sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f26a067b065f2cc15442dc83a19c57519b9fbd4ca60ffa86b6627f6853243945 | Java | 5,669 | 162 | /*
* 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.File;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.Pr... |
e01a4e18211f7c08360966e18ee136b709d872185d1bce31b803b6e24cf1154b | Java | 5,680 | 185 | /*
* 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;
import java.awt.Color;
/**
*
* @author harm-jan
*... |
a309b46606251268cd74b94857d7299853e7cc95d27d3bc9cdb20d46a2ec695e | Java | 5,687 | 210 | /*
* FisherExactTest.java
*
* Created on June 6, 2007, 10:08 AM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
/**
*
* @author ludefranke
*/
public class FisherExactTest {
private double left;
private double ri... |
b491868fa6fae4dbcfb285f2b75094403a05804ce9be35a1cfacad8d3205747c | Java | 5,709 | 177 | /*
* 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.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.charset.Char... |
7c4235a5dc0e9b50f068cbc545b009bc6838e3ecac232217256e53d755bd565a | Java | 5,719 | 183 | package umcg.genetica.math;
import Jama.EigenvalueDecomposition;
import org.ojalgo.matrix.Primitive64Matrix;
import org.ojalgo.matrix.decomposition.Eigenvalue;
import org.ojalgo.matrix.store.MatrixStore;
import org.ojalgo.matrix.store.RawStore;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import umcg.genet... |
142798bd54688a214df65717ed7c2563e84efda1a4d563aa33be94fb35435bbd | Java | 5,728 | 155 | /*-
* #%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 ret... |
513d32753150e1d2ee4e5178ac86e0a522a09758d23b488813aeea90b8ca3df6 | Java | 5,745 | 129 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.gwas;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import umcg.genetica.io.trityper.SNP;
import u... |
7b6713dc5436fdd0dff2e427fc9b6fd28b3900c36b2ff2754ed7c5e00d30f074 | Java | 5,760 | 226 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import org.apache.commons.math3.distribution.NormalDistribution;
import org.apache.commons.math3.exc... |
faae91f96ad1d115b655aeed4bd3424dc6a351c9b150c94e2b861a93aab45199 | Java | 5,774 | 139 | /*-
* #%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... |
77ddbf32bae818a3e73773e8574ddf840ca29f09eb0c4f8efc1f4904c59cbbee | Java | 5,779 | 249 | package org.molgenis.genotype.plink.drivers;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.... |
2ce09362f91eac920c3ee29191b57007a97af0f08d0597dd6760f9f6ae1ec5cb | Java | 5,793 | 246 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import java.util.ArrayList;
import umcg.genetica.io.trityper.util.ChrAnnotation;
/**
*
* @author harmjan
*/
public class MinimalEQTL {
private double pvalue = 1d;
private ... |
7f53204f195b4b0ed3c7b33bd972df97e6a9f17283419029b17401810f1f6cfc | Java | 5,805 | 229 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.genomicboundaries;
import static org.testng.Assert.*;
import org.testng.annotations.Test;
/**
*
* @author Patrick Deelen
*/
public class GenomicBoundaryTest {
public GenomicBoundaryTest() {... |
deb4a3fcc7c63436335c0fcaa8c59f9e4505e942b0c1f4c54b4afc5d3fd928fa | Java | 5,814 | 236 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import umcg.genetica.containers.Pair;
import umcg.genetica.containers.Triple;
/**
* @author harmjan
*/
public class Descriptives {
p... |
febda19da41e76ac3e81af5ad99a6492ab6c385ece126551ae29e8a4812381a1 | Java | 5,816 | 257 | package org.molgenis.genotype.variant;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.util.FixedSizeIterable;
import org.molgenis.genotype.util.Ld;
import org.molgenis.genotype.util.LdCalculatorException;
import org.... |
505242e6a3455cd640a560a90dec6124fb9a63b031b4f58b2b68c90af5d87870 | Java | 5,832 | 157 | /*
* 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.net.URISyntaxException;
import java.text.DateFormat;... |
61958c2c547ec37a6d31c4412dd74391feae428f8daa34f7ba45dfaa70a16f0f | Java | 5,843 | 173 | /*
* 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 au.com.bytecode.opencsv.CSVReader;
import au.com.bytecode.opencsv.CSVWriter;
i... |
ad32124796a9a8dcd1f0a84379905731ace24c4a846e9bec83a314c830a83515 | Java | 5,848 | 189 | /*-
* #%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... |
58af7ad08315f3c53cb33699f8d01cc8648959b197d3cb5e4f206ef9c5167790 | Java | 5,851 | 139 | package deformablemesh.examples;
import deformablemesh.MeshDetector;
import deformablemesh.MeshImageStack;
import deformablemesh.geometry.Box3D;
import deformablemesh.util.connectedcomponents.ConnectedComponents3D;
import deformablemesh.util.connectedcomponents.Region;
import deformablemesh.util.connectedcompon... |
e2a4539382dc1ccef066ae5842875ee9e4449daace9c5503cbffd74e4ff12290 | Java | 5,874 | 159 | /*-
* #%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... |
ae87b2fda28e356924f4c24d78cf3599e61b7ae223c07eac8a8e4c2e562ad2d3 | Java | 5,875 | 202 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.ld;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.bin.RandomAccessFile;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.DataInputStream;
import java.io... |
74682fa217788c701a86f43fc7187cbc420ab2ebb1b7ba5ce009cffe72c36bab | Java | 5,876 | 151 | package umcg.genetica.math.matrix2;
import org.apache.commons.compress.compressors.lz4.FramedLZ4CompressorInputStream;
import org.apache.commons.compress.compressors.lz4.FramedLZ4CompressorOutputStream;
import org.apache.commons.io.input.RandomAccessFileInputStream;
import org.apache.commons.io.output.CountingOutputSt... |
01b8ba12141a3ac0b7c8a81272f9370bfd3211c894cca599bebf31983b236db1 | Java | 5,895 | 175 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.regulomedb;
import umcg.genetica.io.regulomedb.RegulomeDbEntry;
import umcg.genetica.io.regulomedb.RegulomeDbSupportingData;
import java.util.Iterator;
import java.util.List;
import java.util.Ma... |
ccce22f3b45f953355daebe4b872dd4a31ac158906404861d1e03cce0b8f8741 | Java | 5,905 | 170 | package nl.systemsgenetics.genenetworkbackend;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.... |
e6a29c8b288054c12935a228bc3d0c696e96fbdbc99a2735a70c70b541e2ed95 | Java | 5,916 | 159 | /*-
* #%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... |
eaa00632bd5289f76ceca43ad5d721120d2765d8f62cc806b2eaa10c8579cfa5 | Java | 5,920 | 185 | package org.molgenis.genotype.plink;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.Charset;
import java.text.DecimalFormat;
import java.util.Iterator;
import org.apache.logging.log4j.Logger;
im... |
586e24b7415cd9fc4d67d8a520fb7acff7fae8f7e69afb14d37ec40d7cc08763 | Java | 5,934 | 223 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.util;
import umcg.genetica.text.Strings;
/**
*
* @author harmjan
*/
public class BaseAnnot {
public static final byte A = 65;
public static final byte C = 67;
public st... |
97b956e3be36f649cf88ab4aef1d4d29b7ee62653c69caa0d1d45e55394b6cb3 | Java | 5,963 | 189 | /*-
* #%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... |
6a3207e6cf4231471e2821f385744cfe79fb77753e443fd6cc2db2c16963b470 | Java | 5,966 | 220 | /*
* 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.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.regex.Pattern;
import ... |
1c65abeafe31f9ae37ba56521dcd52a13b0e20e636408b4b6ece93f55836e248 | Java | 5,975 | 216 | /* 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... |
8647b168f842cd676abe428e9494d637aea00b0ad9131fcf5ce7812067aa1bc1 | Java | 5,983 | 218 | package umcg.genetica.graphics;
import com.itextpdf.text.Document;
import com.itextpdf.text.DocumentException;
import com.itextpdf.text.pdf.PdfContentByte;
import com.itextpdf.text.pdf.PdfWriter;
import umcg.genetica.graphics.themes.DefaultTheme;
import javax.imageio.ImageIO;
import java.awt.*;
import java.awt.image.... |
f58f9c98726464738033972a1d2475dbc366100061c3aaf92975c5a33999edcf | Java | 5,996 | 153 | /*-
* #%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... |
6dab6ea57efc32ae8c6d9d4bd0c2892ac1e39a11ee62073244197c2788defcfc | Java | 6,007 | 166 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import java.util.ArrayList;
import ja... |
e1108058e3ba5cb1a0a521e5e5911e993705d9e5b316740e768f0d7b69f80a6a | Java | 6,027 | 189 | /*-
* #%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... |
b0a23dca48d9d025b70167a055923f497c0d9e35f4c858b29333478ca2f6a0ae | Java | 6,033 | 180 | package nl.systemsgenetics.geneticriskscorecalculator;
import java.io.File;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons... |
2633aa3b7288a820423d66bd51997f5a817a0212e2466dec9b72b6b66e020360 | Java | 6,051 | 184 | /*-
* #%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... |
78f72f3006f60c7f2e5685514258af9b0603922ffe326fa3fab47f52c7bc97e9 | Java | 6,074 | 158 | /*
* 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;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
impor... |
1374024d7fd41878222322bf3c75f58408f75c670db9a22abaeb73ec770d5462 | Java | 6,078 | 162 | /*-
* #%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... |
a6bbbc7160bf4346fde72f81bd29e98d0246bdfe56bd935a1ce6a50d82b73e22 | Java | 6,084 | 241 | package umcg.genetica.io.bed;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
... |
6c4efc3781649fa068977af7f6989b21353a25ac8aa64746193f7c3139692f7c | Java | 6,106 | 155 | /*-
* #%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... |
dd57eca8583834ed6a7829a9bd8a54fee8ad073163e3b5575d88f82b16d432cc | Java | 6,112 | 198 | /*-
* #%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... |
fff5e46f4da9890c10d0c3e188cd2ad2945df282e1cc6a6851c101890ba56c66 | Java | 6,136 | 217 | package eqtlmappingpipeline.ase;
import cern.colt.list.tint.IntArrayList;
import cern.jet.stat.tdouble.Probability;
import java.math.BigDecimal;
import java.math.MathContext;
import java.math.RoundingMode;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
*
* @author Patrick De... |
ee7a87fa3b85a187728e8d7b038bc8fd5ffc67290bd9c90d578090e1cf6486b3 | Java | 6,139 | 152 | /*
* 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 cern.colt.matrix.tdouble.algo.Den... |
2e67dc3b8e317b6512b9e04cdb1b8461df985dc4105e51bb8082db56553fc2d2 | Java | 6,141 | 210 | /*-
* #%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... |
73953f291c988aff24c1483a1f9a0907d8acad7039abf6de5bc1920614878771 | Java | 6,151 | 223 | /*-
* #%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... |
7ea7773d1cce4cd68ac29471655055200702aab13c5f8432bc0a4366afb440cd | Java | 6,156 | 186 | /*-
* #%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... |
637f9d3abf4dc4e71afed61a7c61fad4e8daed3eb67734e03a599398397faf39 | Java | 6,165 | 155 | /*-
* #%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... |
931304d70bf13e8d3bbf8e759e1586c18a7fd3aafc31104d86028419ebe4d9ae | Java | 6,186 | 191 | /*-
* #%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... |
46801ca2a4f0c08eaf60907ff754b13b92c8df8c74092ab189a49bb320707749 | Java | 6,198 | 183 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.runners;
import cern.colt.function.tdouble.DoubleFunction;
import cern.jet.math.tdouble.Double... |
4039ccf1ca55c21b5bca9ad5848ec36dc6f73ed9d5a6dc64c8731a6dd694a99b | Java | 6,207 | 191 | package nl.systemsgenetics.genenetworkbackend;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import ... |
8c332e69241d4514345b5c23209d58478833f8c2aa3a0856b09fd9f73c3b8ada | Java | 6,218 | 187 | package nl.systemsgenetics.downstreamer.runners.options;
import edu.emory.mathcs.utils.ConcurrencyUtils;
import htsjdk.tribble.SimpleFeature;
import org.apache.commons.cli.*;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import java.io.File;
import java.util.concurrent.ForkJoinPo... |
f4ad9c13e04a3d813a1da3a4d34d1879b071ff995cc6b5d31abcf9cb0012cef1 | Java | 6,219 | 209 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.channels.FileChannel;
import java.text.DecimalFormat;
import ja... |
381c9b56ab22a9f07f03bf807b05c71f9becbb67d299f18288e4c15498240fa9 | Java | 6,220 | 197 | package org.molgenis.genotype.variant;
import static org.mockito.Mockito.mock;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertNull;
import java.util.ArrayList;
import java.util.Arrays;
... |
426512b3be52742c2dc5a6a6972b2c8b766728c4248221f9c689f1a75b0029cf | Java | 6,220 | 171 | package org.molgenis.genotype;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotEquals;
import static org.testng.Assert.assertNotNull;
import java.util.Arrays;
import java.util.List;
import org.testng.annotations.Test;
public class AllelesTest
{
@Test
public void getAlleles()... |
c6cc5c468d22efe748be4868f39d104320995bed41eb56502e8baf78f6ac8c0c | Java | 6,221 | 157 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package imputationtool.preprocessing;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.TriTyperGenotypeData;
/**
... |
a472b9b79690875091258a5105568847024fbca00b3b1fae28305719d6b08032 | Java | 6,227 | 157 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.runners;
import com.opencsv.CSVWriter;
import java.io.*;
import java.util.*;
import java.util... |
4378d6508fbd191288eecfdab662ee9b901d90ea1d587e432f8377d6d97142ba | Java | 6,249 | 181 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta;
import eqtlmappingpipeline.binarymeta.util.Filter;
import eqtlmappingpipeline.binarymeta.meta.IndividualAnalysis;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalyze;
import eq... |
44b85c03dc74a2755c6568eb5e483a32ccd6c699b5fd1833621936d07f65b8da | Java | 6,262 | 178 | /*
* 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;
/**
*
* This format is used to provide called peaks of signal enrichment based on
* pool... |
9e5b041f6906f8bbe94e40656aa9c9e40d58a1caad241f347fe2791400d77b39 | Java | 6,266 | 233 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics.curve;
/**
*
* @author harm-jan
*/
public class ROCCurve extends Curve {
public ROCCurve(int width, int height, boolean outputPDF, String outputLoc){
super(width, he... |
49a3adbcbe3b42bbc5c32a07a99001730e350430390aadfe0099d65665d5053b | Java | 6,285 | 181 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
/**
*
* @author MarcJan
*/
public class SmoothSort {
// by keeping these constants, we can avoid the tiresome business
// of keeping track of Dijkstra's b and c. Instead of keeping... |
46ca374f9e467b26b62fd69259225af6ea4c147dcce841aff01934966962123c | Java | 6,286 | 161 | package ebi.spot.neo4j2owl.exporter;
import ebi.spot.neo4j2owl.N2OException;
import ebi.spot.neo4j2owl.N2OStatic;
import org.neo4j.graphdb.Label;
import org.neo4j.kernel.impl.core.NodeProxy;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.mode... |
0460f5f314a963c2f1a4c40e5832b37e4ba1facfe373f6ddf8be709165075a60 | Java | 6,289 | 183 | /*-
* #%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... |
b403bc003dd084864b28c97f7d6b6153edd88d7ada63e369a7ffeb9d22a4a6db | Java | 6,304 | 206 | /*-
* #%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... |
f6ecc53a446a15e86bf782ad2dff848fd4b353c36f26746d1b66cd9250a77fd8 | Java | 6,309 | 192 | /*-
* #%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... |
f1d71321a55307bdd5821ed9ba1507eed40b6f8be7e78538df1f69eda578a9d1 | Java | 6,313 | 213 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.graphics;
import com.itextpdf.text.Document;
import com.itextpdf.text.pdf.PdfContentByte;
import java.awt.*;
import java.awt.geom.AffineTransform;
import java.awt.image.Buffe... |
28a5538540820946b2dfe9b5b25484c7cfcced9ff7b1fe7b8c234e8ca3ae8ed0 | Java | 6,346 | 186 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.trityper;
import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.molgeni... |
dc23fd354f496fc49e9d5d1491864272c01eda6952445bd9fee8cd9033096715 | Java | 6,378 | 168 | /*-
* #%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... |
9c67d465988701430e0c12c2d319e74a6697a665fea35d994f578c4db5216376 | Java | 6,380 | 219 | package nl.umcg.westrah.binarymetaanalyzer;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
public class MatrixConverterC... |
d8ea0ad0e84d3bcb6ac856e3661c7b9938df49da04ab7ddb85bddbd12dccf76a | Java | 6,389 | 314 | /*
* 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... |
bb44686740d410d1bd7174afe4f2352943577e5ad7f42826fd02202ad53780c0 | Java | 6,393 | 204 | /*-
* #%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... |
cef63d8825d1659f73bf8e4476c786efe00b299aadcc71ccea73f4e5336ded66 | Java | 6,411 | 177 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OConfig;
import ebi.spot.neo4j2owl.N2OLog;
import ebi.spot.neo4j2owl.N2OStatic;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.util.De... |
459f15ee1e754f541135639001b267b30e6af4b67bb3337c03480d0561e70a0c | Java | 6,416 | 214 | package org.molgenis.genotype.editable;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.util.CalledDosageConvertor;
import org.molgenis.genoty... |
218b2391ca4f6a001d83f51c76685f2a9ec89107e31b6ddaa7506bc095b7768f | Java | 6,426 | 234 | /*
* 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;
import gnu.trove.map.hash.THashMap;
import java.io.File;
import umcg.genetica.console.Mu... |
22625892ff7dbe412b058c4953171cacfb0602c9224cbef2cc884b0897a1ab19 | Java | 6,468 | 196 | /*-
* #%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 ... |
6f7102753eb403bb16867cd07c80c7dd7f86199e7697abb459bfba128f07d8ab | Java | 6,473 | 153 | /*
* 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.HashMap;
import java.util.logging.Level;
import java... |
a114d8eb14184220c01f6adb15ef362115f204e37831a8de0f400bb27b5875c5 | Java | 6,486 | 225 | /*-
* #%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... |
a95e7046656539c0441fa6724032fd74bc79f19f00aa86802ff7f5b121d16b23 | Java | 6,514 | 208 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.summarystatistic;
import nl.systemsgenetics.downstreamer.summarystatistic.LocusUtils;
import n... |
5331ce585a1f7c18862bcf6ade66140c0de4fb6d26df1523807fbb5abd08a61f | Java | 6,515 | 183 | /*-
* #%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... |
dc23c524bb27ac4f0a472f8386aa4ab952680ab75caa5d82a8782fb380dcd462 | Java | 6,519 | 191 | /*
* 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.io.RandomAccessFile;
/**
*
* @author harm-jan
*/
public class BufferedSNPLoader {
private RandomAccessFile m_genotypehandle;
privat... |
96309ef095514f5ed07beca3001a77d423391ab41905b47bc11ad0a1408382c3 | Java | 6,525 | 137 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.pcaoptimum;
import eqtlmappingpipeline.util.QTLFileCompare;
import java.io.IOException;
import umcg.genetica.io.trityper.EQTL;
import umcg.genetica.io.trityper.QTLTextFile;
/**
*
* @author... |
948f31e086065dbafd144223ab186dab0d9a5bbf96a1e7701b417ddc3e8879be | Java | 6,539 | 194 | /*
* 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.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.regex.Pattern;
//import ... |
ebd6f8463c8e3bfca5a345b4c36cca3c800a0f4b2abdb2b5c736718c30901426 | Java | 6,541 | 168 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.Map.Entry;
im... |
df9387baebc9dbe2463384cc58fc5fe695a3bb9d33e17c67224a281a330352e9 | Java | 6,552 | 207 | package eqtlmappingpipeline.binaryInteraction;
import au.com.bytecode.opencsv.CSVWriter;
import gnu.trove.map.hash.TObjectDoubleHashMap;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
im... |
f47d7c4e6e5f94c50b9284266aae44c160badc5f35ed7b26d264f2550b485c5e | Java | 6,561 | 163 | package ebi.spot.neo4j2owl;
import ebi.spot.neo4j2owl.exporter.N2OExportService;
import ebi.spot.neo4j2owl.exporter.N2OReturnValue;
import ebi.spot.neo4j2owl.importer.*;
import org.apache.commons.io.FileUtils;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.QueryExecutionException;
import org.n... |
4ecaafa819fd97f87697b24c1d4db338192c5a59b2667505ef4d8a963cd2d5ad | Java | 6,564 | 244 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import gnu.trove.map.hash.TDoubleDoubleHashMap;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.text.Strings;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
public class ApplyFDR {
p... |
9b535b5ad174e871428ae7d1b804fa354f7853faeeb8fca7ee308c78adf32684 | Java | 6,589 | 187 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.trityper;
import java.io.File;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.Map.Entry;
import org.molg... |
d879f4418c2ac2f5590097d98ba5336b92154d262d9e18d9026df0d566ee5e3d | Java | 6,591 | 237 | /*
* 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.io.FileNotFoundException;
import java.io.IOException;
import java... |
532633c6d30039651f6ab63324445d3ae2d38a59535688466defbdb40ac4c5a7 | Java | 6,592 | 195 | package nl.systemsgenetics.genenetworkbackend;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util... |
83fc97f227a9d4ecc33c1d3ca0f8882c872eb9acbbcbb5924226dc0e17e01774 | Java | 6,596 | 180 | /*-
* #%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... |
f8d5fc9dcb86280d4ed83aa5406491b9966bd15ef02a9525997337b893a157c6 | Java | 6,599 | 185 | package org.molgenis.genotype.oxford;
import static org.testng.Assert.*;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import ... |
dbb7cb15cbbbbf8fac574e788554f8f113548cb57f95d4dfe104079e985afc09 | Java | 6,600 | 195 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
import java.io.IOException;
import java.text.DateFormat;
import java.text.SimpleDateFormat... |
534e595fd5f84f75de001b8e7e2d0fc12488827bbfbb5695f18b83acdfa4ade1 | Java | 6,605 | 215 | /*-
* #%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 ... |
a915c36cd93c8f50c9e287ea44ff46638daa3fe919ef4ea2a42ff1bee45b6dce | Java | 6,635 | 195 | /*-
* #%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... |
36cefb009d884422c7f929933128b113d41990d4e95b6ef09301999776aee805 | Java | 6,661 | 214 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import cern.colt.GenericSorting;
import java.util.HashSet;
import org.apache.commons.collections.primitives.ArrayDoubleList;
import org.apache.commons.math3.stat.ranking.RankingAlgorithm;
imp... |
b522e1567c8e9ccc7dc59bf7323b3034fd51f0b121d6d71f8e71f21cbdd37dbb | Java | 6,676 | 166 | /*-
* #%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... |
19b6df331a0e3f9759deac9b479b8ae3ab95d4ee779d8d924d52531aacc56fc2 | Java | 6,678 | 165 | package org.molgenis.genotype.modifiable;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.bgen.BgenGenotypeDataTest;
import org.molgenis.genotype.util.CalledDosageConvertor;
import org.molgenis.genotype.util.FixedSizeIterable;
import org.molgenis.genotype.util.Pr... |
cd3429240b6d812d1a64699d26de3f97f827c34b25ee2371df69979b64981c29 | Java | 6,718 | 192 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.westrah.binarymetaanalyzer;
import it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap;
import umcg.genetica.io.text.TextFile;
import java.io.File;
import java.io.IOException;
import java.util.*;
/*... |
a4d6ff2f27df1a4d5345f36887c89b7f474e2fc52b701d494ee83d72b948113f | Java | 6,740 | 219 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package imputationtool.postprocessing;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import umcg.genetica.io.text.TextFile;
/**
*
* @author harmjan
*/
pu... |
db73f4d5db700d793bad751d062c3dc0a61c02eae7f5ece8782934322e1ce329 | Java | 6,808 | 264 | package nl.systemsgenetics.downstreamer.summarystatistic;
import htsjdk.samtools.util.Interval;
import nl.systemsgenetics.downstreamer.gene.Gene;
import nl.systemsgenetics.downstreamer.summarystatistic.filters.SummaryStatisticsRecordFilter;
import java.util.*;
import java.util.function.Function;
import java.util.stre... |
8c78ad9ed92717c1da474c3653215130e2f44255ba0dd60a009c52f2b4360d68 | Java | 6,812 | 154 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.eQTLFoldChangeCalculator;
import umcg.genetica.console.ConsoleGUIElems;
/**
*
* @author harmjan
*/
public class QTLFoldChangeCalculatorGUI {
public QTLFoldChangeCalculatorGUI(String[... |
dde2f316e8619562bb11403940ff76519c850298a8c726db229d2157d3c000e9 | Java | 6,835 | 121 | /*
* 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.HiC;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map.Entry;
import java.u... |
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