sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f9e82618b707f5d5a90d5e95624589f2240c020b4ed923e481673a95fcb1dcb1 | Java | 1,788 | 53 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.geom.GeneralPath;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew9Stimulus extends Stimulus {
private static double kappa = 0.5522847498;
private int radius; // Radius of the little bump circle
pu... |
e2188a40505d7772c91b03de134a1d88da4e7ac8dfcab1ba3cab5f82b9c47b7f | Java | 1,801 | 95 | package org.molgenis.genotype.plink.readers;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.Charset;
import java.util.Iterator;
import org.molgenis.genotype.plink.PlinkFileParser;
import org.molgenis.genotype.plink.datat... |
693d32e46b094350e17bf6bf178002af42875db5302e21be96110b0f6a7bbfd7 | Java | 1,810 | 92 | package umcg.genetica.graphics.panels;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.themes.DefaultTheme;
import umcg.genetica.graphics.themes.Theme;
import java.awt.*;
/**
* Created by hwestra on 7/15/15.
*/
public abstract class Panel {
protected int width = 0;
protected int hei... |
df0817fe045ade3182d7a7f223d7709a8bf9c43cd96db3d7984e49568edf7ddf | Java | 1,818 | 61 | package org.molgenis.genotype;
import org.molgenis.genotype.bgen.BgenGenotypeData;
import org.molgenis.genotype.bgen.BgenGenotypeWriter;
import org.molgenis.genotype.oxford.GenGenotypeWriter;
import org.molgenis.genotype.oxford.HapsGenotypeWriter;
import org.molgenis.genotype.plink.BedBimFamGenotypeWriter;
import org.... |
6682fa13e746948c6ee05f2cf5d51e9eb031c5cf4a22e36164c3b94ba7437610 | Java | 1,821 | 45 | /*-
* #%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... |
ad5873d665517897dbf6f5d6e97e7f0d821315620d17b584b3d2d72007af9372 | Java | 1,821 | 45 | /*-
* #%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... |
7028f17255a5541fdb1b3dc873cc268d0d7ad5bb1b57c81a3a61803b2bfd365e | Java | 1,826 | 76 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.util.Arrays;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
*
* @author MarcJan
*/
public class SmoothS... |
97b8517897275c7bb0bc212027e582295ab219b34edf4c75cc4a3d805dfecfc6 | Java | 1,828 | 51 | package org.molgenis.genotype.variant;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
import static org.testng.Assert.assertEquals;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.molgenis.geno... |
6c4ec0c2075db86fe4a8c4c370408566650f893af02d595a2fac0547bf76821a | Java | 1,831 | 83 | package umcg.genetica.io.fasta;
/**
*
* @author Patrick Deelen
*/
public class LargeByteArray {
private final byte[][] data;
private long size;
private int blockSize;
private static final int MAX_BLOCK_SIZE = Integer.MAX_VALUE - 8;
public LargeByteArray(long size) {
this.size = size;
long blocks = size... |
8b02e05196961582813bf32e66a2be9d868d97a2c72145223e35b56ccf1cd04b | Java | 1,836 | 79 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression;
import org.ejml.simple.SimpleMatrix;
/**
*
* @author adriaan
... |
abcbd70886b909b99c49ac5b20995cda7c0258a9b57ea2c53e3115e38e15645d | Java | 1,846 | 85 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.pathway;
import java.io.File;
import java.util.Objects;
/**
* @author patri
*/
public class... |
05513edcefec6c11b9379098aaf2353ec168e9dec33e0ee777fc00cc08fb0b34 | Java | 1,856 | 86 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.util;
import java.util.ArrayList;
import java.util.List;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.molgenis.genotype.Allele;
import org.... |
a755f16417629daaba36d0e35b62a824ee8c167d710b7d5831a755bbc3f65bb0 | Java | 1,856 | 63 | package umcg.genetica.io.gmt;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import umcg.genetica.io.text.TextFile;
/**
*
* @author harmjan
*
* $LastChangedDate: 2012-08-24 11:50:07 +020... |
e280e5339a98859442c8dd3ddafe5fff7839c523bf9b0b3fea11376c4f9ccadd | Java | 1,857 | 81 | package edu.cmu.cs.eyetrack.helper;
public class Coordinate<E extends Number> {
private E x;
private E y;
// Since we use timestamps so much in Track-It, just roll it into the coordinate
private long timestamp;
public Coordinate(E x, E y, long timestamp) {
this.x = x;
this.y = y;
this.time... |
06cdcd384546b26e52289411e27b4d155f87e68e5aee57f780e5f9c9a9f13477 | Java | 1,859 | 64 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.util;
/**
*
* @author harm-jan
*/
public class ChrAnnotation {
public static byte parseChr(String chrStr){
byte chr = -1;
try{
chr = Byte.parseByte(c... |
93e17cc9c722bfd0d1e9c29e0dbf403530e4be88587c42c5246a39a61ddd0c84 | Java | 1,861 | 67 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.stats;
/**
* @author juha
*/
public class Binning {
public static int[] getBins(double[] data, double min, double max, int nrBins) {
int[] bins = new int[nrBins];
doubl... |
28074c19cc93747d2b22c0eb55ad3586ac18cf0f32957ab65cfeec27c7a0a865 | Java | 1,882 | 68 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.EQTL;
import umcg.genetica.io.trityper.QTLTextFile;
import java.io.IOException;
import java.util.Iterator;
public class BHFDR {
public void run(String in, dou... |
6f0fd35e365bdbc599f471b9ca48821ef2882a66d3d1ad119ef8e335c9f28cfe | Java | 1,883 | 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.cellTypeSpecificAlleleSpecificExpression;
import org.ejml.simple.SimpleMatrix;
/**
*
* @author adriaan
... |
66bd8d9abb2bf90df2e3295546dd2da3649dc40017d4126f70b053800c699452 | Java | 1,884 | 70 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.molgenis.genotype.GenotypeDataException;
import org.molgenis.genotype.variant.GeneticVa... |
58e595179467089a1eb6d163a041ee60dd0f333c5568a6d05166233dfddfb256 | Java | 1,886 | 45 | /*-
* #%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... |
cb516b11a1da4fbb5871eadd1f104200d8462688222c2bbe6a5b1f3ed7023cd4 | Java | 1,888 | 51 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper;
import gnu.trove.set.hash.THashSet;
/**
* @author harmjan
*/
public class TriTyperGeneticalGenomicsDatasetSettings {
public String name;
public String genotypeLocation;
public S... |
1d250ec2bca904f113be5136ace18a205598fedf18afa232e21b1a3a8ce44542 | Java | 1,910 | 55 | /*-
* #%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... |
51f3d4dfa3848c13af9d14b71a478b8105075615031279a874066f2db1223a7c | Java | 1,911 | 44 | /*-
* #%L
* Utility methods 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 ... |
91432f56d7fcaecc9e0673f6b13088acd9ea0dea393fa77740e5b7ed5d4a458a | Java | 1,914 | 57 | package edu.cmu.cs.eyetrack.gui.shapes.sabine.part2;
import java.awt.Color;
import java.awt.geom.GeneralPath;
import edu.cmu.cs.eyetrack.gui.shapes.Stimulus;
public class SabineNew7Stimulus extends Stimulus {
private static double kappa = 0.5522847498;
private int radius; // Radius of the little bump circles
p... |
add1fb61460464278bfed53560eca5f57becdf6e45afdeced7a51f556d94eabe | Java | 1,917 | 69 | package edu.cmu.cs.eyetrack.analysis.struct.tobii;
import java.util.HashMap;
import java.util.Map;
import edu.cmu.cs.eyetrack.analysis.struct.Trajectory;
public class TobiiData {
private TobiiEventMap eventMap;
private Map<Integer, Trajectory<TobiiFrame>> trajectories;
public TobiiData(TobiiE... |
9951fec04af77e6aa37267d24a5c384fcaa01781e973746ce67cb114315843a5 | Java | 1,921 | 80 | package edu.cmu.cs.eyetrack.analysis.struct;
import java.util.Collection;
import java.util.Map;
import java.util.NavigableMap;
import java.util.TreeMap;
public class Trajectory<E extends Frame> {
private NavigableMap<Long, E> frames;
private long lengthMS;
private long rawTimestampStart;
public Tr... |
305434f70774a62c369b90ec64bf3695bf3aaaa2340e08f111e2ccda3dfeb1d8 | Java | 1,923 | 97 | package umcg.genetica.collections;
import com.google.common.collect.Iterators;
import gnu.trove.map.TIntObjectMap;
import gnu.trove.map.hash.TIntObjectHashMap;
import java.util.HashMap;
import java.util.Iterator;
/**
*
* @author Patrick Deelen
*/
public class ChrPosMap<E> implements Iterable<E>{
private final Ha... |
44e9b3c2e5c90d76fc7136b2e3e8f0ae1ee4000fca071477606d11ecb31d86c6 | Java | 1,925 | 80 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.util;
import java.util.Arrays;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
/**
*
* @author MarcJan
*/
public class inplace... |
816f0fe629e4a071f7430fa24b8d6efad7a6d63c14d59f02cc9cee61fda68912 | Java | 1,925 | 68 | package org.molgenis.genotype.vcf;
import org.molgenis.genotype.variant.GeneticVariantMeta;
import org.molgenis.vcf.meta.VcfMeta;
import org.molgenis.vcf.meta.VcfMetaFormat;
public class VcfGeneticVariantMeta implements GeneticVariantMeta {
private final VcfMeta vcfMeta;
private final Iterable<String> vcfRecordFor... |
b27914f2decc94b6f45a4ff5bdb854a854a7ea59bbbdc1547d90047b351faff3 | Java | 1,930 | 71 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.development;
import cern.colt.matrix.tdouble.DoubleMatrix1D;
import ch.unil.genescore.vegas.Da... |
d2823824fd620b9a1d25e051832aa30499d7e203353eeff789f57873d94a5cd8 | Java | 1,931 | 68 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.io;
import java.io.File;
import java.util.HashSet;
import java.util.Set;
import org.apache.log... |
6baf35ad6bac3b9e71546a9718054651493a7543269d6e094c37518f297f9da1 | Java | 1,932 | 81 | /*
* 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;... |
9f4e437a308237e2b3b41b1db928975ba323fe3510a6338b64fa0e5843dedfe9 | Java | 1,934 | 37 | /*
* 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 java.io.File;
/**
*
* @author patri
*/
public class CompareGenePredictab... |
20146d3a41a6008682f0fc6aba3304f5f66ba36825d11a65646975adfad7d062 | Java | 1,939 | 65 | package org.molgenis.genotype.util;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.util.List;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeDataException;
public class MafCalculator {
public static MafResult calculateMaf(Alleles alleles, A... |
982758f95beb0b1087cba82bc3c84de20f754344bfe5f7edc2bad63ffafb0ad3 | Java | 1,941 | 56 | /*-
* #%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... |
0aaf908bfad01c9d15fd3a5c4cd48a3da7afdf1d400efd20157aadccba0fb6f2 | Java | 1,959 | 53 | /*-
* #%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... |
d58e8163d1bdabdbce212c91a4fed81debeda02ae0f3b696b46afe152cee8ef5 | Java | 1,959 | 53 | /*-
* #%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... |
81f947c83dc33575d4ba78078d5a0f5834993c9d17519ed8e1cc466864090ba2 | Java | 1,962 | 99 | package org.molgenis.genotype.snpeff;
/**
* Note: very incomplete
*
*
* @author Patrick Deelen
*/
public class SnpEffEffect {
//Enum code copied from: ca.mcgill.mcb.pcingola.snpEffect
public enum Coding {
CODING, NON_CODING
}
public enum EffectImpact {
HIGH, MODERATE, LOW, MODIFIER
}
public enum Ef... |
de6597b8a4742f829290e1734f1f314d2173ccd58a2b32b135d4f773ee8350bd | Java | 1,973 | 83 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
imp... |
df69a391a6287c13107b077f14060654e0673de97a2d8b55dcb017290c07df97 | Java | 1,982 | 59 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc;
import nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysis;
import nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysisSettings;
import java.io.IOException;
import java.util.ArrayList;
public class IndependentDatasetAnalyzer {
publi... |
c5d8ebe6448776935e14cf5ce157ac3c2b3e3a4508d186f214be8aae920df01b | Java | 1,991 | 54 | /*
* 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 PathwayEnrichmentRestuls;
import java.io.File;
import java.util.HashSet;
import java.util.Set;
import nl.systemsgenetics.downs... |
46bd9796bba5cc2ce190b4870159a958e78726ff062ffbde6511fafa9774cf7c | Java | 1,993 | 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.cellTypeSpecificAlleleSpecificExpression;
import org.ejml.simple.SimpleMatrix;
/**
*
* @author adriaan
*... |
98d7f3a1bc7ff310f103502a2cbaf18333af6e5212a70fbe08b9c1a54a058efb | Java | 1,996 | 82 | package org.molgenis.genotype;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import org.molgenis.genotype.variant.GeneticVariant;
public class SimpleSequence implements Sequence
{
private static final List<String> CHROMOSOMES = Arrays.asList("1", "2", "3", "4", "5", "6", "7", "8", "9", ... |
7c2220847f872ba19eff58a864466592a8ca1b2a67c861f94bfd8c89efe6aa6b | Java | 2,002 | 61 | /*-
* #%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... |
fa1e6f98c156110e98b09d7dc235824b897e7cbe3d677505ef4d6309b8633ed8 | Java | 2,005 | 62 | package ebi.spot.neo4j2owl;
import java.io.PrintWriter;
import java.io.StringWriter;
public class N2OLog {
//private Log log;
private N2OLog() {}
private static N2OLog n2olog = null;
private long start = System.currentTimeMillis();
public static N2OLog getInstance() {
if(n2olog==null) {... |
f476a5f6e80b2d7f4b54d04a384ba5e4b9165a3ae2877892274e3e395261539a | Java | 2,007 | 54 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
2e6fb74c1ab0f479f7d3284240b3507c6f6f6664f1888be35e37ad79ebf823c9 | Java | 2,009 | 63 | package nl.systemsgenetics.downstreamer.runners.options;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.ParseException;
import java.io.File;
public class OptionsTesting extends OptionsBase{
pr... |
5fc43d48e942ce604e719a21e443d0cd2355b4ac14f1a6d00e9d6146e71730a5 | Java | 2,016 | 51 | /*-
* #%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... |
9af413c49ba1c1042028489232ba0728a7a92a70b1b58181f82d311552f4d134 | Java | 2,016 | 61 | /*-
* #%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... |
271b428182d24920885985df87aad86bbcde955887bbc17b14b9ab3cc471ca52 | Java | 2,023 | 70 | package umcg.genetica.graphics.panels;
import umcg.genetica.graphics.DefaultGraphics;
import java.awt.*;
import java.text.DecimalFormat;
public class LegendPanel extends Panel {
private double min;
private double max;
private double avg;
private int n;
public LegendPanel(int nrRows, int nrCols... |
a8939bfbdae155f848139a8a0be8274f49ebab15f2e41dbc62ddd32d7a0846e3 | Java | 2,027 | 63 | /*
* 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 java.io.File;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Before... |
8b5728f550ecac8ad0c3e295fbf7b0c0a2496d10fc83ed2bfde7a0ee5f70cb3a | Java | 2,035 | 55 | /*-
* #%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... |
9a9fb387e50c62f2b62a7d5709b8a211d55b4b17ec94669a19ac472cb9ddebae | Java | 2,047 | 82 | 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 BatchSplitter {
public void splitPhenotypePerChr(String matrix, String probeAnnotation, String out... |
4897c78daeec59951cdcaee84e015aa08736540c7713f28d495136e05c2b0940 | Java | 2,051 | 50 | /*-
* #%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... |
83b9a94157cacad1a03e00c698920a44d101352634d1d10087de8d64d54ea381 | Java | 2,051 | 50 | /*-
* #%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... |
5f4481aa0fe827ab9fa9e45602abcf2359c9c71a06f2bb7c1356ac1600427b03 | Java | 2,055 | 66 | /*-
* #%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... |
74e48edc22e8715e1c4da4b9979853142a74981ba3e542a7230816c0c0726eab | Java | 2,056 | 64 | package ebi.spot.neo4j2owl.importer;
import ebi.spot.neo4j2owl.N2OConfig;
import ebi.spot.neo4j2owl.N2OLog;
import ebi.spot.neo4j2owl.N2OException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import java.io.File;
import java.io.IOException;
import java.util.concurrent.E... |
14eb352a5ba74f00ec151fd4a9873ef84763c49c12a61b9e13ba75154cb3a56e | Java | 2,060 | 62 | package umcg.genetica.io.binInteraction;
import java.io.IOException;
import java.util.Iterator;
import java.util.NoSuchElementException;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionCovariateIterator implements Iterator<BinaryInteractionQueryResult>{
private final String variantName;
private ... |
46f38b4d520f21ab9e6c7295562f179983bd8060527ea62018c4cc66b419347c | Java | 2,062 | 81 | /*
* 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.util.regex.Pattern;
/**
*
* @author MarcJan
*/
public class SNP {
priva... |
fb4d50ad31d546878bf263fcb37a0c88e77f17cd5c77d2210b0e398a81a845dd | Java | 2,077 | 64 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package imputationtool.postprocessing;
import java.io.IOException;
import umcg.genetica.io.text.TextFile;
/**
*
* @author harmjan
*/
public class TriTypertoPedMapDatExcludedSNPAnalyzer {
public void printSNPsWi... |
ecbeb0c862e91cef2ed34ad22382aaca024401994beeb501df6ff9b6e6b0736d | Java | 2,081 | 81 |
/*
* @Author: Onetism
* @Date: 2020-11-26 18:55:12
* @LastEditTime: 2022-08-21 09:48:08
* @LastEditors: onetism onetism@163.com
* @Description: In User Settings Edit
* @FilePath: \Auto_LF_Deconvolution\src\test.java
*/
import ij.*;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event... |
c15c7016c77cca98aac5abdea74d4de7d1593bc4aa0ac1fe6d15d19d1c8035a4 | Java | 2,084 | 122 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.trityper.bin;
/**
*
* @author harmjan
*/
public class BinaryResultProbe {
private int id;
private String name;
private Integer start;
private Integer stop;
private Byte ch... |
f87f409296027de3129e6220abd74ea2ed462c70748b80bdf706534c9b43ccf9 | Java | 2,122 | 67 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
import gnu.trove.map.hash.TIntObjectHashMap;
import java.util.HashMap;
import java.util.Iterator;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.variant.id.GeneticVari... |
d3cb4aee1b45ce7567b499e0a2500f44df64b5eedb3049915a62e332a94d8b32 | Java | 2,129 | 61 | /*-
* #%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... |
87846b807524778831d10a082acb9227bdc734ee4f1d529910a294db7f9812ce | Java | 2,130 | 53 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend;
import java.io.File;
import java.io.IOException;
import umcg.genetica.math.matrix2.Doub... |
7e5b84a3d3f2ee7bbe411ee153431f2e4159e36d86c0052bf5ace4889b051222 | Java | 2,135 | 76 | package umcg.genetica.collections.intervaltree;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import umcg.genetica.variantAnnotator.GenomicRange;
/**
*
* @author Patrick Deelen
*/
public class PerChrIntervalTree<E extends Range> {
private final Class<E... |
c7b4b25e616be9aea1428f5a00ce197beafb32062f4bca9fff40a8f77ba4bf0d | Java | 2,137 | 68 | package umcg.genetica.math.stats;
import JSci.maths.statistics.NormalDistribution;
import org.apache.logging.log4j.Level;
import umontreal.iro.lecuyer.probdist.AndersonDarlingDist;
/**
*
* Anderson-Darling test for normality. Uses SSJ (GPL) for A-D distribution.
*
* http://en.wikipedia.org/wiki/Anderson%E2%80%93... |
04a879002d91010c4aba0fa14195bb500143e3b85a260a5fc69eb94fce11f866 | Java | 2,138 | 65 | /*-
* #%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... |
071f2f632c7fe8e736b49151d037303898acc22398b365eee4c29f181445d578 | Java | 2,142 | 102 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.stat.dist;
import java.util.Collections;
import java.util.ArrayList;
/**
*
* @author harm-jan
*/
public class Dist {
protected double max, min;
protected double var, s... |
0ebb491e0c470fe83389cac9912aa129eb16a541e8968fcffa9a70615ad0e8eb | Java | 2,145 | 88 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.util;
import com.google.common.base.Function;
import com.google.common.collect.Iterators;
import java.util.Iterator;
import java.util.List;
import org.molgenis.genotype.Alleles;
import org.... |
a3a959b0e08fa50eee29b05c1890043890dddc3f8d633b209484761971ec50c4 | Java | 2,145 | 70 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
import com.opencsv.CSVParser;
import com.opencsv.CSVParserBuilder;
import com.openc... |
05773c261a40b23dd6fcad57db350043cc83b89f5bac846f4e0db95ec8e16dce | Java | 2,146 | 71 | package org.molgenis.genotype.vcf;
import static org.testng.Assert.assertEquals;
import java.io.IOException;
import java.net.URISyntaxException;
import org.molgenis.genotype.Allele;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.ResourceTest;
import org.molgenis.genotype.variant.GeneticVariant;
im... |
02e46e6864bd5b8b08d78186364d35c243331eb3001b21b8f5be50fc95632019 | Java | 2,148 | 112 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
import java.util.HashSet;
/**
*
* @author harmjan
*/
public class Exon {
private HashSet<Transcript> parentTranscripts;
private Chromosome parentChromosome;
private int ... |
64c5ad097f9ab0566b678aea63938aaa743d89e856c6cae9c2f71196e6955cee | Java | 2,155 | 67 | /*-
* #%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... |
3a4565478c72418e9ac9916628fe1b79afe1667a2ce90eed53262077b84f6533 | Java | 2,156 | 61 | /*-
* #%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... |
2852f82fb3c3e61734cfb8417fd6277bb6ae7a3e1a03956276d21b032d58b745 | Java | 2,157 | 73 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variant;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import org.molgenis.genotype.GenotypeDataException;
/**
*
* @author Patrick Deelen
*/
public class... |
b2fb5f982fa3dcb3b0bb626d14c1052812607d592e3b782458c1da269edbd438 | Java | 2,159 | 58 | /*
* 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 static org.testng.Assert.*;
import org.testng.annotations.Test;
import umcg.genetica.math.ma... |
5f49e7eb4144a26a55fcf47e839a236ee365c869371f732e4f73479098f3ad8e | Java | 2,170 | 57 | /*-
* #%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... |
9db20f93c86d0a8e2325bd2b5a3bc200c456a578fbac6eb44ea0c35e25a1e7b6 | Java | 2,174 | 86 | /*
* 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 static org.testng.Assert.*;
import org.testng.annotations.AfterClass;
import org.testng.annot... |
81d3196992a5b1fe87756478672acff11c070f6147574e4247470b481b4d5a8e | Java | 2,180 | 50 | /*-
* #%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 ... |
bc1ad86d3e673023bf928108bbae8e6606494b0abb168d05e5ea5e7ba4fb23e2 | Java | 2,180 | 50 | /*-
* #%L
* Utility methods 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 ... |
a50f92514ccdcb53d5ae0dd30729b4148f423b730b4af422c6e0180bf3a403c5 | Java | 2,183 | 71 | /*
* 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 java.io.File;
import static org.testng.Assert.*;
import org.testng.annotations.BeforeClass;
i... |
d7fbb0fffb22a37b0c90a9e2bde01236f716eed73974d68e91ca1c156a052eb2 | Java | 2,183 | 70 | /*-
* #%L
* Triangulated surface for deforming in 3D.
* %%
* Copyright (C) 2013 - 2023 University College London
* %%
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restricti... |
9d70c472d74346f057618627398cdf93fae9465b082ce1302db3a67061602029 | Java | 2,185 | 58 | /*-
* #%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... |
5569ab1840bd64841d23b23edcda296bba5d10fa6bd303e729a82bb294776e08 | Java | 2,193 | 85 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.table;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import org.molgenis.genotype.Alleles;
import org.molgenis.genotype.GenotypeData;
import org.molg... |
9f21574a8ae3b3107fbb67748e38b32ff48bc05e908e2d8b7e258f2e86db3922 | Java | 2,203 | 77 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.io;
import java.io.File;
import java.io.FileFilter;
import java.io.IOException;
import java.ut... |
111a70655c679f27700776ace7cc4ccbdcd0f50e0931f4be47a9f752ddfea79c | Java | 2,218 | 65 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import umcg.genetica.io.trityper.bin.BinaryResultDataset;
import umcg.genetica.io.trityper.bin.BinaryResultProbe;
import umcg.genetica.io.trityper.bin.BinaryResultSNP;
import... |
de8a6f8db505709e91656a501ad5dbb16fc134c39af16c21d39fd44f55ed6391 | Java | 2,223 | 56 | package main.java.decon_eQTL;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.LineIterator;
public class GenotypeData {
private ArrayList<String> sampleNames;
private... |
17ab47044d02f521420829302df29162ea27bf8f6cf04d832642f1419465c7f4 | Java | 2,224 | 80 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.math.matrix;
import umcg.genetica.containers.Pair;
/**
*
* @author juha
*/
public class MatrixTools {
public static boolean containsZeros(double[][] a) {
for (int i = 0; i < a.leng... |
364ac4df05fe2addbae87ebb2174b95678e48853e86af6882a4a79b5c344a981 | Java | 2,224 | 100 | package umcg.genetica.graphics.panels;
import umcg.genetica.graphics.DefaultGraphics;
import java.awt.*;
import java.awt.geom.Arc2D;
import java.awt.geom.Area;
import java.awt.geom.Ellipse2D;
public class DonutGraphPanel extends Panel {
private double[] data;
private String text;
public DonutGraphPanel(int... |
39fd0c017977a03694d0c196b2f7542c1ca2a8b355f2be5c44a82c1d72d9489a | Java | 2,238 | 57 | /*
* #%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... |
e9a3fa00e27f5310fd48eb9f3eed6cd780f75dd4ad822667d68a7d99a7c42af4 | Java | 2,238 | 57 | /*
* #%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... |
4c222e0bbdb71926ebfde5aab568af36c570816e92ba6bc69c00534246a8f832 | Java | 2,239 | 62 | /*-
* #%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... |
da89168bda31513517a086bff1f5d430276536a43cfc0802bde5b870e7483a7f | Java | 2,262 | 59 | /*-
* #%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... |
fe16f8f77b65500c58411db5d6de9efeb858b9aae6f071feff2ec64d9092fbf7 | Java | 2,263 | 97 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
import java.io.IOException;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
import umcg.genetica.io.trityper.EQTL;
import ... |
960db4430bb18320fb7b3e3258a9494f28af441a716cd97d54bc5f7efbac87c6 | Java | 2,268 | 61 | /*-
* #%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... |
dafe4dc6d567fff899c4586f5ae5ae15bcfb5113180df7f4e35a6ad089f1135b | Java | 2,273 | 80 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.plink;
import java.io.File;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import org.molgenis.genotype.GenotypeData;
import org.molgenis.genotype.Ra... |
0d65347f7ab9045c538f37647ff9d9004bc2353f3a53c2f13115052f7a9569cb | Java | 2,279 | 81 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package imputationtool.postprocessing;
import java.awt.Color;
import java.awt.Font;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.geom.Line2D;
import java.awt.image.BufferedImage;
import ja... |
5954cd7f9feaa123b600354b1938e87a0c7275196078c22efbd809630df2a3f8 | Java | 2,283 | 101 | 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.RawLineQuery;
import org.molgenis.genotype.RawLineQueryResult;
impo... |
46d145a7353d72686fe981852d326d1ade6826d571409090a0225da777403bbb | Java | 2,284 | 62 | /*-
* #%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... |
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