sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
aebcc12e64c82cc246ad1e70f86a54483c41e36579fdd87c23618f715381b85a | Java | 3,465 | 116 | /*-
* #%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... |
842230e9cea7330ba137982f88241699c6301233d36abd4a796060b5a916b711 | Java | 3,469 | 120 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.bin;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.EOFException;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
... |
66d2467ef65df8524329df0ded4d5d79ae5c60bdf21d57264e8a364ce006f905 | Java | 3,471 | 86 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.methylation;
import java.util.ArrayList;
import org.apache.commons.collections.primitives.ArrayDoubleList;
import umcg.genetica.math.matrix.DoubleMatrixDataset;
/**
*
* @author MarcJan
*/
publi... |
9f6361db7cd99e93086cffe491b8ecb1e5535280e4035490583504ca27ce25b2 | Java | 3,473 | 108 | //******************************************************************************
//
// File: NumericRuntimeException.java
// Package: edu.rit.numeric
// Unit: Class edu.rit.numeric.NumericRuntimeException
//
// This Java source file is copyright (C) 2007 by Alan Kaminsky. All rights
// reserved. For further infor... |
dd5dbbfa31b35e6da6ce2e1e7205b8ce4b9c946787b042446ad6f83f919556ec | Java | 3,485 | 95 | package ebi.spot.neo4j2owl.importer;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.io.FileUtils;
import org.json.JSONObject;
import org.yaml.snakeyaml.DumperOptions;
import org.yaml.snakeyaml.Yaml;
import java.io.*;
import java.util.Array... |
03875d288f87dc60c3991cd0ee2fdcfc7fed3f9f86418b25453d3cd5f3e0de65 | Java | 3,493 | 86 | /*-
* #%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... |
2c66b901f2acbc2518a9558436f63ae4c7e9c4b976e634adee46bddf090ed7f5 | Java | 3,503 | 198 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.bin;
/**
*
* @author harmjan
*/
public class BinaryResultSNP {
private String name;
private Byte chr;
private Integer chrpos;
private Integer numsamples;
private ... |
66a05cbe0f4367c6c36fce1fe54efd42888dd95d1c2167293bd62b0325c479ff | Java | 3,514 | 95 | /*-
* #%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... |
34a778ec4b38e83844f7abbd8a6f6134a249cc31ef9e2f59afece6f43d8f24f8 | Java | 3,517 | 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.eqtlannotation;
/**
*
* This format is used to provide called peaks of signal enrichment based on
* pool... |
fc6f6be3b66e04c6d7de8e8651c4cb83738e2a768804f13890a1d5e6c0d784c5 | Java | 3,520 | 112 | /*-
* #%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... |
c87989a0ca5214ac7c397812c43c09383208df1cff7b05c72cc0639be3771a40 | Java | 3,521 | 71 | /*-
* #%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... |
ea8119562d3e8b69c6ff84677d3a7c5685ffdc28ca13b322c6261af6a490d6cd | Java | 3,526 | 135 | /*
* 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.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
import umcg.genetica.io.text.TextFile;
import umcg.gen... |
d5a5a5c84de315cb5a2e481da489f95c9a793718c9da934eafc5acefe0daaa7c | Java | 3,538 | 135 | package org.molgenis.genotype;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import org.molgenis.genotype.annotation.CaseControlAnnotation;
import org.molgenis.genotype.annotation.SexAnnotation;
public class Sample {
private final String id;
private final String familyId;
... |
eb3ccb209e9eb2ee0f5a222bb4eeaeacaa66a1262e2ff1375ec7f5d163d86839 | Java | 3,541 | 80 | /*-
* #%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... |
ee02388e87d0e8a9f1fbecd8138c9a2fc49fd79ad962c24402d84874bb7e52d2 | Java | 3,552 | 123 | /*
* 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.options;
import java.io.File;
import static nl.systemsgenetics.downstreamer.runners.op... |
465cd573d7e0f3d02cc5cb4627573b037c00227976b2f759e299dfe5320503c9 | Java | 3,556 | 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.div;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
2ea347bc358a626ae1f3ab9bcf2c40da682fd18196e6e9a215e321fe10110f89 | Java | 3,560 | 102 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.concurrent;
import java.util.Set;
import java.util.concurrent.Callable;
import java.util.regex.Pattern;
import umcg.genetica.containers.Triple;
import umcg.genetica.text.Strings;
/**
*
* @aut... |
1102a0c64877314671a3fd0f8d900e515cb1257f09a47032c5e4b95c18fa2e37 | Java | 3,570 | 139 | package org.molgenis.genotype.tabix;
import java.io.File;
import java.io.IOException;
import java.util.Iterator;
import net.sf.samtools.util.BlockCompressedInputStream;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.VariantQuery;
import org.molgenis.genotype.VariantQueryResult;
impo... |
f214d7f0c39fb5ab86f6e0a31c5b5761ec8b75924709fe858a7e3d586e14fe8f | Java | 3,574 | 176 | package org.molgenis.genotype;
import java.util.HashMap;
import java.util.Map;
import org.molgenis.genotype.util.Utils;
public final class Allele implements Comparable<Allele>
{
private static Map<String, Allele> pool = new HashMap<String, Allele>();
private static Map<Character, Allele> snpPool = new HashMap<Char... |
1c2020bada883f8defc50115540d98e57ecef4e65a5bd11663163d1f374c0ddb | Java | 3,576 | 109 | //******************************************************************************
//
// File: TooManyIterationsException.java
// Package: edu.rit.numeric
// Unit: Class edu.rit.numeric.TooManyIterationsException
//
// This Java source file is copyright (C) 2002-2004 by Alan Kaminsky. All rights
// reserved. For fu... |
8bcab45229ba39b1bad7c1f514d7c91449430fb623985b1ebc5e36650efa5922 | Java | 3,577 | 91 | /*
* 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... |
03d9076225c36bcdeab4829621b3ea4b979b672b127e47f27900d092cc6cdcf2 | Java | 3,579 | 133 | /*
* WGAFileMatrixGenotype.java
*
* Created on July 9, 2007, 5:08 PM
*
*/
package umcg.genetica.io.trityper;
import java.io.File;
import java.io.IOException;
import java.io.RandomAccessFile;
import umcg.genetica.console.ProgressBar;
//import umcg.genetica.io.bin.RandomAccessFile;
/**
* @author ... |
87eccdc14d4830d13ea535ce92ababf5ba6e21420eca2f3448c90ce24d03511c | Java | 3,580 | 103 | /*-
* #%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... |
357349a25ff42572971e3bd5e9ebf6c12514c5137507bf6fb7bd795184dc766f | Java | 3,585 | 89 | /*
* 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.GenericPermuting;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
im... |
9314074c9bf8d0a0a1dc3d8597b263ed3ea4b423ef58eff4cb9df89136a71acf | Java | 3,590 | 154 | package umcg.genetica.graphics.panels;
import umcg.genetica.containers.Pair;
import umcg.genetica.features.Feature;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.Range;
import java.awt.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
/**
* Cre... |
a6d6c1e23ff670579045cd391b3a7c56fef14e038c50112ea3b1f94d0d583313 | Java | 3,594 | 83 | /*-
* #%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... |
a68bf36eeeb2444326e91b321f48741c90dbf898807f0582b843cad8fff64aa5 | Java | 3,616 | 88 | /*
## Copyright (c) 2019 Thomas Braschler <thomas.braschler@unige.ch>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later vers... |
5e234a8005a3e8d65147a660a97a4c398f2dd23f06d6eb919da0a65efc4f88da | Java | 3,631 | 100 | /*-
* #%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... |
819b05090bce236c932ce1f0b7cb8dbc830378e9abef9c3269ade76c74954f3e | Java | 3,639 | 83 | /*-
* #%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... |
7aca8cf23eb54190bbc6edf40e3fa15dcc8f0019196f1a87ce232ae0c25bf4a4 | Java | 3,640 | 118 | package umcg.genetica.genomicboundaries;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.TreeMap;
/**
*
* @author PatrickDeelen
*/
public class Genomi... |
9ed42ad19a6b0f836f63482015e87f19bf1cbcb64a1b0d72e3048f0c9a5dc2d1 | Java | 3,643 | 85 | /*
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2026 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must reta... |
a266aec9c92609789b4026b214fd9e007d55558766fede22dec9cede5c8fc21e | Java | 3,643 | 85 | /*
* #%L
* Utility classes for BoneJ1 plugins
* %%
* Copyright (C) 2015 - 2020 Michael Doube, BoneJ developers
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must reta... |
3f028a466391bf0dea75abb5171712d5f2c5f2e20a215179589f757183cdb2db | Java | 3,644 | 127 | /*
* WGAFileMatrixRawData.java
*
* Created on July 10, 2007, 11:15 PM
*
*/
package umcg.genetica.io.trityper;
import java.io.File;
import java.io.IOException;
import umcg.genetica.io.bin.RandomAccessFile;
/**
*
* @author ludefranke
*/
public class WGAFileMatrixRawData {
public int nrSNPs = 0;
public... |
975bca380aaace2b8fda6ba85ae0660d7e398ce89cbf47e82b71b0a2beb79448 | Java | 3,646 | 78 | package org.molgenis.genotype;
import java.io.File;
import java.util.EnumSet;
import java.util.regex.Pattern;
/**
*
* @author Patrick Deelen
*/
public enum GenotypeFileType {
BIM(Pattern.compile(".*\\.bim$", Pattern.CASE_INSENSITIVE), ".bim", "Plink bim"),
FAM(Pattern.compile(".*\\.fam$", Pattern.CASE_INSENSITI... |
cb0c009b236bbc8e9f30953f4913916875a960cbc321253cb6894428aa789b0a | Java | 3,649 | 126 | /*
* 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 cern.colt.matrix.tdouble.DoubleMatrix1D;
import cern.colt.matrix.tdouble.DoubleMatrix2D;
impo... |
7f3fc010f3eb1dc44518d9cd75f582bf5eb8f9abb4fdc0ffcfabe9e895d2a350 | Java | 3,652 | 175 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gwascatalog;
import htsjdk.samtools.util.Locatable;
import java.util.HashMap;
import java.util.HashSet;
/**
*
* Locatable is part of htsjdk allowing genomic interval and overlap operations
*... |
706d6c743ed33124f3894525b75401a90bacaf166739fd1bec038b74de868001 | Java | 3,657 | 106 | /*
* 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 umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.tri... |
4c4e7a5188649c379823da37266dd89016163e3b10ac9699eb25e3f92a393db7 | Java | 3,658 | 135 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
import cern.colt.list.tint.IntArrayList;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.var... |
8623a34a450a5a8c5ebe4cd8839e9b0d8aaf45fe2f225d7a7dfc9dd930356e8c | Java | 3,663 | 134 | /*
* 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 cern.colt.function.tint.IntComparator;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
impo... |
89a91d9f3ae703d38a0ded3329f7dd9c712f194b8de56c46f159a088deeaf163 | Java | 3,663 | 125 | /*
* SymmetricShortDistancaMatrix.java
*
* Created on 04 June 2004, 16:03
*/
package umcg.genetica.math.matrix;
import umcg.genetica.io.bin.BinaryFile;
import java.io.IOException;
/**
* Symmetric Short Distance Matrix: A memory efficient matrix capable of performing calculations on all genes x all genes:
*
*... |
c3e3060d54198dafc628910eb99303720914df60bf3cd8c5c6ea60350e995c86 | Java | 3,677 | 82 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer;
import java.io.File;
import java.io.FileNotFoundException;
import org.apache.logging.log4j.Lo... |
1118119cf1d12a27d98781063ce153ead24c4f85ba461deaf37918b9c665f229 | Java | 3,685 | 93 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
import java.io.BufferedReader;
import java.io.FileReader;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.... |
bf265222a7126d4fcc0609e3074bcc72390443dc32fa70d4c782ded434fb5492 | Java | 3,690 | 115 | package umcg.genetica.io.binInteraction;
import umcg.genetica.io.binInteraction.gene.BinaryInteractionGene;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant;
public class BinaryInteractionFileConstructorBuil... |
d0da16f4133525a3446563116b730a08a037ec8fb1276a095e910452b717fad8 | Java | 3,692 | 123 | package eqtlmappingpipeline.ase;
import au.com.bytecode.opencsv.CSVWriter;
import cern.colt.list.tint.IntArrayList;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.util.ArrayList;
import java.util.regex.Pattern;
/**
*
* @author Patrick Deelen
*/... |
78facede254c3020aa29d6304bdd74f1d2ade1d0fa769ecf8b387c78cb2820c6 | Java | 3,694 | 84 | /*-
* #%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... |
60016648837bc1b7717905dc17cdfcad5f62dda45d300fca8cbf76ba862b8192 | Java | 3,715 | 135 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
import org.molgenis.genotype.util.ChromosomeComparator;
/**
*
* @author harmjan
*/
public class MetaQTL4MetaTrait implements Comparable<Object> {
static boolean mapsToChrom... |
55e0166ec24eeece1ac9bc470b25ad12885473e5d6b8852d527d233de3ddc161 | Java | 3,719 | 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... |
17178b22ba5391078551e104154d2b3846d16d95bc1e047590853ddb077285f2 | Java | 3,720 | 142 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.console;
import umcg.genetica.util.RunTimer;
/**
* @author harmjan
*/
public class ProgressBar {
private RunTimer timer;
private long iterations = 0;
private long maxIterations = 0;... |
4599474ac03cfee067ed85436fdf60d428b8ccf0f2cf0a321a0052c080a80d7b | Java | 3,724 | 122 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.regulomedb;
import umcg.genetica.io.regulomedb.RegulomeDbSupportingData;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*... |
b8ae8b50340d0527c4a0b6f73caa5af03c95d0be5a3dabb58f80e0be6b6cc27f | Java | 3,730 | 120 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.cis;
import eqtlmappingpipeline.binarymeta.meta.MetaAnalysisCalculationThread;
import java.nio.ByteBuffer;
import java.util.ArrayList;
import java.util.HashMap;
import java.ut... |
6d08ee25f5cfd23fc991f0b2bfc6db19a34bb7f9ddcf2abfea0f9b872ec4760c | Java | 3,736 | 166 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
import java.util.HashMap;
import java.util.Set;
import java.util.Vector;
import umcg.genetica.util.StringIntegerObjectSorterSortOnInteger;
/**
*
* @author harmjan
*/
public class Tr... |
e4d40859a4717467073caf312ec58876dfda3b4866033ac80b2320f42a6ebb1f | Java | 3,742 | 136 | package org.molgenis.genotype.modifiable;
import java.util.HashSet;
import java.util.Iterator;
import java.util.NoSuchElementException;
import org.molgenis.genotype.variant.GeneticVariant;
public class ModifiableGeneticVariantIterator<E extends GeneticVariant> implements Iterator<E>
{
private final Iterator<Geneti... |
9dc53411000a88679f8ebf2c9955e1a3a959fc552e7685dda69df5d47951e655 | Java | 3,752 | 117 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.div;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import com.opencsv.CSVParser;
impor... |
ae3a1842e9e99ac53723f939b4199e04e49888082dfbf6658d9b1584c139714c | Java | 3,754 | 90 | /*-
* #%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... |
461f695657127f21d8b63ed1a1e6005833212a4f1b1a15f93c14f89be2209395 | Java | 3,756 | 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... |
720a320b7252569ffc8eba2f67a3b90c1fe5900edafd9c140141595e9ae65a83 | Java | 3,782 | 102 | /*-
* #%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... |
4d71960d71967036656563d4f5ed4eae18902b04959920e294aa890065415c0f | Java | 3,784 | 162 | package umcg.genetica.graphics.panels;
import umcg.genetica.features.Feature;
import umcg.genetica.features.FeatureTree;
import umcg.genetica.features.SNPFeature;
import umcg.genetica.graphics.DefaultGraphics;
import java.awt.*;
import java.util.ArrayList;
import java.util.NavigableSet;
/**
* Created by hwestra on... |
1adac78fb59d32d35963e7cc798cf87e127d8324a875959090f1f0732be520ea | Java | 3,795 | 112 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.div;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
ae548b562670dc6d7f95697807fd92aeea29aebf7c7a0b8b9c574480c04e76a2 | Java | 3,802 | 93 | /*-
* #%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... |
4b8686d6f7a9ebe3e8e506137fb1b246b183f5e18e99624ecda0dfa65af264d0 | Java | 3,810 | 108 | package org.molgenis.genotype.annotation;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
import java.util.HashMap;
import java.util.Map;
i... |
6cb29f714c0daf3552656927dcd8f29147ea19d9daa7ce1f03bbc07413914ca9 | Java | 3,818 | 102 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.util;
import java.util.ArrayList;
import static org.mockito.Mockito.mock;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.DummySample... |
3f4d71b6dcb302726dc9aaf673713d74ab3186a227e1e93b2009ab784d32173e | Java | 3,827 | 126 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.editable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import... |
f941889ef47bc2293714e66e31feb4f99a5630dc2627fa55caa134f94881e2c2 | Java | 3,828 | 115 | /*-
* #%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... |
0150312eb4f48287d317d64f884b5c1b41a3db8ebfae11e7f0cd8d49341dc9b6 | Java | 3,829 | 179 | package edu.cmu.cs.eyetrack.analysis.struct.trackit;
import java.util.List;
import edu.cmu.cs.eyetrack.analysis.struct.Trajectory;
import edu.cmu.cs.eyetrack.helper.Coordinate;
public class Trial {
// Individual headers/specifiers for the trial
private int id;
private long length;
private long startTime;
priv... |
1a5d3bbda069b4530dc2dda749987db778deae3c8fc4723b068c59e55dc67fa0 | Java | 3,834 | 96 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline;
import java.io.File;
import java.net.URISyntaxException;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Iterator;
import static org.... |
4a37bcc323ef8c4fc90506046ef32622a4f0f7a08c24ce73914ae63fb8bee943 | Java | 3,838 | 133 | package umcg.genetica.io.pileup;
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.io.UnsupportedEncodingException;
import java.util.Iterator;
import java.util.regex.Pattern... |
4d05cfc3f2ea4706b2faaad7e1df8297714ea3727432a19ef165ff309ad2cc3d | Java | 3,843 | 172 | package org.molgenis.genotype;
import java.io.File;
import java.net.URISyntaxException;
public class ResourceTest
{
public File getTestResourceFile(String name) throws URISyntaxException
{
return new File(this.getClass().getResource(name).toURI());
}
protected File getTriTyperFolder() throws URISyntaxEx... |
db9c38034b5a3c2d04c9376df4b72ac60fbc4a903a52d536acaf9ea9c8f578fa | Java | 3,847 | 154 | 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.List;
import java.util.NoSuchElementException;
imp... |
6ee6842823f849687494ce174bf4e4e468777d0d9ed546834b4cc85c064e6a47 | Java | 3,856 | 140 | /*
* 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.enums;
/**
*
* @author Harm-Jan
*/
public enum ChromosomeUCSC {
ONE(1, "Chr1", 248956422),
TWO(2, "C... |
e83c1774d88d91eba9c25a0d3cbfceb107333e08c17bd5af9acd9f98c643cf6c | Java | 3,872 | 133 | /*-
* #%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... |
9b07eb0bb433a5df1a4bdc1a06ee79ced0554ca38208250284b32d99aaa03202 | Java | 3,877 | 145 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.molgenis.genotype.AbstractRandomAcce... |
322e589b87279735b2710ccdd4475b9cef352d44272a581655671859362db76c | Java | 3,879 | 149 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.umcg.westrah.binarymetaanalyzer;
import umcg.genetica.io.trityper.util.BaseAnnot;
/**
*
* @author harmjan
*/
public class QTL implements Comparable<QTL> {
private double pvalue = Double.MAX_VALUE;
... |
4b90043aa2fdd5ad723167e3c2a47e8ff8c607611167ea4e0fe0c806f3871a36 | Java | 3,879 | 102 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.ucsc;
import java.io.IOException;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.ChrAnnotation;
import umcg.genetica.text.Strings;
/*... |
9e4bd93920943df5fd6af3c2965b6b33922c7b2b9af9e20f1033097f5e7253b4 | Java | 3,889 | 129 | /*
* VectorSorter.java
*
* Created on 23 December 2003, 17:02
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
import java.util.*;
import java.io.*;
/** An implementation of a quick sort algorithm.
*
* Shamelessly taken from Martin Senger's (senger@ebi.ac.uk) Java colle... |
f2b4d6a6122853b5be32fba0094ea394729072f2c7c775c81d282e2617d6de31 | Java | 3,889 | 108 | package nl.systemsgenetics.geneticriskscorecalculator;
import java.util.ArrayList;
import java.util.List;
import umcg.genetica.io.text.TextFile;
import java.util.regex.Pattern;
import java.io.File;
import java.io.IOException;
/**
*
* @author Patrick Deelen
*/
public class GwasCatalogLoader {
private static fi... |
af9bfdd1e3ba8c551ea977226d32f80949b8f4026b781a5474c4ce2024a9edc1 | Java | 3,892 | 174 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl3.containers;
import umcg.genetica.io.trityper.SNP;
/**
*
* @author harmjan
*/
public class WorkPackage implements Comparable<WorkPackage> {
private SNP[] snps; // 1 s... |
60e89a59eb48f393e4e6b9de370822737c7beffc2baec6976358be279cea1bef | Java | 3,897 | 91 | /*-
* #%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... |
8aba8e166fa7ab87cf995d8ee0e654cf075641be8793bd4a8b72d3eb3dfdd7ba | Java | 3,897 | 91 | /*-
* #%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... |
fced89717ef247148c9ec1de9aa2cb66b645afa3d1a64c623deb1bb0668604b9 | Java | 3,915 | 87 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.examples;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.HashSet;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.... |
d45942ecc21c17a9818fcf3e79e7aae47c302a7081bc1a8e6093b19d93b02e1e | Java | 3,918 | 106 | /*-
* #%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 ... |
ef2ab9ef8acfd6828a60848e261d6daa29076bdbbcc722252eaa2dfd844f154f | Java | 3,939 | 141 | package org.molgenis.genotype.vcf;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.varian... |
316dbec3e7e0125b1c38b278f25e2fab4e6aa8d5db5addbbf0035f479b3e85d2 | Java | 3,946 | 210 | package org.molgenis.genotype.variant.id;
import java.util.List;
public abstract class GeneticVariantId implements Iterable<String>
{
public static final String DEFAULT_ID_SEPARATOR = ";";
public static final BlankGeneticVariantId BLANK_GENETIC_VARIANT_ID = new BlankGeneticVariantId();
/**
* Get the Id as str... |
80b94587c355930f391129c1bde8aa28f8eccfb0f5062949c7f5853822d153c1 | Java | 3,949 | 221 | package umcg.genetica.graphics;
import JSci.maths.ArrayMath;
/**
* Created by hwestra on 7/16/15.
*/
public class Range {
private double maxX;
private double maxY;
private double minX;
private double minY;
private Double unitY;
@Override
public String toString() {
return "Range{" +
"maxX=" + maxX +
... |
c8e9dc84c6dcd752f7125f177296daa929cf8b4cb0bc8b36afc683432e81afbb | Java | 3,952 | 138 | package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.ProbeAnnotation;
import java.io.IOException;
import java.util.HashMap;
import java.util.HashSet;
public class ExpressionSampleFilter {
public void filter(String efileIn, String efileOut, String sampleList) th... |
3a9424acda91abcf8f4300f72e135bfc5a8a4f48e64d152ef22e0bb5a9d811c9 | Java | 3,968 | 195 | package nl.systemsgenetics.downstreamer.summarystatistic;
import htsjdk.samtools.util.Interval;
import java.io.Serializable;
/**
* The type Snp.
*/
public class SNP extends Interval implements Serializable, OverlappableGenomicRange {
/**
* The primary variant id.
*/
protected String primaryVaria... |
74c3bc7dd7fbbdb39269fc3ced1817f4cd0a1ca41df31826612e88681720319f | Java | 3,979 | 135 | package eqtlmappingpipeline.util;
import com.mastfrog.util.streams.HashingOutputStream;
import umcg.genetica.console.ProgressBar;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
public... |
4d17d2c93c7a131e558a844ab9f3416e93237c1cb4fad7c1c7e140cbef616aba | Java | 3,996 | 168 | /*
* 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 transeqtlcrossmap;
import umcg.genetica.enums.Chromosome;
import umcg.genetica.enums.Strand;
import umcg.genetica.text.Strings... |
ca8fb82b3c167b18064751e854118267e97efbd2838ee6b34af4d992aaf471dc | Java | 4,005 | 130 | package org.molgenis.genotype.plink;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.... |
25f5bf3e8ff7e7cabb85b3d12c38e2f37ad00a2566f357fe920d968ef788b859 | Java | 4,009 | 164 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import java.util.HashSet;
import umcg.genetica.io.trityper.EQTL;
import umcg.genetica.io.trityper.bin.BinaryResultSNP;
/**
*
* @author harmjan
*/
public class MetaAnalysi... |
158c3daefa3e1a9bb60c5cde8c159341ecb09e13616fb202bafe36a9d371aaad | Java | 4,010 | 98 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math;
/**
*
* @author harmjan
*/
public class PCA {
private Jama.EigenvalueDecomposition eig;
private double[][] eigenVectors;
public void PCA() {
}
public static Jama.Eig... |
ad49681ce2b8e058a97eaefde92a37400c13fd62e50d14e45553b428f92619d7 | Java | 4,010 | 100 | /*-
* #%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... |
c9dac03760a2ce780dd24ee06c43482f78c072b26bbc84cab2e29c3188fb3e71 | Java | 4,011 | 130 | package org.molgenis.genotype.plink;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.... |
3687756e4c110928a2d69349476cbe7c153a0bec40d8995b79836fd78d378be8 | Java | 4,014 | 119 | /*
* 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.io.RandomAccessFile;
import org.molgenis.genotype.ResourceTest;
i... |
9c5fda58569112fa742eb483ea13cdf2d7c146d7d5c5d7da482f5489d77a5e26 | Java | 4,016 | 130 | package org.molgenis.genotype.plink;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.... |
6aab4e81746c5b832ce15e382f57d385474566cfaa4da73437dccecc574564e0 | Java | 4,021 | 103 | /*-
* #%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... |
bc4e077aacf7d227f1d6104724b0cf1ac1ca3a7f530262caab50af38cb0c6f0f | Java | 4,024 | 100 | /*-
* #%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... |
cbc2b73858735f3b572e5aa18a4bc5e6b5e2adadf9530871b86ceeeb8e7aa965 | Java | 4,036 | 134 | /*-
* #%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... |
d195c610b593a53758fd5488eba946fe0ac6047410e1682e3280f9cc041c052c | Java | 4,045 | 127 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.pileup;
import org.molgenis.genotype.Allele;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotatio... |
5c90566de0464b8e6a6637e20179a819f731703c322ec6f477b52a99f32580e3 | Java | 4,070 | 107 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.causalinference;
import umcg.genetica.console.ConsoleGUIElems;
/**
*
* @author harmjan
*/
public class IVConsoleGUI {
public IVConsoleGUI(String[] args) {
String settingsfile... |
330066a88a329c86f436b8007ae2a98d341c906d5e136b2c580d4f7c32955230 | Java | 4,071 | 124 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
import java.io.BufferedReader;
import java.io.File;
import java.i... |
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