sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
861d1a958611dbd79ce591ff37a18b78948dd8dd6e5ddf70a9d21135ef60222e | Java | 2,285 | 64 | package network_code_v5.proc;
import network_code_v5.func.*;
import network_code_v5.beans.*;
import java.io.*;
import java.util.*;
public class NetworkInteractionsProc
{
public NetworkInteractionsProc(){}
public void genNetworkFromFimoOutput(ConfigBeans configBean)
{
NetworkInteractions handler = new Netw... |
cc85ff29d5839a8ccf1c493e3408736b663307626152646b6c33fc10958c41bd | Java | 2,287 | 54 | /*-
* #%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... |
f76dcc2094999f53654f57ac4c2d6891f9af303d539c2cf7f172b27b45da0c58 | Java | 2,287 | 75 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.oxford;
import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import or... |
6a5b29ded124750219761a71528143867b6cd0c2e59dbd38d76ce8b671ba1ab2 | Java | 2,315 | 64 | /*
* #%L
* Utility classes for 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 must reta... |
89303b2ee5a9900825a6323115a7ffeeac6057c587628fec202ba37355d42efa | Java | 2,315 | 64 | /*
* #%L
* Utility classes for BoneJ1 plugins
* %%
* 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 reta... |
d485e7c312be700647743b367787165f89acdeb90e52c34475e315614d277eb2 | Java | 2,320 | 80 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.cis;
import java.io.IOException;
import java.util.HashMap;
import java.util.concurrent.ArrayBlockingQueue;
import umcg.genetica.console.ProgressBar;
import umcg.gene... |
4aded9fa1deb2392edb37cccdb26473bb14fd8090d8fb7b7b42609767e2299d0 | Java | 2,328 | 75 | /*
* 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;
import java.io.File;
import java.net.URISyntaxException;
import java.util.ArrayList;
import j... |
88c30bc0779eaf4fdc464d563ad88292e834e36cb6c7d755a05c4c7ef546274d | Java | 2,334 | 63 | /*-
* #%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... |
615560d4f423e926c469d747a31bd8dcc10359778982aaf2225b084017732326 | Java | 2,338 | 98 | /*
* 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;
import htsjdk.samtools.util.Interval;
import java.util.Objects;
/**
* @author patri
... |
83f7b17041a313a10c66f60ca8a330d78f1e1189d9675e633c9f7faabfc39858 | Java | 2,339 | 63 | /*-
* #%L
* Utility classes for 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 must ret... |
e46a4178d1f75c2462bf22dab6f10568b127bd16258e25837c11ea625f7776bd | Java | 2,339 | 98 | /*
* 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;
import htsjdk.samtools.util.Interval;
import java.util.Objects;
/**
* @author patri
... |
02c83f0fa8895618759ea2cb8402cca29d82e81b2fece51710436432c67c335c | Java | 2,343 | 70 | /*-
* #%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... |
c2a3f5a0ec66aa62991c2f49aa862394cd4d972de3343cbf24d1a3831f27be81 | Java | 2,348 | 92 | package umcg.genetica.features;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.enums.Strand;
import java.util.ArrayList;
import java.util.NavigableSet;
import java.util.TreeSet;
/**
* Created by hwestra on 5/3/16.
*/
public class FeatureTree {
// setting comparator to true removes all overlapping el... |
d763e59cd4b7a49ff4ad2a4f2b532ebfbb3503ae53a3e787ba8314b008434100 | Java | 2,350 | 120 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
import java.util.HashMap;
/**
*
* @author harmjan
*/
public class Gene {
private Chromosome parentChromosome;
private HashMap<String, Transcript> transcripts;
private in... |
fc6d67169b9fa6e6ec5802a5ad94f01360705b96d75f8e134bcc8e74343455ec | Java | 2,350 | 72 | /*
* 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 com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
0c48450714a2d63f71b6c3a7acfbc53d94a9bd0bfa4e70f182d55bc6da6bb544 | Java | 2,351 | 73 | package org.molgenis.genotype.snpeff;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
/**
*
* @author Patrick Deelen
*/
public final class SnpEffAnnotationTranslator {
private static final int EFFECT_TYPE_FIELD = 0;
private static final int EFFECT_INPACT_FIELD = 1... |
b6e05a7aa3f1775265eb002e1f062ca669cee78e505f1916387f3a29447a23ac | Java | 2,365 | 68 | package ebi.spot.neo4j2owl.importer;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
class RelationTypeCounter {
private final double threshold;
RelationTypeCounter(double threshold) {
this.threshold = threshold;
}
private Map<String,Map<String,Integer>> mapCounte... |
0b5bb7623826f7a9682209a8bcbde8278f21895c9216876d91b03af913444792 | Java | 2,366 | 83 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import java.io.IOException;
impor... |
1ad42390e51d05d398f31d0239fd825848aa8efefa37a3e8223e49aaea501c75 | Java | 2,366 | 75 | /*-
* #%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... |
9ae0de2c76d55c5c325fa8f5775f7752239db2c20a1dbaa2c9837793ed173081 | Java | 2,367 | 106 | package org.molgenis.genotype.util;
import java.util.ArrayList;
import java.util.List;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
public class CalledDosageConvertor
{
public static float[] convertCalledAllelesToDosage(List<Alleles> sampleAlleles, Alleles alleles, Allele refAllele)
... |
115a67780c6502159317cd05f2e874542f70536176aec5b8449759146b908269 | Java | 2,390 | 78 | package deformablemesh.meshview;
import deformablemesh.geometry.DeformableMesh3D;
import deformablemesh.track.Track;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.utils.picking.PickResult;
import java.awt.event.MouseEvent;
import java.util.List;
import java.util.Optional;
import java.ut... |
3f59792fec673d52ba50ee496aac43329acc08cca0657c78002ad0def6ecf4b4 | Java | 2,390 | 60 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.bedgraph;
import java.io.File;
import java.util.Iterator;
import java.util.List;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
import umcg.genetica.collections.intervalt... |
1d3c11dc80eec622f0f9fb62e83a42898b352f99aea8f6de9d8c10fb5af2c2ee | Java | 2,392 | 121 | package umcg.genetica.individuals;
import umcg.genetica.enums.DiseaseStatus;
import umcg.genetica.enums.Gender;
import java.util.ArrayList;
/**
* Created by hwestra on 6/28/16.
*/
public class Individual {
String name;
Individual father;
Individual mother;
ArrayList<Individual> children = new ArrayList<>();
... |
60ce1778f55edcbb23cb80704507a0a9a3575d0fbec9896ac999f8f674995424 | Java | 2,398 | 69 | package main.java.decon_eQTL;
import java.util.ArrayList;
import java.util.List;
public class DeconvolutionResult {
private List<String> celltypes;
private String qtlName;
private List<Double> pvalues = new ArrayList<Double>();
private InteractionModelCollection interactionModelCollection;
private double wholeBl... |
8b8205be335672ec6c42b28501548b0ab8408193b813276dda66e2a40670b796 | Java | 2,398 | 59 | /*-
* #%L
* Utility methods 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 ... |
4cfc355c36eb77a33e5d85cb070d097f501ce3e7b0ccff14d15466ab25df343e | Java | 2,399 | 61 | /*-
* #%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... |
b8e705212ca328bf421f5fd7c93228b700492d468676dd9c5d1a5c6166bd7cac | Java | 2,399 | 61 | /*-
* #%L
* Mavenized version of the BoneJ1 plugins
* %%
* 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 mus... |
ce7a1c06fb877577628d07e5b75da6df8e2a9953ceaf58ea3480a9e3a15f8c09 | Java | 2,399 | 69 | /*-
* #%L
* Utility classes for 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 must ret... |
7d3647da6579a6928fb1a91195ef67d76bb347fed600b08996d30ff863d95deb | Java | 2,400 | 86 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import cern.jet.random.tdouble.StudentT;
import cern.jet.stat.tdouble.Probability;
/**
*
* @author Harm-Jan & Marc Jan
*/
public class TTest {
/**
* Calculate t-test ... |
06498837715f5ead7093e5a882e344010cd1779a768cb239e28ea46c152a1ed8 | Java | 2,401 | 73 | /*-
* #%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... |
dffe9af480a3d1df8331903c6d9647bf6cc288ab4e1596f9e8d236b756e8cc96 | Java | 2,401 | 59 | package main.java.decon_eQTL;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.LineIterator;
public class ExpressionData {
private ArrayList<String> sampleNames;
priva... |
170aad63c28335b13eb54dc53cd09c5f26473f2da68b0e321c63b6019595523b | Java | 2,409 | 67 | /*
* #%L
* Utility classes for BoneJ1 plugins
* %%
* 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 reta... |
8a833a752e5ddf3c28cb133dff94ed9be7a2dd58d8f9acc5977947836f999e8c | Java | 2,409 | 95 | package org.molgenis.genotype;
import java.io.Closeable;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.annotation.Annotation;
import org.molgenis.genotype.annotation.SampleAnnotation;
import org.molgenis.genotype.variant.GeneticVariant;
/**
* Interface that rep... |
d42a78b98abf6d7801794d7f15ecc26f4eec6b53f5e516b54c81f72058339cc3 | Java | 2,409 | 67 | /*
* #%L
* Utility classes for 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 must reta... |
663bbca7cf966cec67ad906fd60679da730d1edd82523a36b0aa6b0965a76733 | Java | 2,415 | 52 | /*-
* #%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... |
82acede8fb99aae6b66ad52057073e8cc2dface33f16909e808d03da84cb0824 | Java | 2,417 | 116 | /*
* 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 java.io.Closeable;
import java.io.IOException;
import java.sql.ResultSet;
import java.sql.S... |
2e5b5dab49bf78d41309aa9e5339fd8ebdd2fc861bd50abc115e8c3cf0007da1 | Java | 2,424 | 98 | /*
* 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.simplegeneticriskscorecalculator;
/**
*
* @author MarcJan
*/
class RiskEntry implements Comparable<RiskE... |
fd8a47422b95438e308f04d8d7cb9e5f8481fcab54ce6f163cd1ed77f79abdff | Java | 2,425 | 97 | package org.molgenis.genotype.annotation;
import org.apache.commons.lang3.math.NumberUtils;
import org.molgenis.vcf.meta.VcfMetaInfo;
public class VcfAnnotation extends Annotation
{
public static final int NUMBER_UNKNOWN = -1;
private final Integer number;
boolean unbounded;
private final boolean perAltAllele;
... |
6717165e7d28aa2c5ed8a4b33f50a5eed47fe044647dd8845bf0615024a6a241 | Java | 2,436 | 100 | package org.molgenis.genotype;
import java.util.HashMap;
import java.util.List;
import org.molgenis.genotype.variant.GeneticVariant;
import org.molgenis.genotype.variantFilter.VariantFilter;
public interface RandomAccessGenotypeData extends GenotypeData {
/**
* Get all sequence names
*
* @return List of Stri... |
f1e4d257a2f0905328139c01bc4356624a416e78e845e6d8b7f6490a1b765931 | Java | 2,438 | 72 | package network_code_v5.proc;
import network_code_v5.func.*;
import network_code_v5.beans.*;
import java.io.*;
import java.util.*;
public class PutativeRegulatoryRegionsProc
{
public PutativeRegulatoryRegionsProc(){}
public void genPutativeRegulatoryRegion(ConfigBeans configBean)
{
PutativeRegulatoryRegio... |
051d2da2b16553114fdbd5dfa196af87e19ad97a42ae1ffe2d47171c321cf2c0 | Java | 2,447 | 70 | /*-
* #%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... |
a002de9d35fb52697aea16c045a9c8244a2f8c0b48b66484dc68b8ff09555ad4 | Java | 2,449 | 72 | /*
* 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;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.IOException;
impor... |
efae86562020ac2f196d3651bfb29cc6b497379f712614413a7e80063975e039 | Java | 2,460 | 78 | /*
* 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.eqtlannotation;
/**
*
* @author MarcJan
*/
public class TfbsOverlapResult implements Comparable<TfbsOver... |
d064097688047a1ad2f90e50245c8063f5aac66082d605a5bf3d3b4cb58ee9f3 | Java | 2,469 | 87 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.regulomedb;
import java.util.regex.Pattern;
/**
*
* @author Patrick Deelen
*/
public class RegulomeDbSupportingData {
private final String supportClass;
private final String supportMetho... |
2cca6823fb1883cca29970ef825952ecc3ede3ec8df6be33f18e671cc091fbf9 | Java | 2,470 | 89 | package org.molgenis.genotype;
import java.util.List;
import org.molgenis.genotype.util.CalledDosageConvertor;
import org.molgenis.genotype.util.FixedSizeIterable;
import org.molgenis.genotype.util.ProbabilitiesConvertor;
import org.molgenis.genotype.variant.GeneticVariant;
import org.molgenis.genotype.variant.Genoty... |
e42f1556ab28b204fb2a2bf14d675ae556f93fbd9466849be704655cfdccd0e1 | Java | 2,474 | 87 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
import cern.colt.list.tint.IntArrayList;
import java.util.Random;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public clas... |
6339749eaf5ccce884b092ebba4209121c17fea0ebc83ccbec2c9d02e5fbfc16 | Java | 2,481 | 79 | package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import java.util.HashSet;
import java.util.Map;
/**
*
* @author Patrick Deelen
*/
public class CompareToGeuvadis {
/**
* @param args the command line arguments
*/
public static void main(String[] args) {
Expre... |
071813ef149940aa82e5ad445a96217e228a340288f766aa9bd4c40273adaed6 | Java | 2,488 | 98 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
/**
*
* @author harmjan
*/
public class SortableSNP implements Comparable<SortableSNP> {
public static enum SORTBY {
NAME, ID, CHR, CHRPOS, CHRANDCHRPOS, EFFECT
... |
f4c56296a5129390cb9abf8ea1c08f4da2a0a25018addf49e104ab668a689814 | Java | 2,492 | 121 | //
// Source code recreated from a .class file by IntelliJ IDEA
// (powered by FernFlower decompiler)
//
package mbqtl.datastructures;
import java.util.ArrayList;
import java.util.Objects;
import umcg.genetica.util.Primitives;
public class Dataset implements Comparable<Dataset> {
private String name;
private int[... |
1f554a473724856219a53db3cf06e43d32fd42226f2bb162b1b8a529ae053680 | Java | 2,498 | 84 | package org.molgenis.genotype.util;
import static org.testng.Assert.assertEquals;
import java.util.Arrays;
import java.util.Comparator;
import org.testng.annotations.Test;
/**
* This comparator can be used to sort chromosome names. In this order: 1-9
* 10-19 etc ending with X Y MT
*
* @author Patrick Deelen
*... |
29eea94b097289f62d1513d3efbcba300cda6d01384557b0a6d7790c433cbad8 | Java | 2,504 | 75 | /*
* 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.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import java.io.IOException;
import java.util.Map;
impor... |
e2c049cf13096ad77e1914b02242e2b12c8d9ebd14e57dd0ac5fd431db4801a5 | Java | 2,515 | 75 | package deformablemesh.geometry;
import deformablemesh.meshview.MeshFrame3D;
import deformablemesh.util.Vector3DOps;
import java.awt.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class SplittingSpheres {
public static void main(String[] args){
MeshFrame... |
6ff1661c2aa30df7f691d1d0cc5cda51823709f0f8ad6e22fab9d8d85b93c4f1 | Java | 2,531 | 93 | package org.molgenis.genotype.util;
import java.util.Iterator;
import org.molgenis.genotype.GenotypeData;
import org.molgenis.genotype.variant.GeneticVariant;
/**
* Check if two GenotypeData or GeneticVariant objects contain then same data.
* Be careful in using this, only use for testing as this can be very expen... |
9c157eeb6723eed859037716d568f5d0bdb526559f943e175eb8e7690f8af6a1 | Java | 2,531 | 68 | /*-
* #%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... |
48ffa9918d380f3b55483e6eec9af68a5cd3b4c79b217a5f415758fb85c5b737 | Java | 2,552 | 115 | package edu.cmu.cs.eyetrack.analysis.struct.tobii;
import edu.cmu.cs.eyetrack.analysis.struct.Frame;
import edu.cmu.cs.eyetrack.helper.Coordinate;
public class TobiiFrame extends Frame {
private long timestamp;
private Coordinate<Double> gazeLeftPt;
private int validityLeft;
private Coordinate<Double> ... |
5e81d0829717f99094744bc3b27000f99869b59f476cb1f792769b3faae79773 | Java | 2,564 | 99 | package umcg.genetica.collections.intervaltree;
import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
/**
*
* @author Patrick Deelen
*/
public class IntervalTree<E extends Range> {
private final Interval... |
6c401fea020e16c6074748daee4d6338bbd3d70a30b3c10c902ac2caa76d5e89 | Java | 2,566 | 100 | /*
* WGAFileMatrixGenotype.java
*
* Created on July 9, 2007, 5:08 PM
*
*/
package umcg.genetica.io.trityper;
import umcg.genetica.console.ProgressBar;
import java.io.File;
import java.io.IOException;
import java.io.RandomAccessFile;
//import umcg.genetica.io.bin.RandomAccessFile;
/**
* @author ludefranke
*/
p... |
6bbeea5b1cdde4fd513989702db7fb088a8b505b661c6d969fbfa348b12ff792 | Java | 2,567 | 130 |
import org.jtransforms.dct.DoubleDCT_2D;
public class DCTEntropy {
protected final int mWidth;
protected final int mHeight;
protected final double[] array;
protected DCTEntropy()
{
array = new double[0];
mWidth = 0;
mHeight = 0;
}
public DCTEntropy( final int pWidth,
final int pHeight,
... |
5b1c9ab88b7bc5fd7ce36d6f164215dde09f275b0a6969c8988c3e94cfb59f45 | Java | 2,582 | 120 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.regulomedb;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.I... |
2b8637ff20249c6adff22c8cf2e387150b405b18df29e105ef38ed4041571f05 | Java | 2,585 | 73 | /*
* Copyright (C) 2016 adriaan
*
* 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.
*
* This program is distribute... |
ba89d1fd9bc3b4886273291371e4e36b1e57d76444a3d170cf43ce93986a2fd9 | Java | 2,600 | 69 | /*-
* #%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... |
cc6ed0f2e2f38a99d4a496da65a570dd5f007af7adec84a315ebc866112d0d3f | Java | 2,600 | 67 | package org.molgenis.genotype.vcf;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import or... |
5639b03043c129be32002f040d1dce6bc08014b5d5bd66ea73206e2ce084aa76 | Java | 2,604 | 67 | /*
## 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 vers... |
7cf56ace61f3597b168c26df32f7856daecb458263f4c948ea9627483d12edd9 | Java | 2,613 | 134 | package umcg.genetica.genomicboundaries;
/**
*
* @author PatrickDeelen
*/
public class GenomicBoundary<V> implements Comparable<GenomicBoundary>{
private String chromosome;
private Integer start;
private int stop;
private V annotation;
public GenomicBoundary(String chromosome, Integer start, int ... |
e2136288520476382000958644a3492485c5f86f28daffa48850804a4b05de3c | Java | 2,617 | 95 | package org.molgenis.genotype.variant.sampleProvider;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.util.FixedSizeIterable;
import org.molgenis.genotype.util.Probab... |
545f7b36aef6d017c405a20af291cc74fb8df6f0aaf92496a4ae7cc45768c726 | Java | 2,622 | 79 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
/**
*
* @author MarcJan
*/
public class HWE {
public static double calculateExactHWEPValue(int obs_hets, int obs_hom1, int obs_hom2) {
//System.out.printl... |
c0f3f60c6319aad04fbc50cc36689fea616043f0a09db72860cd2db7fd6e0f2c | Java | 2,631 | 81 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.methylation;
import umcg.genetica.math.matrix.DoubleMatrixDataset;
/**
*
* @author MarcJan
*/
public class ConverteUandMTo {
public static DoubleMatrixDataset<String, String>... |
3c0df85f5279696089e44c12ebabaadd8f2b414fcb20bc8203cd039b24644242 | Java | 2,635 | 80 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import JSci.maths.ArrayMath;
import cern.colt.Arrays;
import java.io.IOException;
import org.apache.commons.collections.primitives.ArrayDoubleList;
import umcg.genetica.io.text.TextFile... |
0197506aa660cbf596d62485cacc2927bb9ce1fc3a8cf492942e8640476fd1de | Java | 2,646 | 83 | package mbqtl.stat;
import org.apache.commons.math3.analysis.MultivariateFunction;
import org.apache.commons.math3.optim.InitialGuess;
import org.apache.commons.math3.optim.MaxEval;
import org.apache.commons.math3.optim.PointValuePair;
import org.apache.commons.math3.optim.nonlinear.scalar.GoalType;
import org.apache.... |
1f580719b7f97059e7ac4ba09319d0787da32255a6b2c0f4a3bf17a849dfdb31 | Java | 2,658 | 84 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.regex.Pattern;
impor... |
408df3b4c9775c8e881f417cf3f0ac8470a285bcf89a9063eb026cd44488de70 | Java | 2,690 | 86 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.collections.intervaltree;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import o... |
393544ccad48c52f99bc0d410c094b7fea35f5a0d62a8cb917e4f43b152ee1c8 | Java | 2,692 | 114 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.ucsc;
/**
*
* @author harmjan
*/
public class UCSCDataObject implements Comparable<UCSCDataObject> {
private byte chr;
private int positionStart;
private int positionEnd;
pri... |
7b5d23476a29c3c8976ede3917cc9ba74ff11664739f38d213deaf4a342d9bf9 | Java | 2,713 | 106 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gwascatalog;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
*
* @author harmjan
*/
public class GWASTrai... |
0824b53c4fc11eedd1d5c97fad18078509bf4645c4b5e45b77cc0f86ed51aa7a | Java | 2,729 | 83 | /*-
* #%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... |
d3650f460f25656fd7e04bd0e91b8b5fb7cad18896ed558097418a6d0ea876d5 | Java | 2,732 | 72 | /*
* 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.plink.readers;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
impor... |
faf3b1fd1191fd8f22c7349f89706021909ad85fc9bb3f72a7493c4da27456fb | Java | 2,733 | 116 | /*
* 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;... |
533dc81b9f81dbf51cbfaf00daf8fe239864973ee1396e24434f9c773737babb | Java | 2,735 | 76 | package mbqtl.junk;
import mbqtl.stat.BetaDistributionMLE;
import umcg.genetica.io.text.TextFile;
import umontreal.iro.lecuyer.probdist.BetaDist;
import java.io.IOException;
import java.util.Arrays;
public class ShuangTest {
public static void main(String[] args) throws IOException {
String permfile = ... |
b7507909bce3cdf930a9425fae0f08c4d7242edf760dd552f6126bb4ea985437 | Java | 2,735 | 85 | package main.java.decon_eQTL;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import main.java.decon_eQTL.Utils;
public class CellCount {
private List<String> cellTypes = new ArrayList<String>();
private List<String> sampleNames = new ArrayList<String>();
private double[][] cellCou... |
7431ee498933893f6be1942887400bd997e458db54f4e0868d6f99cde371140b | Java | 2,737 | 104 | package eqtlmappingpipeline.util;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
public class QTLFileMerger {
public void mergeChr(String loc, String out) throws IOException {
... |
7b26fd4de0e7edf1c93377fc7433e97f8decbcd09e5ae6c2732595f5a3d1ae63 | Java | 2,742 | 81 | /*-
* #%L
* Utility methods 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 ... |
f58c18af315d05fabb430d3177e0fd9d844c7de7ff926d37a49baca31ac37733 | Java | 2,744 | 84 | /*-
* #%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... |
3ba52e1cb0ad59a341dc1c78bc7c2b93d3150b418c140537f180f131a5d3046d | Java | 2,747 | 124 | package edu.cmu.cs.eyetrack.analysis.struct.trackit;
import java.util.HashMap;
import java.util.Map;
public class Experiment {
public static enum TrialType {ALL_SAME, ALL_DIFFERENT, SAME_AS_TARGET};
// Descriptors for the entire experiment
private int numDistractors;
private int objectSpeed;
private TrialType... |
33244d07fdc56e2c6ab47fc41f427b6efa0dd8260bd53809a97054415f189be5 | Java | 2,750 | 97 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.eQTLFoldChangeCalculator;
import eqtlmappingpipeline.metaqtl3.MetaQTL3;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.SNP;
import umcg.genetica.io.trityper.SNPLoader... |
0c932fc6fff8e8baa68e01a73dd908c1ac9113c7b2272d00d4e9e8313cad7d10 | Java | 2,756 | 76 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashSet;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.ProbeAnnotation;
import umcg.genet... |
5efccf812b8e1f0b495008cbdf7a735eb978a1dabbe7d52e6922080b6135ef1b | Java | 2,760 | 110 | /*
* 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 java.util.ArrayList;
/**
*
* @author Adriaan van der ... |
ab7a39d29dcd0efe31bed8adc9dcedb55f9fd6b783e3bdf2501f6f14b602bb98 | Java | 2,760 | 142 | package org.molgenis.genotype.variant.id;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
public class ListGeneticVariantId extends GeneticVariantId
{
private final List<String> variantIds;
protected ListGeneticVariantId(List<String> variantIds)
{
sup... |
db6f214bed283bbbe0d7077b424826230442962de4c1aad64a9c23f481ab6014 | Java | 2,771 | 113 | /*
* 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 org.apache.poi.ss.usermodel.CellStyle;
import org.apache.poi.ss.usermodel.DataForma... |
5ebb40bdd1a93c02aba432de6ebc062ac1a9b7b706726fbab020f59d2317c0dc | Java | 2,773 | 81 | /*-
* #%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... |
cd96a294ec3c659baa336cfc4d8446803a8f42f6b568bb5a1f23114ea2b883e1 | Java | 2,776 | 90 | /*-
* #%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... |
37853482f5dab9f5b260ec56ccaba1afe3d1730d026a3832f2f704258f577d61 | Java | 2,795 | 71 | /*-
* #%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... |
b1cdcb32a1acbf7e432b82b2a3f04198aeee6b96310010404826cb5e59be23ba | Java | 2,802 | 95 | /*
* 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.sophie;
/**
* @author Sophie Mulc
*/
import com.opencsv.CSVParser;
import com.o... |
bd6d39cb7d5c95b6b268bf04e03b348fef35a44aacb3cbcd8597ad88cfec7586 | Java | 2,802 | 88 | /*-
* #%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... |
0deab6627465252a25de9adcd6def4fdd58a6d1e5c1382d6d331094bd6430522 | Java | 2,812 | 94 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
*
* @author MarcJan
*/
public class RankArrayNGTest {
publi... |
a2f47654fb21cc20064d6b2dacebafd35beb81b1a039395c979ea3cd50303237 | Java | 2,816 | 124 | package umcg.genetica.graphics.themes;
import java.awt.*;
/**
* Created by hwestra on 8/26/15.
*/
public class ComplementaryColor implements Theme {
public final Font LARGE_FONT = new Font("Helvetica", Font.PLAIN, 14);
public final Font LARGE_FONT_BOLD = new Font("Helvetica", Font.BOLD, 14);
public final Font S... |
30942b1bc6a9258a18e513297859bb9123c319d7dfc78a2c3cb71a87f3c5d7f4 | Java | 2,833 | 82 | /*-
* #%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... |
6f62c7869cfa658008536627bc614398790dc29795d7e9e7de2dd93cfffe0793 | Java | 2,833 | 104 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.examples;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgen... |
f8e477ad10c214d305054a132daa37b6716407bccd79c50f60221bdab08314bb | Java | 2,847 | 85 | /*-
* #%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... |
8a880290e6b73254c32eca0db194bf25ce0ab03a4afa7ad331d3c3007f8d7a90 | Java | 2,848 | 87 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.IOException;
import java.util.HashMap;
import java.util.TreeMap;
import java.util.regex.Pattern;
import umcg.genetica.io.text.TextFil... |
562b4d8815d909436a1cc6b3825011b2fb32eb99df6ec03bc70adabf995272d1 | Java | 2,857 | 80 | package org.molgenis.genotype.oxford;
import static org.testng.Assert.assertEquals;
import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import org.molgenis.genotype.GenotypeData;
import org.molgeni... |
bdc29701cbf829f8f4cd531fac14f3638138174ed4d568a44593c0bb1ba1604f | Java | 2,858 | 99 | /*
* 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 com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
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