sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3b6f4ac5c4d0bf046fca84e0451b120719351766f2610cb829b6a162f31e525b | Java | 2,220 | 60 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
2f57f8d130bddf641223a20502daf51d04475cb537e6c5cdafab7ad6e80b90e1 | Java | 2,227 | 74 | /*-
* #%L
* ComDet Plugin for ImageJ
* %%
* Copyright (C) 2012 - 2025 Cell Biology, Neurobiology and Biophysics
* Department of Utrecht University.
* %%
* 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 Softw... |
d6ec4ad08695f8c242640bfc1174eb9ea599855687a9cd1fb7163c1ea1520cbb | Java | 2,231 | 57 | /*
* MIT License
*
* Copyright 2024 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
79408ccb875e87d2ec2e40ee6775452076b05dd396cd3c2e4c250e3d7f8f97e5 | Java | 2,243 | 52 | package org.broadinstitute.dropseqrna.utils.editdistance;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.broadinstitute.dropseqrna.metrics.UmiSharingMetrics;
import org.broadinstitute.dropseqrna.metrics.umisharing.ParentEditDistanceMatcher;
import org.broadinst... |
09fb097ab08d1ce722ccd079ac6ddb3b44d6cc87fad89f641beb458ef92402df | Java | 2,244 | 68 | package org.broadinstitute.dropseqrna.metrics;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import org.broadinstitute.dropseqrna.utils.CompareBAMTagValues;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.... |
04f0feeebe83b8fc7aeba5d15d8c06c649620c259532682fab8655470bf99f10 | Java | 2,255 | 73 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
17577e01971762de78b881192388e57d1088204330283596a5ea0e5b0fdb7f68 | Java | 2,266 | 72 | import java.awt.dnd.*;
import java.awt.datatransfer.*;
import java.util.*;
import java.io.File;
import java.io.IOException;
public class MLDropTarget extends DropTarget
{
/**
* Modified DropTarget to be used for drag & drop in MATLAB UI control.
*/
private static final long serialVersionUID = 1L;
... |
0dcccddfc32b5bfd072a8f9371aac3e541d8aa74a9115c749e11447d90c9c1f5 | Java | 2,268 | 83 | package arcade.core.util.distributions;
import sim.util.distribution.Uniform;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
/** Container class for uniform distribution. */
public class UniformDistribution implements Distribution {
/** Minimum of the distribution. */
final double min;
... |
979c8995877d5683a721af891a2f8ced1c2b8edea5aff19825b3655410dbf936 | Java | 2,270 | 79 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
eaefd89a5a8407fd37dcc392d63fa616e80be891237cc1a9997e87bf10b2ca7d | Java | 2,274 | 70 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import arcade.potts.agent.cell.PottsCell;
import static arcade.potts.util.PottsEnums.Region;
/** Configuration for {@link AdhesionHamiltonian} parameters. */
class AdhesionHamiltonianConfig {
/** Associated {@link PottsCell} instance. */
final Po... |
0ceaefa1098f7a672aa6282fcb9a871318c7d803296ee8b07054bcdbffe38567 | Java | 2,277 | 64 | package arcade.potts.agent.cell;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.Location;
import arcade.core.util.GrabBag;
import arcade.core.util.Parameters;
import arcade.potts.agent.module.PottsModuleQuiescence;
import static arcade.potts.util.PottsEnums... |
ac6c871ab6a23be0550456e5bab09bf921d2b6c79c3f87bf9ce09f5aac4966f1 | Java | 2,287 | 82 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
2865f38fd4bd487ed4536ac9afe849376e2dc14a88a19c0d2ea655ca3e2169d1 | Java | 2,288 | 64 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
f6acb0aed6137b6ccf7b2f747235854de90e8e39783182c593c2ab64c15187fd | Java | 2,290 | 82 | package arcade.util;
import java.util.logging.Logger;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import org.xml.sax.Attributes;
import org.xml.sax.XMLReader;
import org.xml.sax.helpers.DefaultHandler;
import arcade.Main;
/**
* Custom XML file loader that uses SAX parsing to iterat... |
0dc7d7b6fff4a8971ab17b275a7f8ce894a27e455b03fcbfd3d2496f0c110370 | Java | 2,310 | 74 | package arcade.patch.env.lattice;
import java.util.HashMap;
import ec.util.MersenneTwisterFast;
import arcade.core.env.lattice.LatticeFactory;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
/**
* Implementation of{@link LatticeFactory} for {@link PatchLattice} objects.
*
* <p>Each lattice is initi... |
c133d8d2ac38badc1835782eef4171979731411266f7f843330837260f99950f | Java | 2,311 | 76 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
ea58d95b90ff660fb6eff580bf0d4157b478f3269162ee1baa26e9f1dbcf1468 | Java | 2,313 | 64 | /*
* MIT License
*
* Copyright 2018 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
841f404d4ec44a988ccc75802ebc9b8e5e629249d401266f909ffe2c7070fb68 | Java | 2,314 | 82 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.HashMap;
import arcade.core.util.Vector;
import arcade.potts.util.PottsEnums.Direction;
import arcade.potts.util.PottsEnums.Region;
import static arcade.potts.util.PottsEnums.Direction;
import static arcade.potts.util.PottsEnums.Region;
/... |
2185fc78175d44633b12e7995e662363e3ea8c9230a25eac3ffc805849fe84e0 | Java | 2,315 | 68 | package arcade.potts.sim.hamiltonian;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static arcade.potts.util.PottsEnums.Region;
/** Extension of {@link AdhesionHamiltonian} for 2D. */
public class AdhesionHamiltonian2D extends AdhesionHamiltonian {
/** Neighborhood size. */
public... |
59b08435c0a06d8c165c39dfb3989ee7e7290573f6869734cf5c48e6ddbfad29 | Java | 2,327 | 70 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
8b4456d3f41be7526c7d7a4cc30cb5bf416dff5dfab048a15ca1bcba0587ac6e | Java | 2,328 | 66 | package org.broadinstitute.dropseqrna.vcftools.filters;
import htsjdk.samtools.util.Log;
import htsjdk.tribble.util.popgen.HardyWeinbergCalculation;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.dropseqrna.utils.FilteredIterator;
import or... |
d946db6738538191b93fd9b40375854865f1fc7863e0645c9df794af1a6125e6 | Java | 2,329 | 90 | package arcade.core.util;
import java.util.NavigableMap;
import java.util.TreeMap;
import ec.util.MersenneTwisterFast;
/**
* Container for weighted collection of integers.
*
* <p>{@code GrabBag} objects are collections of integers, where each integer has a weighted
* probability of selection. For example, integer... |
2b2536f57c5603f8ebb837c6a8bd9fb94f763e6a77fa629c457b9708f963123d | Java | 2,332 | 66 | package org.broadinstitute.dropseqrna.utils.referencetools;
import java.io.File;
import java.io.IOException;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
public class MaskReferenceSequenceTest {
private s... |
a1447cd4f631fe1e63e7ef6581220371f4a36cee32da3895c62c3a18a5ac37b7 | Java | 2,333 | 66 | /*
* MIT License
*
* Copyright 2019 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
e5cb9ca54e0c0b600550d035a1bf26009bf3f8c203d02039bf0fd5ffed40edca | Java | 2,340 | 81 | package arcade.sim.profiler;
import java.io.*;
import sim.engine.*;
import arcade.sim.Series;
import arcade.sim.Simulation;
/**
* A {@code Profiler} object captures simulation data and writes to a JSON file.
* <p>
* More than one {@code Profiler} can be scheduled for a given {@link arcade.sim.Simulation}.
* When ... |
1c6a579e98f2f52f46a12897ba6030450f40a16405763ace1d77d4e9d91a778d | Java | 2,341 | 48 | /*
* MIT License
*
* Copyright 2019 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
548d940638e015187f1edffd59188dd76cd71ea3a8920fa976556818a51bb066 | Java | 2,345 | 65 | package org.broadinstitute.dropseqrna.vcftools.filters;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.variant.variantcontext.... |
1f3536713aa0a8b9dd02c07d592d59f702933ffadd1a7ffa7138a14fb8313874 | Java | 2,352 | 70 | package arcade.patch.agent.cell;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.Location;
import arcade.core.util.GrabBag;
import arcade.core.util.Parameters;
/**
* Extension of {@link PatchCellCancer} for cancerous stem cells.
*
* <p>{@code PatchCellCa... |
16c89208ffa9569a24a5d5643551e4cb99c096465fbdf85b6a7a42a240749634 | Java | 2,353 | 61 | package org.broadinstitute.dropseqrna.vcftools.filters;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
public cla... |
6bf1fc8e516a0185c3f16779e90b1aa15be39e36c76561aa0cd2ad485799cdf1 | Java | 2,359 | 62 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
1ffce8ef713e9a688ffda2338b5d64e377130f922af7dd0d9c7f91b10c6ba63e | Java | 2,361 | 70 | package arcade.patch.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCell;
import arcade.patch.agent.cell.PatchCellCART;
import arcade.patch.env.location.PatchLocation;
import static arcade.patch.util.PatchEnum... |
7c2fa5b93299fb2c42f779d7d84e71b9458087505ae14900bd57df370901de9d | Java | 2,363 | 52 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
4af1a4181d7c964debb3ffbe40e045b43f383926041327fb4949fabe250795f7 | Java | 2,364 | 79 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import java.io.File;
import java.io.PrintStream;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.broadinstitute.dropseqrna.utils.io.Er... |
de999a381220043da6a1fc668d98fba9a231969def588e1b885ff8e00b629fbe | Java | 2,365 | 71 | /*
* MIT License
*
* Copyright 2018 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
f620b118ac187f977a6096721172bbf9bc89844c09a37671e784114a4b590d32 | Java | 2,389 | 86 | /*-
* #%L
* ComDet Plugin for ImageJ
* %%
* Copyright (C) 2012 - 2025 Cell Biology, Neurobiology and Biophysics
* Department of Utrecht University.
* %%
* 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 Softw... |
6295a5858fe57556b575b6f0357646e437fc556b1bfbb8394418971bf7a9fac8 | Java | 2,392 | 71 | package arcade.patch.agent.module;
import java.util.ArrayList;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.Cell;
import arcade.core.env.location.Location;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCell;
import a... |
ce321017586c4df2ecb8fe13d02fa100ff1e076358690f5f1027ee6d0c44c904 | Java | 2,404 | 72 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
3137ce6c9d30d7c7793d072ad9ab042858a27a8560b8eeabfea1f29fb604b28a | Java | 2,412 | 65 | package org.broadinstitute.dropseqrna.censusseq;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import org.broadinstitute.dropseqrna.vcftools.filters.MonomorphicVariantContextFilter;
import org.testng.As... |
6936bd6e5bba725f0cb60935cef9ba1649805aaa20cb2cfdc3fe0f89a16c6637 | Java | 2,413 | 69 | package de.uol.neuropsy.recorda.recorder;
import java.io.IOException;
import edu.ucsd.sccn.LSL;
public class RecorderFactory {
@FunctionalInterface
public interface RecorderConstructor {
StreamRecorder createRecorder(LSL.StreamInfo info) throws IOException;
}
enum RecordingSa... |
ee41feff71ac265c18b47252be5ee35ed5cad8d6c014d8ea4bd21ec00f994019 | Java | 2,438 | 52 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
3c14cabd271df0a25183e60930ac2c60e8c3f42a0c63d208d5a5bcbc0f6ccd5f | Java | 2,447 | 75 | /*
* SequenceParserTest.java
* JUnit based test
*
* Created on June 27, 2002, 6:48 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.classifier.train.LineageSequence;
import edu.msu.cme.rdp.classifier.train.LineageSequenceParser;
import java.io.File;
import java.io.FileNotFoundExce... |
dc862daa999d53e427f4582cdb8b3c1ab1bec528c4d70dbbd62c1d555b9e1825 | Java | 2,451 | 83 | package arcade.potts.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSimulation;
import static arcade.potts.util.PottsEnums.Phase;
... |
824ada3255f5cec66caf12426c4787bea4452048bd6df1f7b681727e985f5585 | Java | 2,457 | 69 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
3775b7090430c485a06f433b314a1ff7735b7c7083e42e2d35100753129e270c | Java | 2,458 | 79 |
/*
* TreeFactoryTest.java
* NetBeans JUnit based test
*
* Created on June 25, 2002, 3:59 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.classifier.train.LineageSequence;
import edu.msu.cme.rdp.classifier.train.LineageSequenceParser;
import java.io.File;
import java.io.FileReade... |
643c2030fe23ed06a32247597244e6f807c1b023c476a74fed5dbdda5f889e63 | Java | 2,495 | 83 | /*
* Copyright (C) 2014 wangqion
*
* 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 2
* of the License, or (at your option) any later version.
*
* This program is distribut... |
7f096af029434e96945a8026919203a407d690dcba526c31c9477d88a4384ef8 | Java | 2,521 | 69 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
bc9cecd3c19d5424af6bfeef22bb95ddc09923192ccabb79e608204bedc3aa33 | Java | 2,521 | 56 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
a859853fdc502572c8b2b06f42317b0350fb8425377e0a759a9dfcee12f9fab4 | Java | 2,538 | 68 | /*
* MIT License
*
* Copyright 2018 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
a6371a4ce19e4ceb9965f1b83c1c19c4b07f5ec9c7219a0670474b793cf5219f | Java | 2,540 | 85 | package org.broadinstitute.dropseqrna.utils;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.testng.annotations.Test;
import org.testng.Assert;
public class ObjectCounterTest {
@Test
public void test() {
ObjectCounter<String> o = new ObjectCounter<>();
... |
4d07c8b4e4cf454b590ea3c737078c868591d54ebb571aaa57ca13823cc511ae | Java | 2,542 | 61 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
398210de06d66fe1c9b3f049ecbf1cda41d49df710510d72e098e04f8aba18c1 | Java | 2,549 | 87 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
33137cc98ea99bc76dfd3a0d05408b2e4add1f828f4675c78f18b7fade3e9c93 | Java | 2,551 | 66 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
6ea8361530798b941d4f8518df15efcb37ff5a5d8f30023a056c464e671167c4 | Java | 2,551 | 83 | /*
* TreeFileParserTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 11, 2003, 12:07 PM
*/
package edu.msu.cme.rdp.classifier.rrnaclassifier;
import edu.msu.cme.rdp.classifier.HierarchyTree;
import edu.msu.cme.rdp.classifier.utils.HierarchyVersion;
import edu.msu... |
641ff8c5bb92f1fad656bf5555d956e36e0450ed3037a75e3a717f940b93a92d | Java | 2,552 | 70 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import org.broadinstitute.dropseqrna.utils.FilteredIterator;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMTag;
import htsjdk.samtools.util.... |
0c8b761c9dd2a3b7bd7973eac4f312b8927a1feff12e6928a4cf999cd5488b4e | Java | 2,553 | 95 | package arcade.sim.checkpoint;
import java.io.*;
import java.util.logging.Logger;
import sim.engine.SimState;
import arcade.sim.Series;
/**
* A {@code Checkpoint} object saves and/or loads simulation checkpoints.
* <p>
* Checkpoints do not save the entire simulation state; instead, it saves
* subsets that can th... |
3c23670cbde9f9d9bacf77f4f93dc8b62ec0d4ed15ed8c0d30d24f9e34370f0c | Java | 2,555 | 72 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
2150723df0fa23c5fcf368b2943da330f790fb52da6eef374c34cd8c2d9be12a | Java | 2,557 | 62 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
41106fc4ea3c120f5e1efabeee248adf0b2a1291b5f574cd9763e481cc008527 | Java | 2,558 | 67 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
f9aa42eb132c6a13e89c3b82e839cb497a1de4f77f584fb2f6cfe5a0349db7e6 | Java | 2,562 | 68 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
f6a3e3b6087749f5dd230f01bf053e9c795b534b6356834e2e869e0bac6b016c | Java | 2,571 | 58 | /*
* MIT License
*
* Copyright 2021 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
a7c88b1b649faf6d70551d87cc9b937e65f31f37c4519dc1bd15dc8d7f4963f3 | Java | 2,575 | 87 | package arcade.sim.checkpoint;
import sim.engine.SimState;
import arcade.sim.Series;
import arcade.sim.Simulation;
import arcade.env.comp.GraphSites;
import arcade.util.Graph;
import arcade.util.Graph.*;
/**
* Extension of {@code Checkpoint} for saving graphs.
*
* @version 2.3.1
* @since 2.3
*/
public abstra... |
8a00a732a6bc35820075aa57bb293724bd757e627666dd7e101ad0bb359c6f32 | Java | 2,593 | 60 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
9eeae9bfd3222988ec5b71e4303d9610217a3759961ee2f87afa5578b514b2da | Java | 2,595 | 64 | /*
* MIT License
*
* Copyright 2018 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
7b6ec7e99163a935bdce6a3c49c0417d34cbecd13209e394be760312add77194 | Java | 2,607 | 84 | /*
* ParsedSequence.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on November 7, 2003, 5:46 PM
*/
package edu.msu.cme.rdp.classifier.utils;
import edu.msu.cme.rdp.readseq.readers.Sequence;
import edu.msu.cme.rdp.readseq.utils.IUBUtilities;
import edu.msu.cme.rdp.readseq.utils.Se... |
4181f31575f0761174a72f9cebd13c8c0790e7c06b70a241675d3c621e2ecf1e | Java | 2,610 | 87 | package arcade.core.util;
import sim.util.Double3D;
/** A plane in 3D space. */
public final class Plane {
/** A point on the plane. */
public final Double3D referencePoint;
/** The unit normal vector to the plane. */
public final Vector unitNormalVector;
/**
* Creates a plane from a Double... |
1cb3698d6d94af56a94fe5a1c3a56920dda506b4ed4b9d8683cd83147a06ae0d | Java | 2,616 | 72 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
6cb34bb7644f474022020da47fa6e6f48de70771f48ca8fed0324beb47b894ce | Java | 2,620 | 58 | /*
* MIT License
*
* Copyright 2025 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
3230fe19050558136ccda5c53254ccf75978a2e63b6e2f6d3bfbb9be4edabc45 | Java | 2,621 | 81 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
public... |
414a5e83f5c75c0e6a269fd08990437697058c6392ed46e6cc100e82078924a7 | Java | 2,623 | 73 | package arcade.potts.sim.hamiltonian;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static arcade.potts.util.PottsEnums.Region;
/** Extension of {@link AdhesionHamiltonian} for 3D. */
public class AdhesionHamiltonian3D extends AdhesionHamiltonian {
/** Neighborhood size. */
public... |
efe0fac8d8d65d4521ceca2a266bae44afb56d14cbfc70c48abb5beeba465f63 | Java | 2,639 | 79 | package arcade.env.comp;
import arcade.sim.Simulation;
import arcade.env.lat.Lattice;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.comp.Diffuser} for triangular lattice.
* <p>
* {@code TriDiffuser} also check if the triangle is pointed up or down based
* on the row and column, where the top l... |
4e270c4e19e9fbdeb15c42da69653f93eb921e46015d5ab133c6b77475617e53 | Java | 2,640 | 73 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
63e8058ffebbcf71db201d9f7637c37e5ec74634a7a6f425da6ed7819cfe3df1 | Java | 2,643 | 95 | /*
* Ztable.java
*
* Created on April 12, 2005, 3:09 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.Properties;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.StringTokenizer;
import java.util.Hashtab... |
ee79b93be326f6fd2454ebfa5206f36b84480add995a80cff909538ee4d9f954 | Java | 2,652 | 64 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
ea1a464f9dd945ab168a4e054d0fa513540bc3708d8794123f7e4228750d74e9 | Java | 2,653 | 77 | /*
* MIT License
*
* Copyright 2018 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
630b3af565c229bcdb630656c49f605cb52f7c9e9e73b298d7e0d18be25ecfa1 | Java | 2,658 | 58 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
32d9ff4d1869923f12a6f29345827a252c18e483acc06b0853185909873bbccd | Java | 2,660 | 87 | /*
* Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
*
* 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 2 of the License, or
* (at your option) any later v... |
2d7c5bb3171966ff88ed7efeb9df70765e85c460136d3a0541346db3b201277e | Java | 2,667 | 89 | package arcade.agent.helper;
import sim.engine.*;
import arcade.sim.Simulation;
import arcade.agent.cell.Cell;
import arcade.agent.cell.TissueCell;
import arcade.env.loc.Location;
/**
* Extension of {@link arcade.agent.helper.TissueHelper} for cell movement.
* <p>
* {@code MoveTissueHelper} is stepped once after t... |
1748c09fc316202cd14cd2ff5dd6be434df03049a7625bd36d1b2ffc20b0729d | Java | 2,678 | 121 | package org.broadinstitute.dropseqrna.eqtl;
import java.io.File;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.yaml.snakeyaml.Yaml;
import htsjdk.samtools.util.IOUtil;
public class ParseContigGroups {
/**
* Build a map fro... |
b882874e44e8297733c6c2fbbf2487e3ec338a17e3befbb8a42c43a8c6249fc3 | Java | 2,680 | 70 | package arcade.patch.agent.process;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCell;
import arcade.patch.env.lattice.PatchLattice;
import arcade.patch.env.location.PatchLocation;
... |
3eaadf1c441c1c2a9b39a9a12e4d6f3c78fbcc3d0eda99a8bbbf0e7c34c00f24 | Java | 2,684 | 74 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
a24285da12a74dfac689901bed5a35b17ae33f817bd857011d3cc618062b365d | Java | 2,685 | 60 | /*
* MIT License
*
* Copyright 2022 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
2e48d2600af82f152ed26fc753496907768fcd8f8ad11453c9611550c7e1a24c | Java | 2,691 | 100 | package arcade.core.util.distributions;
import sim.util.distribution.Normal;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
/** Container class for normal distribution. */
public class NormalDistribution implements Distribution {
/** Values for distribution bounds. */
final double[] boun... |
45887924bc3ce419465d555ac87a5dfacc7460a22de2a03f0655df76bf4989a1 | Java | 2,691 | 74 | package arcade.patch.util;
import java.util.HashMap;
import java.util.Map;
import arcade.core.util.EventLog;
import arcade.patch.env.location.Coordinate;
/**
* Concrete implementation of {@link EventLog} for lysis events.
*
* <p>{@code LysisEventLog} objects are created when a CD8 CAR T-cell successfully kills a t... |
662eff4b83172889f124c32f5cd3b87d8165f7e6d029ece460901a0e7d2fdd77 | Java | 2,691 | 62 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
aaea20ab503ca3b16e0651aabfc8921b5cf4bf9b9e28f09732c07f7121675651 | Java | 2,703 | 67 | /*
* LogWordPriorFileParser.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 18, 2003, 5:38 PM
*/
package edu.msu.cme.rdp.classifier.io;
import edu.msu.cme.rdp.classifier.TrainingDataException;
import edu.msu.cme.rdp.classifier.utils.HierarchyVersion;
import java.io.*... |
2142e6e5cdac3b45ab644932526a4d5b37e352c415e26b3b754384ac513666e2 | Java | 2,711 | 104 | package org.broadinstitute.dropseqrna.utils.readpairs;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
public class ReadPairTest {
@Test
publi... |
bd4fb7973400d51d32d29b7fe8015e8838774bef6a80b652700ae43927a1fe27 | Java | 2,727 | 81 | package arcade.potts.util;
import java.util.ArrayList;
import java.util.EnumSet;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.potts.util.PottsEnums.Direction;
import static arcade.potts... |
ac8a8b3c8e71f50ddb24c187b4c751c5d4b63c249e6ef4625cacbcb8cc48f9c0 | Java | 2,744 | 59 | /*
* MIT License
*
* Copyright 2022 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
2e3778ecb0da5cf432620f1b30068e50bc8c26001c8c801ff00ff6b04e0d98d3 | Java | 2,747 | 74 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
1fa5f19598cbb4c72254d3cc1c051e69cf296c10b09020352ee190afb3530934 | Java | 2,751 | 91 | /*
* ClassificationResultFacade.java
*
* Created on May 11, 2007, 4:02 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.classifier.train.LineageSequence;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
/**
*
* @author wangqion
*/
public class Vali... |
a8d4db0d62a48a2ac03267fe49b9fea7d27ddbb6936a4dae87840a38bfe270e6 | Java | 2,755 | 80 | /*
* MIT License
*
* Copyright 2022 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
c90e3579a4bcadd764dea57108a50b854e065ec769186b3b08d6215b01264c5f | Java | 2,757 | 63 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
c643cc9dc22f397013943204cce73be852d6eba2494df1ef95dd35f234e4530f | Java | 2,758 | 78 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
a2ea283dc1230c475ec57e50395cffe363263a9e30c33259dd591163822c88e6 | Java | 2,759 | 76 | package arcade.patch.env.operation;
import ec.util.MersenneTwisterFast;
import arcade.core.env.operation.Operation;
import arcade.core.sim.Simulation;
import arcade.core.util.MiniBox;
import arcade.patch.env.lattice.PatchLattice;
import static arcade.patch.util.PatchEnums.Category;
/**
* Extension of {@link PatchOpe... |
8b3a4df72d0a34b0c0e7fe5db549c8b1842d82fa8999f3ecc96373acde336e25 | Java | 2,760 | 72 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
9d0072078ddaae5ab9ac589668c12ed62605ef2068fbf878f6e5dbb57ba66976 | Java | 2,760 | 68 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
b3aedbd8837f43d54d83b9dc797daf924dc0e8f79e0a43ea02ed4b973a57f471 | Java | 2,760 | 70 | /*
* MIT License
*
* Copyright 2020 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
781fb5fc8b9235278ef9a57cfffc8fa880496af100e8f2404997be251a3d0799 | Java | 2,770 | 85 | package arcade.patch.agent.cell;
import sim.engine.SimState;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.Location;
import arcade.core.sim.Simulation;
import arcade.core.util.GrabBag;
import arcade.core.util.Parameters;
import static arcade.patch.util.Pat... |
df32cda21bdf3190ecbd2dfb7f5bdea65578307059fc9c47f990c734d513ece0 | Java | 2,776 | 78 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
943731212ca1d67c6ba9a54d4d00057493ff227f49193b77e3660f1ecfc19b4b | Java | 2,777 | 86 |
/*
* RawHierarchyTreeTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 25, 2002, 3:59 PM
*/
package edu.msu.cme.rdp.classifier.train;
import junit.framework.*;
import java.io.*;
/**
* A test class for RawHierarchyTree.
* @author wangqion
*/
public class RawHierarc... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.