sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d10c820a0a9781c71cfa08eb8ad2139ecc6627b1e58d7d2e6894b860b536e5db | Java | 10,252 | 248 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.ensembl;
import umcg.genetica.containers.Transcript;
import umcg.genetica.containers.Exon;
import umcg.genetica.containers.Gene;
import umcg.genetica.containers.Chromosome;
import java.io.IOExcepti... |
3392bf10653a6b75cf6c6ab40828b2c7f04425fd56d9b3f112834a523acf8415 | Java | 10,256 | 251 | /*-
* #%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... |
c3f9c43fe30db65d86e586f7f3932bea084ac92351f11b70d0a303b3fe4abbba | Java | 10,274 | 265 | /*-
* #%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... |
611cead022166c79ace4836e84593725e0d40dff085914467cdb2331eec1013a | Java | 10,305 | 285 | /*-
* #%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... |
677ff5eef0adffa4a879b571ec5ea087663591629bdb3f263bc1d95b2f4238c7 | Java | 10,305 | 316 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.EQTL;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.u... |
03cd492609eecb7e078925e5b266ba491f947422051862ccc1e7bb1141cc0804 | Java | 10,318 | 225 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.chromosomeyexpressionplotter;
import java.awt.*;
import java.awt.image.*;
import java.io.File;
import java.util.ArrayList;
import umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset... |
53b4186a25a8b7dd8fe72b81ca3357a47f645b63164af32c9cd610bd2ad783ad | Java | 10,347 | 395 | /* 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... |
7a92cd3df245fdd5d73ed0696cd2af689a2bef44d585cca33ff89a462bc0c23f | Java | 10,349 | 306 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.bin;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.nio.ByteBuffer;
impo... |
9a7889843dfa6debd2e00c5d578fa4d2b8ce36fdc7f8c3d188bc8f47b7b3ef41 | Java | 10,351 | 305 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
import java.io.File;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.... |
573fbbe6bb4b44692d8895f6da5266d31c772727b924187091455fc9be91f043 | Java | 10,404 | 305 | /*-
* #%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... |
14d7836e17a5b1619ba8feef6970c1cfc3de22b488b6b7d3e586671633fe2f89 | Java | 10,421 | 266 | /*-
* #%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... |
a6eef74b3f4e812e0bd13c4633775c4bde12c6b67f6a5496ca7304e89f09089b | Java | 10,458 | 373 | /*
* 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 java.io.IOException;
import java.io.RandomAccessFile;
import java.nio.ByteBuffer;
i... |
8b021611ffd62e9bd0eff507c67912ac3993625197c31573d07669afed39029f | Java | 10,467 | 240 | /*
* 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.util;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map.Entry;
imp... |
159b028ccebcd85c9f48fdcffd0bf55acb2ffd21d96e39748ec4a61f87982a62 | Java | 10,481 | 371 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
impo... |
360c7287ad1cd48b8cd41a55d08298ead6374246b606e49abe8c03c3c0a98962 | Java | 10,484 | 267 | package mbqtl.gfx;
import com.itextpdf.text.DocumentException;
import umcg.genetica.io.text.TextFile;
import javax.imageio.ImageIO;
import java.awt.*;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
public class QTLDotPlot {
private long[] cumChrPos;
private int[]... |
93960f6b021d91c68f370cb26e7152fd275d5a5548a8b168be7651263458b9ba | Java | 10,499 | 250 | package umcg.genetica.io.trityper;
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
import java.util.*;
import java.io.*;
import java.util.regex.Pattern;
import umcg.geneti... |
4a07f7ba33818da5b2b8d5f88ac9472f87245e1cc2d2bc1639c14f55df7eee61 | Java | 10,530 | 354 | /*-
* #%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... |
e1541e6bc274488cdc1bcdbe93dea5ef86fc8d287b8d169f81b17830bba19de8 | Java | 10,560 | 460 | package network_code_v5.beans;
import java.io.*;
import java.util.*;
public class ConfigBeans
{
private String workingDirectory = "";
private String geneInfo = "";
private String geneExpr = "";
private String fpkmFile = "";
private String putativeRegulatoryRegionFolder = "";
private Strin... |
3b071190274c3dfbdd7e588ee5574a1c1378a119191932bd09bc050099958bb7 | Java | 10,569 | 163 | /*
* 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 static java.lang.Math.abs;
import junit.framework.Assert;
... |
65e7960432e5f957accaab53c63e1de6a34d34aea9f727f86f4da4b04467ecb1 | Java | 10,631 | 264 | /*-
* #%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... |
a52251881c2e588bdd0ea280e208ef1ac65cd5e0640e2020d26bc357ac793868 | Java | 10,633 | 198 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.causalinference;
import java.io.IOException;
import java.util.Iterator;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.containers.Triple;
import umcg.genetica.io.tex... |
4036ce095e433b1f862ab8d4c9f3f6c0571022de57842f945ef62a88c0c3380b | Java | 10,635 | 287 | /*-
* #%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... |
c3779e343c5e919eee1e44dc1d42905da56443b807898e5dce74395ee1e481c6 | Java | 10,647 | 336 | package org.molgenis.genotype.plink;
import gnu.trove.map.TIntObjectMap;
import gnu.trove.map.TObjectIntMap;
import gnu.trove.map.hash.TIntObjectHashMap;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
i... |
65b17528d711ddf60e114fce30293937724a15911b2fdfba27e1d79e6288a96b | Java | 10,741 | 285 | /*-
* #%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... |
3fc4039bc1937965f6660d24f1c4cfe42a91666bc0c4709ca50809f92435b205 | Java | 10,744 | 368 | /*-
* #%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... |
6c4de770d8e377c4f4be0706ba4d8903ff3fbdce40432b77216dd5c3ebfd071d | Java | 10,785 | 269 | /*
* 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.File;
import java.io.IOException;
import java.util.ArrayList;
import java.ut... |
cfc8e3a93aee80e913ba744e78fe68166581ee820e831f5cac7dc08f09dd2b52 | Java | 10,863 | 391 | /*-
* #%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... |
82dee22720f8f2cc9352b7de664ca8b4902f46cec10a2ccebb7c948f4528bdef | Java | 10,864 | 314 | /*-
* #%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... |
931a3c84003b8d84d88d67bfa52a0a229518496626d25cc35cd067b6fad98e8d | Java | 10,975 | 314 | package nl.systemsgenetics.downstreamer;
import nl.systemsgenetics.downstreamer.runners.options.DownstreamerMode;
import nl.systemsgenetics.downstreamer.runners.options.DownstreamerOptionsDeprecated;
import nl.systemsgenetics.downstreamer.runners.*;
import java.io.File;
import java.io.IOException;
import java.text.Da... |
fa1b3dbb3b506bcc074e26a9902241825c28bc5d8e39bccf6d6ed0de2fb72f72 | Java | 11,018 | 315 | /*-
* #%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... |
732a35a5e971d826c8dff65fd3a03bf3c951187e41e1ce4c73ee49da4b3aca73 | Java | 11,023 | 343 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics.histogram;
import eqtlmappingpipeline.graphics.Graphics;
import eqtlmappingpipeline.mixupmapper.stat.dist.Bin;
import eqtlmappingpipeline.mixupmapper.stat.dist.DiscreteDist;
/**
*
... |
89f7f58a59b7e6299b7a9360448b27385fc4c880c90a5a342bd83d7437db731d | Java | 11,065 | 299 | /*-
* #%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... |
c4cdc1304c3c6be1ae357aa1ebb2b78dd2e4758796ed1876e6cb95bf49c94b98 | Java | 11,081 | 295 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OConfig;
import ebi.spot.neo4j2owl.N2OStatic;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.util.mansyntax.ManchesterOWLSy... |
d80cdc2ebc32cd0b4269c54fbaeeb22d2181147635b5de241db67ee8cfe375f1 | Java | 11,113 | 295 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.graphics;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.Bu... |
16fdb5f0839cacb3ed30fd8b4cbba60a6839d56694a3367f8aa66a7acdca4b72 | Java | 11,121 | 278 | /*-
* #%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... |
80b70f45531b618d836ad9bc5b8b24d542107e68b42f211c898e3548a703acb4 | Java | 11,141 | 367 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
i... |
857b72357e42fa48792d5f33573be6a57383ff6da9c3194df8dc57ae666a5985 | Java | 11,191 | 314 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics.map;
import java.awt.Color;
import java.awt.Stroke;
import java.awt.geom.Rectangle2D;
import java.util.HashMap;
import java.util.ArrayList;
/**
*
* @author harm-jan
*/
public cla... |
ca31518eab02c80cb80f36cce6a7d0e841f341b2ceb40fbc23fd2658571c407d | Java | 11,209 | 283 | package mbqtl.vcf;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.Set;
import mbqtl.enums.AnalysisType;
import umcg.genetica.features.Feature;
import umcg.genetica.features.SNPFeature;
import umcg.genetica.io.Gpio;
public class VCFVariantProvider implements Iter... |
588193fa5e1e16035a49d793b1fb1f2052a391512e05621aebc251882bad4b37 | Java | 11,286 | 267 | /*
* 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.Arrays;
import java.util.HashSet;
import java.util.List;
import org.apache.commons.collections.primitives.A... |
5c40f4ae5f8cb97629ad24b229453fb57fc24cc62bd9758883c0a8b82489c124 | Java | 11,305 | 289 | /*-
* #%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... |
19cd8b57010edca94d6ecd2f859756a1bb93fcf3251547b2bcc337a4df21ff38 | Java | 11,375 | 369 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.text;
//import it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap;
import it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap;
import java.io.UnsupportedEncodingException;
import java.text.... |
0d40f8a8499451b73302b6a1635b073aa4632f1c3e290a36cc95eca3c3463016 | Java | 11,480 | 332 | /*-
* #%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... |
5af186252031a8e51f1fbc08c685b7a80396ddda76dc3330b36cfab28de36692 | Java | 11,524 | 296 | package edu.cmu.cs.eyetrack.test;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Vector;
import au.com.bytecode.opencsv.CSVWriter;
import edu.cmu.cs.eyetrack.analysis.io.Loader;
import edu.cmu.cs.eyetr... |
cd89ad15d03266ca652a89d9d5e709e5f95aa45154ad04ae6b480ced39ca3391 | Java | 11,548 | 322 | /*-
* #%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... |
3c85fe0165272b3464698be65e16dd3d31dbb2486eda40440f81871d44579d62 | Java | 11,553 | 452 | package org.molgenis.genotype.tabix;
import java.io.Closeable;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.charset.Charset;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import jav... |
c8c9885689e06485cdfd4f0001c2cc78ceed67358e594064796ce56ee0468c19 | Java | 11,553 | 275 | /*
* 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.metaqtl4;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.util.ArrayList;
import java.util.Collec... |
51543901d84993577a3608adb659bdfc4dade057706ae17afe597e85840fc70f | Java | 11,559 | 283 | package umcg.genetica.io.pileup;
import gnu.trove.map.TIntObjectMap;
import gnu.trove.map.hash.TIntObjectHashMap;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java... |
0841cae714911c17e700caafac9babe4a65f8dd50bff345106f7a5e9c8f2b534 | Java | 11,561 | 313 | /*-
* #%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... |
0ab5ff2de2a9626786dd47a892c01b17b39bd6cc9ad4c947651a5d2f4b33324f | Java | 11,619 | 342 | /*-
* #%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... |
c84d163a6e719258969e543db27388ea077d65f50ee0c255264458d0c9de13d9 | Java | 11,642 | 321 | package umcg.genetica.graphics;
import com.itextpdf.text.DocumentException;
import umcg.genetica.graphics.panels.AssociationPanel;
import umcg.genetica.graphics.panels.Panel;
import java.io.IOException;
/**
* Created by hwestra on 7/15/15.
*/
public class Grid {
int marginBetweenPanels;
int marginX;
i... |
2daab8aeb65f62de4132522095c4e31a7d0bdbde4220518ad731b8afbe0f2dad | Java | 11,649 | 368 | /*-
* #%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... |
d2ecfb437aa274dc2b632e07ae25edcc3b9a0b5c6e3bc03b696ea1c9a3722df2 | Java | 11,697 | 264 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.pcaoptimum;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import umcg.genetica.console.ConsoleGUIElems;
import umcg.genetica.io.Gpio... |
356ddf60f1dd9a39f4517ba5eea3e9bf7a1ed415b3fbf99cf4be408bb063807d | Java | 11,737 | 339 | /*-
* #%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... |
7661f841e40db06ed3b80c9c24fba14a70a539b38961c02363bf576f93b3d134 | Java | 11,760 | 327 | /*-
* #%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... |
bd7208d768ed93b9f71eb3e997e1b9a8504fd712da58da4e1d0979e209302030 | Java | 11,771 | 313 | /*-
* #%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... |
bdcbbaf1eab02f4ae6812b5308ad5801431658ccc49bede96041769bed1f728b | Java | 11,779 | 298 | /*-
* #%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... |
ffd1a8e255673752ad0dcb14c4898e9c7c307fbc05ef2f782258ceea4a5b7ed1 | Java | 11,817 | 384 | /* 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... |
c0959c25867f7e3b5f3277fc1f9b15b19ff4dfd5fa9d8d344fda5dd625ecb9ac | Java | 11,878 | 241 | /*
* 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.IOException;
import java.util.HashMap;
import java.util.HashSet;
import umcg.genetica... |
37b1833f32185090d1abb88e26a3989b06f02948a2681a0317f2395923711fe2 | Java | 11,886 | 376 | /*-
* #%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... |
a2e45136ca4885de1baedcdb150ed06ee36fbdf4822a4d8e492cede301999cf5 | Java | 11,886 | 279 | package org.molgenis.genotype.util;
import static org.mockito.Mockito.mock;
import static org.testng.Assert.assertEquals;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import org.molgenis.genotype.Alleles;
... |
b8f78c8586a5fd6f0058feefb76b47ca518d1c7603dad6c8b44f657673e461f6 | Java | 11,897 | 367 | /*-
* #%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... |
3b434f9e2580b8ec937f9fbe26cfe013e09feec817558202b9cce67b3e3bc7bf | Java | 11,919 | 422 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.converters;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.regex.Pattern;
import umcg.... |
5c77b9cbd2e9ea9d632f017a402380c33ac480ece7154fbbd7d128e8652b67e2 | Java | 11,927 | 300 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatr... |
8f559b7b36be3227738699e6a1fdd35fa609acfbdf27584599331e8835817983 | Java | 11,948 | 304 | /*-
* #%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... |
25ad558c210581d8a2d565afbca9343adf6bc53d17421d541116200adb994bd6 | Java | 11,963 | 356 | /*-
* #%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... |
16d7af1a8f4edf84c2592288e46e854322c7cedcc54424015b4fcc943adea3e2 | Java | 12,012 | 307 | /*-
* #%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... |
33f6e9c531fb77e5cd3f70cee006942b1a02ebbbea58544bede8c314b0ae917d | Java | 12,012 | 307 | /*-
* #%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... |
45e21e230f0a77b059cf26dd7542e913b6a9690f02fddc2caf4d6864f1cfecf8 | Java | 12,049 | 332 | /*-
* #%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 ... |
db81d05f14a1cc8c289535bfed164229b16c991bfaf2b7caf3469df999184f17 | Java | 12,108 | 276 | package transeqtlcrossmap;
import org.apache.commons.cli.*;
import java.io.IOException;
public class Main {
public static void main(String[] args) {
Options options = new Options();
options.addRequiredOption("m", "mode", true, "Mode: [makeseq|quantify]");
options.addRequiredOption("e"... |
10857ccf6184e61cb945b73cc792438924399a96bc66c4bba1f10a8a41cb6e14 | Java | 12,116 | 389 | /*-
* #%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... |
b068cb56b6f15dbc96a292f0379fe2904da2b1d09bd758ff68bc727433956d7f | Java | 12,140 | 335 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.oxford;
import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.molgenis... |
64a9f4402e2ba50832b302f86e771533952f81dfb9d0858fc9d1d5eeed6cfff6 | Java | 12,264 | 357 | package network_code_v5.func;
import java.io.*;
import java.util.*;
public class UCSCbrowserData
{
public UCSCbrowserData(){}
/*
* TF binding tracks
* integrate files generated from NetworkInteractions.genNetworkFromFimoOutput()
*
*/
public void printUCSCTFBindingBedFiles(String networkFolder, String u... |
ac6da062cd7de64877277df314dbdf442ae83c660822d2c866706646f31dc19d | Java | 12,265 | 313 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import umcg.genetica.io.gmt.GMTFile;
import umcg.gen... |
d05dc3831482bf0136a3dc0e7e1c44e0c8cfbaffe02869c4994bb103ec962230 | Java | 12,288 | 318 | /*-
* #%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... |
06f1dd94268f619d91bd0cbc9d4686577e038537c30a73096cd5aa68b4d8912c | Java | 12,300 | 261 | package org.molgenis.genotype.variant;
import java.util.ArrayList;
import org.molgenis.genotype.Alleles;
import static org.mockito.Mockito.mock;
import static org.testng.AssertJUnit.assertEquals;
import org.molgenis.genotype.DummySampleVariantsProvider;
import org.molgenis.genotype.variant.sampleProvider.SampleVari... |
af5309d1a52bf14fcd675663d254b9179b451c8ff161bd5c15bb7ade151b6b8d | Java | 12,362 | 297 | package main.java.decon_eQTL;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Properties;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineP... |
c8c79e6887e3fd7c91256ab9020ff85e313e23cd11abdc11245fad8cf58c5814 | Java | 12,383 | 369 | package edu.cmu.cs.eyetrack.state;
import java.awt.Color;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Random;
import org.jdesktop.core.animation.timing.Interpolator;
import org.jdesktop.core.animation.timing.KeyFrames;
import org.... |
18893757659e94869eead5128f6ee230111613c33c3cc6e586a23d0b2eec6075 | Java | 12,495 | 354 | /*-
* #%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... |
1ae460e7d750e7140b439a97ece8d5db619256665bcb5e81e6eb52e1c688d808 | Java | 12,508 | 327 | package ebi.spot.neo4j2owl;
import ebi.spot.neo4j2owl.importer.LABELLING_MODE;
import org.apache.commons.io.FileUtils;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.yaml.snakeyaml.Yaml;
import java.io.File;
import java.io.FileInputStream;
import java.io... |
b2966aefe0be52981c7de2eff1a502cbb9ff20c8aeb491afae2fe1ba9c662d20 | Java | 12,515 | 414 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import com.opencsv.CSVParser;
impor... |
343fc2843de4f2b3673aaf57b623dd25a65ad8190269213c5a2c1626ad82a194 | Java | 12,516 | 309 | package eqtlmappingpipeline.util;
import com.google.common.collect.Lists;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
imp... |
4304bad892a77880d6047d29bb7e9c8c881ec00cc8ddb0f93cfa1785681bcf92 | Java | 12,550 | 329 | /*-
* #%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... |
12fd3e431ef777fc1b5c310ae3c811a16bf953865ede85db2258629e8d2e1fe0 | Java | 12,646 | 360 | /*-
* #%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... |
cf06129dc0e1ea351038220f79d0355204a45e9a78c970676c3648d8a15fd550 | Java | 12,651 | 303 | package org.molgenis.genotype.variant;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.util.FixedSizeIterabl... |
d97c04c12c35c65b3a336b130f5bf1cfeffdcf2b7d6bf7920d9d19d3418bf22e | Java | 12,679 | 402 | /*
* 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 cern.jet.stat.tdouble.Probability;
import umcg.genetica.containers.Pair;
import umcg.genetica.containers.Triple;
import ... |
4fd934bc1d1d0a801268f2d8ab387bc711c6b3f032e9b7f7d5d09d3a403ee73e | Java | 12,713 | 327 | 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.semanticweb.owlapi.model.OWLEntity;
import java.io.File;
import java.io.IOException;
import java.util.*;
public class N2O... |
c7ab25d1504819ed10ffe34455c0dd78ac6f0ec6cc36c591a842844d62a7a6e2 | Java | 12,796 | 433 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics;
import java.awt.*;
import java.io.File;
import java.awt.geom.*;
import java.awt.image.*;
/**
*
* @author harm-jan
*/
public class Graphics {
private com.itextpdf.text.Do... |
265ab6bb2118552ea7d3beddc8cf533b1fac48c24da39d3534ada6bcca3c8d00 | Java | 12,820 | 337 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix;
import java.io.*;
import java.util.*;
import org.apache.logging.log4j.Level;
import umcg.genetica.graphics.ForestPlot;
/**
*
* @author lude, juha
*/
@Deprecated
public class DoubleM... |
ec4a2318b23e6298493c6c702c13ad7e31b963786f8dd392ea38f2773e6a9526 | Java | 12,833 | 361 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import ... |
567191053349af526bea33cd1111727f700d4a0ee7987abd7d81b1a52db802a2 | Java | 12,851 | 434 | /*-
* #%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... |
a2216c7018c6cadaa5aa455c7a318d9f49331e90bdf9a1a1c00f0bd3f8790552 | Java | 12,882 | 441 | /*-
* #%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... |
d598aac0420576746a9d7a1fc3e79dc722a4eb917ed080638cfaaaecee3eaf8b | Java | 12,896 | 396 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.containers.Triple;
import umcg.genetica.enums.SNPClass;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import umcg.genetica.graphics.themes.DefaultTheme;
import umcg.genetica.math.Gon... |
6bd4f077f10cf754bfa4b7a02fa726d08989007a82081082e4127744fd3dcc5e | Java | 12,988 | 325 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.stream.IntStream;
import com.google.common.util.concurrent.AtomicDouble;
import org.apache.commons.collections.pri... |
b4710c050cb1f20e1d9902bd888d80b5d7eb3e1b6e649742bb4cce7c3dbae8be | Java | 13,002 | 380 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatr... |
f8dbe9ddd33981f08500d1291dab19b1b1c922002f8356478fce87c6d5f3aae3 | Java | 13,035 | 350 | package eqtlmappingpipeline.binaryInteraction;
import au.com.bytecode.opencsv.CSVReader;
import eqtlmappingpipeline.Main;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import... |
0090eec44377466e6d8d6a698a92772cc49fd0188e7ed11b9d79fb29ba67a227 | Java | 13,111 | 362 | package nl.systemsgenetics.downstreamer.runners.options;
import org.apache.commons.cli.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.File;
public class OptionsModeRegress extends OptionsBase {
private static final Logger LOGGER = LogManager.getLogger(Option... |
e0e22202dae6f185f49a2c1320ecb7cf0d42de68c4675cb9e71d404f76028dd3 | Java | 13,140 | 391 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics.map;
import eqtlmappingpipeline.graphics.Graphics;
/**
*
* @author harm-jan
*/
public class Heatmap extends Graphics {
protected int r, g, b, a;
protected boolean useAlp... |
1957836a171e962fbed7041dd428cef4e3bf46888e62b3a937bef4f5b249f4b5 | Java | 13,177 | 394 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.molgenis.genotype.Allele;
import org.molgenis.geno... |
d548062ea35f2a46bda18cd5602156d4c29a269c171b23c574edcd5f258a6cec | Java | 13,181 | 264 | package edu.cmu.cs.eyetrack.state;
import java.awt.Color;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Random;
import java.util.Set;
import javax.swing.ImageIcon;
import ... |
f0cf888b9185f2cbf37bcd5b64f2ff6f19fefcf694ada891e6e17326e3d95f3d | Java | 13,203 | 449 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import umcg.genetica.math.stats.Descriptives;
import umcg.genetica.math.stats.HWE;
/**
* @author harmjan
*/
public class SNP {
private byte chr;
private int chrPos;
pri... |
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