 63 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.containers;
/**
*
* @author harm-jan
*/
public class Result {
public double[][] correlations;
public double[][] zscores;
public int[] numSamples;
public int[] nr... |
1926c34fe6dab1af6cce5b1c3a549f301348e9dcc789469c0b7b5d00b65d8ccb | Java | 1,706 | 67 | package umcg.genetica.io.binInteraction;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionQtlZscores {
private final double[] zscores;
private final int[] sampleCounts;
private final double metaZscore;
private final static double[] emptyDoubleArray = new double[0];
private final static int[]... |
b62d52350ac02f4958ef4f3683db2c9a00b37855c27859eb3fddac1665c311d8 | Java | 1,708 | 40 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
6a0a8b9c2a0977216b7f8946c2e667ee7ae7e776f9adca00e6120834335e3d3f | Java | 1,716 | 79 | /*
* 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
... |
f42349f0915f1d82ba84a67b893cf6c7df9f9fb5ea30e86c1954d4d53c486ac4 | Java | 1,727 | 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 nl.systemsgenetics.gadocommandline;
import java.io.File;
import java.io.IOException;
import umcg.genetica.math.matrix2.DoubleM... |
eb86fdc83b0e628453aa3d6ac7163b00d7982dab38429726574eced5363e313e | Java | 1,736 | 44 | /*-
* #%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... |
2f9e96476470efc374b9153ee34ac6020f6f7a069e8f9453ef594aa4a62d5325 | Java | 1,744 | 94 | package org.molgenis.genotype.multipart;
import java.util.Iterator;
import java.util.NoSuchElementException;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.Sequence;
public class MultiPartSequencesIterable implements Iterable<Sequence>
{
private final Iterable<RandomAccessGenot... |
7bc71900c1f891cdee5f648c455ec29c11b022cc2e8a1281557ccd910c7dd4bb | Java | 1,744 | 63 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.IOException;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.ucsc.UCSCDataObject;
import umcg.genetica.io.ucsc.WigFile... |
d9bd07d7e919c0253a0d789f0875d958fdca8f4e290acd2c1c65fdd0855fe9bc | Java | 1,745 | 94 | package org.molgenis.genotype.multipart;
import java.util.Iterator;
import java.util.NoSuchElementException;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.variant.GeneticVariant;
public class MultiPartVariantsIterable implements Iterable<GeneticVariant>
{
private final Iterabl... |
646c3d84e076bb4e5e1ca4b2dcdff9fe62d06ed957553442a08b1c76152013d8 | Java | 1,746 | 66 | /*
* 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 java.util.NoSuchElementException;
import org.molgenis.genotype.util.ChromosomeComparator;
import org.molgenis.genotyp... |
b771e5d9e6ddadf2fd3f814386d2535914315a9088bfbe2fe871bb99da07e907 | Java | 1,746 | 91 | package mbqtl.vcf.filter.variantfilters;
import mbqtl.vcf.VCFVariant;
import java.util.ArrayList;
/**
* Created by hwestra on 3/21/17.
*/
public class VCFVariantFilters {
ArrayList<VCFVariantFilter> filters;
public boolean hasRegionOrSetFilter = false;
boolean filterschecked = false;
public VCFVariantFi... |
f47b4c8a767f141fb8af15aa98a6853c1b8b1443b53bc2aa0842147936843f09 | Java | 1,747 | 54 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import cern.jet.stat.tdouble.Probability;
/**
*
* @author harmjan
*/
public class ChiSquare {
public static double getX(int a, int b, int c, int d) {
r... |
d6b108da6c79f62e03526e457d046da49840a535821c52192ad6e6312a5c13da | Java | 1,749 | 63 | package test.java.decon_eQTL;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import main.java.decon_eQTL.Statistics;
public class StatisticsTest {
Statistics statistics;
@Before
public void init() {
}
... |
32c9661a7361ca8a744788d5e1d47c33537b8136913ca7790dc292a0d8b287f7 | Java | 1,756 | 69 | /*
* 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 java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import j... |
8a4324b9d806c754e9d40de98331df36180b3f273ebcec4c2563f8f12f4286b6 | Java | 1,756 | 99 | package org.molgenis.genotype.variant.id;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
public class SingleGeneticVariantId extends GeneticVariantId
{
private final String variantId;
protected SingleGeneticVariantId(String variantId)
{
super();
th... |
2a05b0ac6c579e3989549d9ec0f8877f2fe37c98f93c4cf5b505be4facbfa90e | Java | 1,760 | 55 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.Polygon;
public class StarStimulus extends Stimulus {
private Polygon polygon;
private int numArms;
private double innerRadius;
private double outerRadius;
public StarStimulus(String name, Color color, int numArms, doubl... |
2def95d08290d24b045f0d6a65201c244d73c35e9f21f15bfb2d3e5871c21175 | Java | 1,762 | 74 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.HashSet;
public class CompareSNPProbeCombosBetweenFiles {
public void run(String f1, String f2, String fout) throws IOException {
TextFile tf = new T... |
09e4ed0cc2414a4fa26d9f48558ab984eace4f9356bfd104ecb6889f82cf3da4 | Java | 1,767 | 55 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.awt.geom.GeneralPath;
public class HeartStimulus extends Stimulus {
final static double topCurveFrac = -0.1;
final static double startCurveFrac = 0.4;
final static double widerByFrac = 0.15;
public HeartStimulus(String name, ... |
e93a9e0708b5571e75473be1146d35e3eb87c95b1c0863da69bb87fe3c69adbd | Java | 1,767 | 48 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the... |
3c6cef163e8f97a0e79a2946fb216ff0713a513e699c5a4d7dfbc2d4fcb7d089 | Java | 1,773 | 46 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
/**
*
* @author harmjan
*/
public class TwoStepLeastSquares extends Regression {
// for IV analysis, this would be trans, cis, snp
public static double[] tsls(double[] y, do... |
6fcfc5171b498b0716bdbd6f46447629deba214a008d34b256334427cd509906 | Java | 1,775 | 54 | /*
* 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.gene;
/**
*
* @author patri
*/
public class JamaHelperFunctions {
/**
*
* @param data... |
e75909e98bc43585f82aa7d6a1c7424761fe0c49060cce01340cb0ab1eac2591 | Java | 1,775 | 47 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code mus... |
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