sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
34e886f738f3599b629f2866d45bc5a90938e6b173b7230ad48ded67cfce64f0 | Java | 2,859 | 109 | /*
* 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.File;
import java.io.FileNotFoundException;
import java.io.IOExcep... |
a708cec08913fad50ff3dd5663b57f5063b6d5b78f35a9a73eacf29848c743ca | Java | 2,860 | 79 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import java.io.IOException;
import java.util.HashSet;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.SNP;
import umcg.... |
06924cdda5c8e77dd6155992ab4a173c059523774c99691180607e0ca7e561ad | Java | 2,864 | 97 | /*
* 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 ... |
5c12c01b526e0348c3cc872606b0c502a376839dd17b19f25de21b15a2f6d783 | Java | 2,866 | 103 |
/*
* 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.open... |
9ff9d901ccc07f1a137af3f6df1a6a3c5603eeb28eba5740adc289a981c0a4a1 | Java | 2,871 | 75 | 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.... |
ea2b8afe790b38b13fa91e271811c20b9f4d2585b93b3dcaa813474a054e3853 | Java | 2,874 | 76 | /*
* 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 com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.ope... |
0c2535396d7d08074e44b918a6f822885a5d7f8c2ae676665b68f7f3af04d06f | Java | 2,880 | 84 | /*-
* #%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 ... |
efa85d670544d8668f4d57cc21776fd66298f32048f675ea0551b19c391d6346 | Java | 2,884 | 118 | package mbqtl.gfx;
import com.itextpdf.text.DocumentException;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Grid;
import java.io.IOException;
import java.util.ArrayList;
public class QTLPlot {
public static void main(String[] args) {
// generate some test data
double[] x = new ... |
78800be0c5995692108a04e417588c4b832a10684beb15781a607f9626d32ef1 | Java | 2,895 | 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... |
52211aeb61a22a339d7a4db592c51835f141854e60c70a778a7aead4ca9ab58d | Java | 2,906 | 115 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.containers;
/**
*
* @author harm-jan
*/
public class Matrix {
private double[][] mat;
private String[] rowNames;
private String[] colNames;
public Matrix(int ... |
b64b8183177ef2c55dbf25bea6b9056b8861a667af1f7ae0a3ea77b56dfeeb1a | Java | 2,913 | 103 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
/**
*
* @author harm-jan
*/
public class RunTimer {
private long start = System.nanoTime();
private long prevstart;
private Granularity g = null;
public enum Granularity ... |
c0fc89225ffe87e3a2aea6d3525e3f89946fae90753281519caecbfe29c12c79 | Java | 2,926 | 88 | /*-
* #%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... |
8f965bb70dcf988b24d3f755cbc6e33605b27944c5ce9cf971cf88201bc8d8bf | Java | 2,928 | 86 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OConfig;
import ebi.spot.neo4j2owl.N2OException;
import ebi.spot.neo4j2owl.N2OStatic;
import org.apache.commons.io.FileUtils;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxObjectRenderer;
imp... |
529e8484a2d1dac98877f3a8d0fd987c36e42a505a228f56f24959c08f5241f0 | Java | 2,929 | 110 | package org.molgenis.genotype;
import java.util.HashMap;
import java.util.Iterator;
import java.util.NoSuchElementException;
import org.molgenis.genotype.variant.GeneticVariant;
import org.molgenis.genotype.variantFilter.VariantFilter;
public abstract class AbstractRandomAccessGenotypeData extends AbstractGenotypeDat... |
5d9e95a0069467da822060247a2f388607c52f02eab82df60231ef536d72ea3d | Java | 2,929 | 64 | /*
* 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.util.Iterator;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
*
* @author ... |
8867f945b9802df4009fd66f933fe81d7acbd3d7cfdef0ccdc9807b56916454d | Java | 2,929 | 99 | 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 umcg.genetica.util.Primitives;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
impo... |
9a47bff57fa0a9b558d69aaccda9cca432cbc2689b5a45db271ae8d652b0b873 | Java | 2,930 | 82 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D;
impor... |
8306af239b33c462a0683a94b6ccb648e932df0e8924d4b880b41f6efee17dd0 | Java | 2,934 | 127 | package edu.cmu.cs.eyetrack.analysis.struct.tobii;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class TobiiEventMap {
public static enum TobiiEventType {
SCREEN_REC_STARTED("ScreenRecStarted"),
IMAGE_START("ImageStart"),
IMAGE_END("I... |
465a32d996b234cc79bcfab55e780e6fcf91a4e4ac8aa52fcf7abc407a8f4063 | Java | 2,937 | 99 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.pcaoptimum;
import eqtlmappingpipeline.graphics.Graphics;
/**
*
* @author harmjan
*/
public class PCAOptimumPlot extends Graphics {
PCAOptimumPlot(int i, int i0, boolean b, String ou... |
ccf3c9f9de1cddba64ff5fd524bdc187414b209f8490f50cfcd37efa92a60237 | Java | 2,940 | 106 | package nl.systemsgenetics.downstreamer.gene;
@Deprecated // TODO: If this ends up being used, make it integrate with LinearRegressionResult
public class GenePathwayAssociationStatistic {
private String pathway;
private String gene;
private double beta;
private double standardError;
private double ... |
c8257d76ad02e7824fc2f6f122e203d064822c8488e6a0fbe7af53e70903ec19 | Java | 2,944 | 97 | /*
* 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.matrix2;
import java.io.File;
import java.net.URISyntaxException;
import java.text.DateFormat;
import java.... |
b078fb0bd798ab7d37eabaf097270f32215579a6ad38461eb36ca1e6d48be303 | Java | 2,945 | 82 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats.concurrent;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D;
import cern.colt.matrix.tdouble.impl.DenseLargeDoubleMatrix2D;
impor... |
e8c4df533b3f9bf0e98fb3d3beba9f9a45a7651e9c05640dc42aed9a739aec95 | Java | 2,945 | 93 | /*-
* #%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... |
758d8848e68600842b34e8f85342fa2938b3c11473c6a7edfd1d4c7dad2c7d73 | Java | 2,959 | 85 | package edu.cmu.cs.eyetrack.gui.trial;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.image.BufferedImage;
import java.util.List;
import javax.swing.ImageIcon;
import edu.cmu.cs.eyetrack.gui.EyeTrack;
import edu.cmu.cs.eyetrack.io.ResourceLoader;
import edu.cmu.cs.eyetrack.state.Settings.Experime... |
8dd60cf088fbd057eb463e3dd0b6d89febf4ce89af98c1d918849bc2841de2ea | Java | 2,961 | 92 | package edu.cmu.cs.eyetrack.gui;
import java.awt.BorderLayout;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import javax.swing.ImageIcon;
import javax.swing.JLabel;
import edu.cmu.cs.eyetrack.helper.Util;
import ... |
fed6b6a8a3dae1fc6f94fa2611904426429c21136ba246affa6e7d0bfba6ac41 | Java | 2,966 | 107 | package umcg.genetica.genomicboundaries;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Set;
import java.util.TreeMap;
import java.util.regex.Ma... |
459e5cd81b036ef7d5bb787cc6395c55da7f9d54753a3ea19d0310c14b90a93e | Java | 2,974 | 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.io.hpo;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileN... |
110905be279e8c501bb4a2f1592c5c1245beb460d9cb96ccee6ddb6de0ad81eb | Java | 2,978 | 106 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.cis;
import umcg.genetica.containers.Pair;
import umcg.genetica.io.trityper.bin.BinaryResultDataset;
import umcg.genetica.io.trityper.bin.BinaryResultSNP;
import ja... |
628f1c29ed3e905cd483106435443b624e338d52e03097e0d1548769ca3ac864 | Java | 2,979 | 112 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
/**
*
* @author harmjan
*/
public class KolmogorovSmirnov {
public static double getProbabilityKolmogorovSmirnov(double d, double n1, double n2) { //Numerical recipes code
... |
a1aab03c2a1326dc129993e2ef4a97747da92b51b68103e3f096a4fa7f54d65c | Java | 3,001 | 100 | package org.molgenis.genotype.variant.sampleProvider;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.util.FixedSizeIterable;
import org.molgenis.genotype.variant.GeneticVariant;
import org.molgenis.genotype.variant.GenotypeRecord;
import org.molgenis.genotype.variant.ReadOnl... |
5738ee80efe9e40ad22c72b6e9770522705783f0e477dacaaf7408539f513418 | Java | 3,002 | 66 | /*-
* #%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... |
58fe6f8881109dbaa8c62c0f2dd90995908fa48bad80ccbb86dfaba21fd642d6 | Java | 3,002 | 66 | /*-
* #%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... |
8ce9a87d96c3f752a0a779d111252717703ed6d87e3a6afe7f9ff689861db2be | Java | 3,009 | 94 | /*-
* #%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... |
dbb3e3c79a23e6e33d78773376a1ceeee4797e31c90396770c97d0a8d6c18cae | Java | 3,018 | 90 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.toolbox;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
i... |
b247d8730a778cc5877aa09f9f98b801eb79781e66dcbcc7ab76e23e8228a560 | Java | 3,029 | 99 | package nl.umcg.westrah.binarymetaanalyzer;
import org.apache.commons.io.FilenameUtils;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
import java.io.*;
import java.util.Arrays;
import java.util.zip.GZIPInputStream;
/**
* Created by harmbrugge on 30-06-17.
*/
public class MatrixConv... |
509fb18867e88cb6e80816d3c7f89a0294089ab26e0d7cf4e99e2a5fe0a5922a | Java | 3,030 | 81 | package eqtlmappingpipeline;
import java.io.File;
import java.util.List;
import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypedDataWriterFormats;
import org.molgenis.genotype.RandomAccessGenot... |
c98a93a9a8d790be5cc8d8a009846778581e9a02cb154eac0911b8007931ea3d | Java | 3,031 | 118 | package umcg.genetica.console;
import com.google.common.base.Strings;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.util.RunTimer;
import java.text.NumberFormat;
public class MultiThreadProgressBar {
private final RunTimer timer;
int[] ctrs;
int[] subtasks;
boolean[] complete;
NumberFormat def... |
7c85285bd35908299ec921a30dcce30661d3e6b513b3d799fb8925dfc5ec3ddf | Java | 3,034 | 102 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.util.Vector;
/**
*
* @author harmjan
*/
public class VectorSorter {
/****************************************************************************
* A default constru... |
ed91e6136e8854e420a674470509d87184fb2b012b89a2f45de3c6356c1c10bf | Java | 3,035 | 73 | package org.molgenis.genotype.plink.drivers;
import static org.testng.AssertJUnit.assertEquals;
import java.io.IOException;
import org.molgenis.genotype.Allele;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class PedFileDriverTest ext... |
e7be2e14f49791c61ace2699f7c1a299d4522806e00ce9bc20b86ef68b9faa14 | Java | 3,041 | 96 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix2D;
import java.util.ArrayList;
import java.... |
3e741ccfbff24067a424e1dcf861f12f82631f9c784c48c0ebae8a645a1c3026 | Java | 3,046 | 149 | package eqtlmappingpipeline.ase;
import cern.colt.list.tdouble.DoubleArrayList;
import cern.colt.list.tint.IntArrayList;
import cern.jet.stat.tdouble.Probability;
import java.util.ArrayList;
import org.apache.commons.math3.stat.inference.AlternativeHypothesis;
import org.apache.commons.math3.stat.inference.BinomialTes... |
28c1498c7b67dcec505c19c7eb1d8e55c6f9540891fcd629ece6db1795039cd6 | Java | 3,049 | 86 | package org.molgenis.genotype.vcf;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNull;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.variant.GeneticVariantMeta;
import org.molgenis.vcf.VcfRecord;
impo... |
36a5e7188d1739b00781c4b0f76609216b35c90d1410c926baf4f8b091da8be9 | Java | 3,056 | 76 | /*-
* #%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... |
a0a5e202e6c186fa6562d869cfc37195a34846d74edb1a8177e25da7c21d035a | Java | 3,061 | 85 | /*-
* #%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... |
28eaad0c44b227af424473da0255de677e7d0bc8e0fc4eb7aa99a73507324166 | Java | 3,063 | 61 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* 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... |
95ae41f04b57edfe38f190f1b99a6b140892ac2e4253fbc6ae0f9427f72130a0 | Java | 3,069 | 82 | /*-
* #%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 ... |
332e21d5c50b5adb202720e5ec1dc640822922c886a55d9923ce97f3d98aa05f | Java | 3,078 | 94 | package umcg.genetica.math.matrix2;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.stream.IntStream;
public class DoubleMatrixConverter {
public static void TextToBinary(String in, String out) throws IOException ... |
545c6bb9fad2d7e109b9df7d27b6af36ff8b51d6401f9310875238dc9175acf8 | Java | 3,078 | 98 | package edu.cmu.cs.eyetrack.analysis.score;
import java.util.List;
import edu.cmu.cs.eyetrack.analysis.score.compare.PointComparator;
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;... |
d4b0731f28b3d312ef193a45c6804d6ca4db31f4798b673ef932973e2a796598 | Java | 3,080 | 133 | /*
* 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.stat.tdouble.Probability;
import gnu.trove.list.TDoubleList;
import g... |
b440d48004fad2d3d647e08048ea06e830d7a816961c99a9416f4234cbf776a9 | Java | 3,109 | 80 | /*-
* #%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... |
0c1fae8d425dab0c8a3e693d68e47dc1c4711ddf712c1bd3a4f002cd13cd18a5 | Java | 3,113 | 87 | /*-
* #%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... |
af6590d4f34dda3f9409c38fff21dbb9d32b2dff558f3c9a44ee2c43ae7b1200 | Java | 3,113 | 92 | /*
* 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... |
cd9c5cca5132d3421cc09e5d3500ffe6fb4a55629a4b11575b8807dccb03da7f | Java | 3,116 | 109 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.bin;
import umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset;
import java.io.*;
import java.util.ArrayList;
/**
* @author harm-jan
*/
public class BinaryResultProbeSummary... |
a1a18aab862a0dad916e4efb083936ccaaeec08b64dff2237f5d415bca744a1c | Java | 3,122 | 69 | /*-
* #%L
* High-level BoneJ2 commands.
* %%
* 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... |
e928842eb96ed444e79368c30ac3ef17d14b3e9a2a1f19e30cdf13a0ec280c7f | Java | 3,130 | 109 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OConfig;
import ebi.spot.neo4j2owl.N2OStatic;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology... |
5326f347426c6d070273bc9f2decece430704e45e8d8451a6016f5abc5f7a008 | Java | 3,140 | 98 | /*-
* #%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... |
3fd7d64a73d2cad5327d7e4c0e953ea1ecae4f7bec5d826b4288903f80df4acb | Java | 3,144 | 106 | /*
* 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 com.opencsv.CSVParser;
import com.o... |
89e883c4fd062e1db56aee5dddefa972062a1a09eb5eb8b82ef07a9d1fc788e2 | Java | 3,153 | 97 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cer... |
e4a1523b2edf7a34027e51f8d3db5e8576286bbebc5b96851ea939195bf84c2d | Java | 3,168 | 97 | package nl.systemsgenetics.downstreamer.summarystatistic.filters;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
* The enum Filter type.
*/
public enum FilterType {
/**
* Variant id filter filter type.
... |
5e2bb5c261407239f998a8a5b31d5ff0501001c37396d2f62299b76354b1a160 | Java | 3,172 | 69 | /*-
* #%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... |
e77c7a8385e0928a3be03847d4b527eccb8d5ab358f00a9f6b70f6bd0886a61a | Java | 3,172 | 114 | package edu.cmu.cs.eyetrack.state;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
import edu.cmu.cs.eyetrack.gui.shapes.StimulusFactory;
import edu.cmu.cs.eyetrack.gui.shapes.StimulusFactory.StimulusType;
/**
* Order1 Order2
trial1 1 2
tri... |
fee186e4ca469db42ac0fdf837c40a6aec718cc7b0b4d61bf0bade9d1abe82c1 | Java | 3,172 | 89 | /*-
* #%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... |
b31b1633ea421bb1be98a1854399c66b09ba5a5cdbf086d8211fba0c355b687c | Java | 3,180 | 96 | /*-
* #%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... |
193bad18b9a058a1209c47fa060f8632b2372777d5843d8796fc30d36cebdc6f | Java | 3,195 | 81 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.util.Arrays;
import java.util.Random;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import static org.testng.Assert.*;
/**
*
* @author MarcJan... |
2d3c0b353691728320a0f9b2d582ab5a5e6b2508094df3cf0b0a5c11ed2431d3 | Java | 3,202 | 109 | /*
* 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 com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv... |
f2b8f03f27f12f4ac7354c26bd1bcca8c9bb526c21f13891cb2381432552edae | Java | 3,204 | 140 | package umcg.genetica.graphics.themes;
import java.awt.*;
/**
* Created by hwestra on 7/16/15.
*/
public class DefaultTheme 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 MEDIUM_... |
1dfdd40608969b2103a416ab56917e59651faaa27a716d238b43544e13cb4877 | Java | 3,205 | 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.development;
import java.io.IOException;
import java.util.LinkedHashMap;
import java.util.Link... |
a9df08df35e5fa2d8d4efbbb1eacb2a9a0b4d9495cb3860a572775a4244fe1bc | Java | 3,207 | 108 | package org.molgenis.genotype.util;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.mo... |
b31dc83284f7413e906e50fe60b6997d47115b6c035455d2498b864d0551d0c2 | Java | 3,211 | 154 | package edu.cmu.cs.eyetrack.analysis.struct.tobii;
import java.awt.Dimension;
import java.awt.geom.Rectangle2D;
import java.util.Date;
public class TobiiHeader {
private String sysOS;
private String sysUser;
private String sysMachine;
private String recName;
private Date recDateTime;
private Lon... |
2531e7edec69015bd73f93c85ec1969b75e414deeb0e84f65a94c5eb99431871 | Java | 3,215 | 74 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OConfig;
import ebi.spot.neo4j2owl.N2OLog;
import ebi.spot.neo4j2owl.N2OStatic;
import ebi.spot.neo4j2owl.N2OException;
import org.apache.commons.io.FileUtils;
import org.neo4j.graphdb.QueryExecutionException;
import org.neo4j.kernel.internal.GraphDataba... |
0b6c08fbc70eb8ff2309aaffb3da9a82a94ba6f9663bcc092c5accc2c5814055 | Java | 3,217 | 160 | package umcg.genetica.collections;
import com.google.common.base.Function;
import com.google.common.collect.Iterators;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.NavigableMap;
import java.util.TreeMap;
import org.molgenis.genotype.util.ChrPos;
/**
*
* @author... |
f52861d48c3a3d7958019eb417af981c9b83b5cb5118f21a9ab5a09c3e200994 | Java | 3,222 | 96 | /*
* The MIT License
*
* Copyright 2013 Tim Boudreau.
*
* 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 restriction, including without limitation the rights
* to use, copy, m... |
43c7857733a62e33b2939a99a0d93a59af301fae4de0597ed637c4f142c283ad | Java | 3,226 | 123 | package umcg.genetica.graphics.panels;
import umcg.genetica.features.Feature;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import java.awt.*;
/**
* Created by hwestra on 11/27/16.
*/
public class AnnotationTrackPanel extends Panel {
private double[][][] data; // [dataset][g... |
53c98d70142ab5079e4abb6b71c0e23bb53ea24e0d42dccbd32dd6967b06983f | Java | 3,233 | 99 | package eqtlmappingpipeline.ase;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import org.apache.commons.lang3.StringUtils;
import org.molgen... |
3ae385248e9e4383a17a3a42d168c39d80388b9b79a7f8a46d7a0e44796380b4 | Java | 3,244 | 89 | /*-
* #%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... |
6f5ce25d1c9de8718f92fbf5af6c5a6c2ed685fcdd9d0b2ac344b112b4b4a00f | Java | 3,246 | 94 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.methylation;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import cern.jet.math.tdouble.DoubleFunctions;
/**
*
* @author MarcJan
*... |
bccc037759468b06f091a3d9a0420c06d51c7b568420258a9e73947a9d0058cd | Java | 3,252 | 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 org.ejml.simple.SimpleMatrix;
/**
*
* @author adriaan
... |
636c25183a10fd619a341f81eaea18edb7ee6623a82eba8bd71478126e428260 | Java | 3,268 | 120 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gtf;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.util.Iter... |
3bb64575750a689b7ef01d02dd8c229e8690349b3fc76fb1cba739e76d5f0faf | Java | 3,271 | 148 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gtf;
import java.util.Collections;
import java.util.Map;
import umcg.genetica.variantAnnotator.GenomicRange;
/**
*
* @author Patrick Deelen
*/
public class GffElement implements GenomicRange... |
7bcaf8c9494558fb9d7838ff1867afe83e18661b78655be30eb7ff8081dce477 | Java | 3,280 | 116 | /*
* The MIT License
*
* Copyright 2013 Tim Boudreau.
*
* 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 restriction, including without limitation the rights
* to use, copy, mo... |
cd50d89a6d55cd5298a0d9b486c59eb31f6686c0ab83a0032d6a8677705a6a6b | Java | 3,281 | 66 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
public class FDRFilter {
public static void main(String[] args) {
FDRFilter f = new FDRFilter();
String[] filesin = new String[]{... |
2e222ea6ba81298971156680912d52a31d0cdbc6a11b54548872deffb2d535b0 | Java | 3,292 | 114 | /*
* 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 java.io.File;
import org.apache.commons.cli.CommandLine;
import org.apache.commo... |
c446c262d434b0af97acbef130c2d79f6cf648d4a12b64de4a93773e0483d7e3 | Java | 3,304 | 98 | /*-
* #%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... |
e50ff28adf75956c332519dfa1165080bd1b3c9120e61dac1843e0d5d56cdf9a | Java | 3,313 | 123 | package edu.cmu.cs.eyetrack.gui.shapes;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Random;
public class StimulusFactory {
public static enum StimulusType { BOTH, TARGET, DISTRACT... |
7342ee4f18fa0fb7696319b114daccfe8774a13e723e75e02f8a73b48e687687 | Java | 3,332 | 101 | /*-
* #%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... |
18a69ced26e3c5660ae54c54733db27219568c227d9bb470a488a95e1973846b | Java | 3,371 | 85 | /*
* 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.genetics.tableAdaption;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.uti... |
38d4cbdab4e4578645e93bf40cef9a02ffc97c38da555df415ad55f640044595 | Java | 3,377 | 94 | /*-
* #%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... |
5e157704a477d7417fad3e347da513cb63b14b753866219cdb0a650a1b6bcdd7 | Java | 3,377 | 94 | /*-
* #%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... |
b98308aa49724772a9ef49be50bd4172ac3522011491a8a5577f20d6382de0bd | Java | 3,380 | 125 | package umcg.genetica.features;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
/**
* Created by hwestra on 2/24/17.
*/
public class BedFileGroup {
// HashMap<String, Integer> groupIndex = new HashMap<String, I... |
fd4c469d72f66c31a885941fd6df28a88a935a9d07c904868bfe5d3186e3562a | Java | 3,386 | 99 | /*-
* #%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... |
1b9ecee20219b6555e50f60bfd85a9153336eb029fca03ac6dc0174568371947 | Java | 3,387 | 100 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.containers;
import cern.colt.matrix.tint.IntMatrix2D;
import umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset;
/**
*
* @author harmjan
*/
public class QTLResultContaine... |
b32e1fb3955d9091757e97b60c5ba34f6e287e6447689711154bd17df6e128ad | Java | 3,387 | 87 | /*
* 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.util;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.loggin... |
64e5dadd89cc90aea42d3d008d003df20d6a1b83dba60c168ecf0fb1fb773911 | Java | 3,407 | 72 | /*
* 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.util.ArrayList;
import java.util.Iterator;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import org.testng.annotatio... |
78b3edf78654703a9a022a33fb7489c0116b7c166106415e2398015c116ce9e3 | Java | 3,412 | 121 | package edu.cmu.cs.eyetrack.io;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FilenameFilter;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import javax.swing.ImageIco... |
84c4fb46e96f70fe4cead2cad9fb21a87e5def2a12ba99350372dbe688749443 | Java | 3,422 | 126 | package umcg.genetica.graphics.themes;
import java.awt.*;
public class ColorBlindTheme 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 MEDIUM_FONT = new Font("Helvetica", F... |
fa02ef6baf2f13dfe4f2e0b03e6b0a2315aaf50994bdbe1c26a4fb9820662876 | Java | 3,428 | 101 | /*-
* #%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... |
67f661185b86e900518dc1f43483ac75d4fd9c1a112ca87470c61313813c1ee7 | Java | 3,430 | 120 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics.histogram;
import eqtlmappingpipeline.mixupmapper.stat.dist.Bin;
import eqtlmappingpipeline.mixupmapper.stat.dist.DiscreteDist;
/**
*
* @author harm-jan
*/
public class Frequenc... |
f0657a2573884c562c02d8c99f3e772ce2f7e68463d0eba31f07736102581eea | Java | 3,434 | 128 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import static org.testng.Assert.*;
/**
*
* @author MarcJan
*/
public class CorrelationNGTest {
public CorrelationNGTest() {
}
@org.testng.annotations.BeforeMethod
... |
80943439f629d915d9dc2e53e603e57aa20cd17afb305eda1b835a7d5976ce70 | Java | 3,456 | 123 | package org.molgenis.genotype.tabix;
import static org.mockito.Mockito.mock;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.io.IOException;
import java.net.URISyntaxExcept... |
229994cfcbb72cec01b0f5262d27f91c612f5f68b37792d7b754c6f944f0c025 | Java | 3,458 | 150 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import java.io.IOException;
import java.util.HashMap;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.ChrAnnotation;
/**
*
* @author harm-jan
*/
public... |
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