sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b9109c3303ebf6491eb8acb563938f743044c647f2f884b79475f3a1dd4edeab | Java | 4,373 | 129 | package arcade.potts.agent.module;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.env.grid.Grid;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import arcade.pott... |
18a248058ac9bca5653e3665462ba6e79b1975cdcc6380d65b1921549b483745 | Java | 4,401 | 153 | package arcade.env.comp;
import java.util.logging.Logger;
import sim.engine.SimState;
import arcade.sim.Simulation;
import arcade.env.lat.Lattice;
import arcade.env.loc.Location;
import arcade.env.comp.SourceSites.SourceSite;
import arcade.util.MiniBox;
/**
* Implementation of {@link arcade.env.comp.Component} for c... |
4787ec8c28f29617150b5c67afe6d70acd8b8320d6fc4b0056c731e1d74d45a2 | Java | 4,405 | 126 | package arcade.potts.sim.input;
import java.util.ArrayList;
import java.util.HashMap;
import org.xml.sax.Attributes;
import arcade.core.sim.input.InputBuilder;
import arcade.core.util.Box;
import arcade.core.util.MiniBox;
import arcade.potts.sim.PottsSeries;
import static arcade.core.util.MiniBox.TAG_SEPARATOR;
import... |
e97fdce63e0ad147eed48b00d3bbcf739b1edce641470c68a298799abd4baa89 | Java | 4,406 | 140 | package arcade.core.util.distributions;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.randomString;
public class UniformDistributionTest {
private static final ... |
23e6120a1528add0bee87e95e6ee2af6c552fa28c32ef9322f0c7d425a8b32ab | Java | 4,408 | 128 | package arcade.sim.profiler;
import java.util.Map;
import java.util.ArrayList;
import sim.engine.*;
import sim.util.Bag;
import arcade.sim.*;
import arcade.env.loc.*;
import arcade.agent.cell.*;
import arcade.util.Parameter;
/**
* Extension of {@code Profiler} to output cell parameter values.
* <p>
* The output J... |
aa5e235ba8a23263605bfd8bae2ffcc1fa8588149ba8399d3b07d6b4eb3b075b | Java | 4,408 | 129 | /*
* 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... |
6de68b15df390d4fd9cd6185f62d5e0bbd9f8a6f219f2a85332e460694ab475d | Java | 4,419 | 100 | /*
* 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... |
0fa17134ec7251d968b67a1bd3b1579433e89aabc3d0bbf952a5b83d55552b39 | Java | 4,429 | 184 | package arcade.util;
import java.util.ArrayList;
/**
* Container that maps a key to a tag category and a series of attributes.
* <p>
* {@code Box} objects use two {@link arcade.util.MiniBox} objects to map between
* key, tags, and attributes.
* Rather than nesting the key to attribute to values, the class automa... |
f87a40d1b9f51b45ab8c40228b52be21808f76e3434a2e69d37c3b2fd4a3dfb7 | Java | 4,436 | 125 | package arcade.sim.profiler;
import java.util.ArrayList;
import sim.engine.*;
import sim.util.Bag;
import arcade.sim.*;
import arcade.env.loc.*;
import arcade.agent.cell.*;
/**
* Extension of {@code Profiler} to output cell properties and molecule
* concentrations.
* <p>
* The output JSON includes:
* <ul>
* ... |
83d14a0fcb6915a71931abe9ab608f9ebe071e114feb816933d4c5c5d841f3d2 | Java | 4,442 | 118 | /*
* 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... |
1c36bb84f758f0c13307f5822d5e2703f2357c941a26780b86fa50e2c12b972f | Java | 4,452 | 111 | /*
* 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... |
80246fd83b290eeac8f9a11478c19a0e5246f754f4b192fca01a944da716224e | Java | 4,457 | 101 | /*
* 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... |
a7c78f78a1446cce7c30a186d1c3f5526718ed2286adaf3d996744e1a6dff08d | Java | 4,478 | 102 | /*
* 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... |
947950389589ccfb59289caec1770b730f5c00b7f55926e9351741e6a354c8d7 | Java | 4,495 | 121 | /*
* 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 3 of the License, or
* (at your option) any later v... |
7e2ebae23d7f9fe929de06ec4114bad283465708a6a508b640156bedd73bf34c | Java | 4,514 | 126 | /*
* 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... |
4f4eb0b71dbd707de3f52de4297571c8791c9db33919452f0906eaf355449a76 | Java | 4,542 | 101 | /*
* 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... |
6c9419958c9b063e00f26678188362b719a772021c178731e0c9fac0d83bf6fe | Java | 4,549 | 110 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import org.broadinstitute.dropseqrna.annotation.AnnotationUtils;
import org.broadinstitute.dropseqrna.barnyard.Utils;
import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
import picard.annotation.LocusFunction;
import java.util.*;
/... |
d7e572dd3649c1f69c8052dfc32fe72ef9ee5e3ec478c02e9e14d89342ed9f13 | Java | 4,570 | 125 | package org.broadinstitute.dropseqrna.utils;
import java.io.File;
import java.util.Arrays;
import java.util.Collections;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import org.testng.Assert;
import picard.ann... |
115a4a445b45b45a78f47f7c8a2ab3f3a8a38212c6964e1d31594353767e83e9 | Java | 4,578 | 147 | /*
* 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... |
8d84a75c02a1373e83989b26a0939707e478ea3f72a040e5ac9f567ce4ca9410 | Java | 4,589 | 90 | /*
* 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... |
b037b8d05c200db5121352d324bcbadcc2b6aa5b1222ce0a8477ba61da6e66a3 | Java | 4,598 | 102 | /*
* 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... |
64c6384fbb6aaec0da6de4f4a981b531939c58d0895a2323328d088c6fc3e8bc | Java | 4,619 | 146 | /*
* 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... |
0915f578bec822fc4037c34d8ac2f0edb76380c04b228b460a25c978564c241c | Java | 4,634 | 153 | package arcade.potts.env.grid;
import org.junit.jupiter.api.Test;
import sim.util.Bag;
import arcade.core.agent.cell.Cell;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
public class PottsGridTest {
private static Cell createObjectMock(int id) {
Cell object = mock(C... |
f48aa14cfcefc3ce1b1574ea466f8000c759f278e3b80acf7b5d717c56315aad | Java | 4,642 | 119 | /*
* 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... |
1c0e76cb6da2ad5f87d7aa4a4bab2ed198191b7a4dd13d1929c454daf450ed73 | Java | 4,652 | 113 | /*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2017 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever.
* Neither the Broad... |
dc54c276e87dfe2e2b429b74a912d173bb659b65228b4cc7b58b5bea7bc1ae6e | Java | 4,662 | 97 | package org.broadinstitute.dropseqrna.utils;
import java.io.File;
import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.nio.PicardHtsPath;
public class BaseDistributionAtRe... |
04d36553f46e255b4586f0d1fa8c92b34dc7c1486111a309063a1659861ad4d7 | Java | 4,665 | 115 | /*
* 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... |
8ebba4c9782e18463c5a998391d032b9bd798ca90c78a38cd42c7db0ce9386a0 | Java | 4,692 | 177 | package arcade.env.comp;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.comp.PatternSites} for triangular lattice.
* <p>
* The pattern unit cell for pattern is given by:
* <pre>
* -----------------------------
* \ / \ / \ 2 / \ / \ /
* \ / \ / 1 \ / 1 \ / 1 \ /
* ---... |
70cb9e3aa942e66512d5b630da9c3629d8d381f1232d32ad5a6d4b32346001db | Java | 4,693 | 110 | /*
* 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... |
52fb1c434d3fdb022de0c6f436901c179accb90be40aae6cc770e4ab05c877e5 | Java | 4,722 | 99 | /*
* 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... |
2023b0c673fa8a8e1549a33a33a42c757cf16286b9b0600132f524716a3fd2db | Java | 4,734 | 125 | package arcade.core.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonDeserializationContext;
import com.google.gson.JsonElement;
import ... |
0a26785ccb019449246f9e17207501351c1679052eaa7c46ce538893068676ab | Java | 4,737 | 116 | /*
* 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... |
1bd86ad82e96ee5e3ecfd72ba3b38b0bf9437e65366eebe601dbac3537d294be | Java | 4,750 | 138 | /*
* 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... |
1f82c3e7621227d28c16eb396270e96d005f042daedaf18064e0d1b27d2d27e4 | Java | 4,750 | 152 | /*
* SigCalculater.java
*
* Created on February 8, 2005, 4:28 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
/**
*
* @author wangqion
*/
public class SigCalculator {
private static final int FREQ_LIMIT = 5;
private int s1Total;
private int s2Total;
private int combinedTotal;
pri... |
b96c3c0ed4d311ea1ec279747ea718e732177df4abc60925991db36c6a210da3 | Java | 4,753 | 135 | /*
* 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... |
eaee318a7c3308642d92cf8356ed199c29461be8fc1c169fc528ffecf10d70ed | Java | 4,755 | 112 | /*
* 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... |
4d48ed14b7ece3537dc275fd5dcfa0fe0ac72c4088328d4a332030a0ae7cda4f | Java | 4,759 | 138 | /*
* 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... |
a1352a5c72434bdac4d6b1fb065db19e85703a2a5f4c3765a3bc11771bd3c056 | Java | 4,773 | 126 | package arcade.patch.agent.process;
import java.util.Arrays;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.mockito.Mockito;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCellCART;
i... |
f015b44e8538ba709c1f47b6c0db0315b675c880c122afe9196a02bffd3b7659 | Java | 4,775 | 120 | /*
* 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... |
50d7e5108bc83216decdf5a71df259417883b9102c8e87224170a52c87c740dc | Java | 4,795 | 104 | package org.broadinstitute.dropseqrna.utils;
import java.io.File;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.dropseqrna.barnyard... |
c14d32e082cf897e8cd82d73c6b1d8ebec72f5fccd3603957d294968f6a6b0e1 | Java | 4,796 | 190 | package arcade.env.comp;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.comp.PatternSites} for rectangular lattice.
* <p>
* The pattern unit cell for pattern is given by:
* <pre>
* -------------------------
* | | | | | 1 | 2 |
* -------------------------
* | | | | ... |
76084197dc537e26b05d1ee82180e023507f56a7f513864f108423622379b4d3 | Java | 4,797 | 91 | /*
* 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... |
48e6571c0c8bb31b92eaa18ebb82bc0433e5a5ff90260f93f5c76ea6d2dddfc1 | Java | 4,804 | 169 | /*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2017 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever.
* Neither the Broad... |
ed25b31974757eff7bfd4129bd3bdddf4c46cc35226f8b2f317a21a11febb384 | Java | 4,804 | 154 | package arcade.vis;
import java.awt.geom.Rectangle2D;
import sim.engine.*;
import sim.field.grid.DoubleGrid2D;
import sim.portrayal.Portrayal;
import sim.portrayal.grid.FastValueGridPortrayal2D;
import sim.portrayal.grid.ValueGridPortrayal2D;
import sim.util.gui.ColorMap;
import arcade.sim.Simulation;
/**
* {@link a... |
980fa8b92578628ad99d19cd05e3bb6f210cbf410d28d0adafa3d344fc23485b | Java | 4,813 | 152 | package arcade.agent.module;
import java.util.Arrays;
import arcade.sim.Series;
import arcade.sim.Simulation;
import arcade.agent.cell.Cell;
/**
* Extension of {@link arcade.agent.module.Metabolism} for random metabolism.
* <p>
* {@code MetabolismRandom} will uptake a random fraction of glucose and oxygen
* from ... |
d46abd0dec4f5c41c2f16e61a48eeb6a12411d2128485677ddbb5c9f0dd3b30f | Java | 4,816 | 111 | package org.broadinstitute.dropseqrna.annotation;
import java.util.List;
import htsjdk.samtools.util.StringUtil;
import org.testng.annotations.Test;
import org.testng.Assert;
public class GTFRecordTest {
@Test
public void testAddError() {
GTFRecord r1 = new GTFRecord("1", 1, 10, false, "g1ID", "g1,Name", "t1Nam... |
1ec8aa2cb30445d06de00e7ab209ddc0112fe193d44665d8cfc0d31f975973c2 | Java | 4,832 | 116 | /*
* 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... |
e97d632918f88aecfd38c0d04df3694f0b665b569fb9d10607a3aaf967c1faef | Java | 4,835 | 158 | package arcade.core.sim;
import java.lang.reflect.Type;
import java.util.ArrayList;
import com.google.gson.reflect.TypeToken;
import sim.engine.Schedule;
import arcade.core.agent.action.Action;
import arcade.core.agent.cell.CellContainer;
import arcade.core.agent.cell.CellFactory;
import arcade.core.env.component.Comp... |
f2b051793982bfdad40beb04cf01d9cd93c236fb02572de0b074953d650f07b3 | Java | 4,838 | 143 | package arcade.patch.util;
import java.util.ArrayList;
import java.util.Arrays;
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.patch.util.PatchEnums.AntigenFlag;... |
abec71b1b02a85b263acbcfad9f999d7a31b63ee81ca90b8f9456d0390d0d619 | Java | 4,884 | 146 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.EnumMap;
import arcade.core.agent.cell.CellContainer;
import arcade.core.env.location.*;
import arcade.potts.agent.cell.PottsCellContainer;
import static arcade.potts.util.PottsEnums.Region;
/**
* Implementation of {@link LocationContain... |
0e8edef333a2de913565c8aab03e50dbb1d076b87bf6ffb7b426cb3ddb991621 | Java | 4,913 | 107 |
/*
* DecisionMakerTest.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;
impor... |
91bc72a0d2cfedba889ff5c90b11d69c7a1d83892a4d2115eecdccda7cd2bd31 | Java | 4,916 | 103 | /*
* 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... |
15e2f07e21470e1262c4757bdd8729890173af9c20336e3cb716e45493784965 | Java | 4,921 | 118 | package org.broadinstitute.dropseqrna.barnyard;
import htsjdk.samtools.util.*;
import org.broadinstitute.dropseqrna.barnyard.digitalexpression.UMICollection;
import org.broadinstitute.dropseqrna.utils.OrderAssertingIterator;
import picard.util.TabbedTextFileWithHeaderParser;
import java.io.File;
import java.util.Arra... |
2eac32dbde3aad417802f470dac4255dbb97affc68190ee1573138c608f3b6c1 | Java | 4,931 | 135 | /*
* 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... |
c2a5d7b73725a75a1ea0884aff4f93a38ef0319e2f33c55dd54379472bf97865 | Java | 4,942 | 102 | /*
* 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... |
fdb351d93f80301cfd5f55805153949aa648d78ce5da11a4c352a923a03771c9 | Java | 4,946 | 158 | package arcade.potts.sim.hamiltonian;
import java.util.HashMap;
import java.util.Set;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static arcade.potts.sim.PottsSeries.TARGET_SEPARATOR;
/** Implementation of {@link... |
5bb8a24ae353f67494b893a2930a40b2ac247e80ace9e1d21eec219064499d18 | Java | 4,954 | 103 | /*
* Copyright (C) 2013 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... |
775bddeb25739b7ae435c43fdd4fabf3639a83b5ee4cfc77d4a95d5cb9d0cf31 | Java | 4,959 | 149 | package arcade.agent.module;
import java.util.Arrays;
import arcade.sim.Series;
import arcade.sim.Simulation;
import arcade.agent.cell.Cell;
/**
* Extension of {@link arcade.agent.module.Metabolism} for simple metabolism.
* <p>
* {@code MetabolismSimple} assumes a constant glucose uptake rate and constant
* ATP p... |
9670f177ff11a33197d2a8342cbffe4a73abec830ad5b3a090dd74423d97e24c | Java | 4,974 | 164 | package org.broadinstitute.dropseqrna.barnyard;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.broadinstitute.dropseqrna.barnyard.ChimericUmi.CHIMERIC_STRATEGY;
import org.broadinstitute.dropseqrna.barnyard.digitalexpression.UMI... |
9f7368507f9e6f3aca9f9acbd73d363dc0d740dadae1209bc20f96c561882435 | Java | 4,981 | 135 | /*
* 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... |
a95cdaac708cacb8850c6c6e60340e94cadb2620912d3276297c1d4fdf5df727 | Java | 4,982 | 130 | /*
* 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... |
8b185396c1e53e46e3950386d1d0fa0d11349dac75e521850561af68c408a46f | Java | 5,002 | 171 | package arcade.agent.helper;
import java.lang.reflect.Constructor;
import java.util.ArrayList;
import sim.engine.SimState;
import arcade.sim.Simulation;
import arcade.agent.cell.Cell;
import arcade.env.grid.Grid;
import arcade.env.loc.Location;
import arcade.util.MiniBox;
/**
* Implementation of {@link arcade.agent.... |
f6ff462005c0102762a72d280d2caa2a5d2b07edb292ed3e90b7a2218bdb9564 | Java | 5,004 | 161 | package arcade.vis;
import java.awt.geom.Rectangle2D;
import sim.engine.*;
import sim.field.grid.DoubleGrid2D;
import sim.portrayal.Portrayal;
import sim.portrayal.grid.FastValueGridPortrayal2D;
import sim.portrayal.grid.ValueGridPortrayal2D;
import sim.util.gui.ColorMap;
import arcade.sim.Simulation;
import arcade.ag... |
23fd88eaeec759c04be399e9404d4432b04efabd0132bdcf2897cba29c6c0073 | Java | 5,006 | 121 | package arcade.patch.env.location;
import java.util.ArrayList;
import org.junit.jupiter.api.Test;
import arcade.core.env.location.Location;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.randomIntBetween;
public class PatchLocationRectTest {
@Test
public void g... |
f0068ef3884d3ad0999c0ed9729e7a273421519f7427a14de7a714c16023596d | Java | 5,029 | 204 | package arcade.env.loc;
import sim.util.Bag;
import java.io.Serializable;
/**
* A {@code Location} object defines agent coordinates within the environment.
* <p>
* Each agent has a {@code Location} that identifies where they are within the
* {@link arcade.env.grid.Grid} (relative to other agents) and the
* {@l... |
8d8ec578637e35752e2b7d554c82266e7806b7ea7a8c7bfc193fd241cc4b3a06 | Java | 5,031 | 150 | package arcade.agent.helper;
import sim.engine.*;
import sim.util.Bag;
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 division.
* <p>
* {@code MakeTissueHelper} i... |
a1292d3576101a534e1c50047df5b81ff391584471da1c76c0aa61da2c2e7120 | Java | 5,056 | 128 |
/*
* NBClassifierTest.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 edu.msu.cme.rdp.readseq.utils.orienta... |
638f69d4a75e43d3f776ea36b94777280e32ee7815d0434f672e5bf1d5145bfa | Java | 5,059 | 155 | /*
* 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... |
065f8fc165bb99285b411e766ba02411a3ba38926af5ee63c619fcf80a116d84 | Java | 5,098 | 138 | package arcade.vis;
import sim.engine.*;
import arcade.sim.Simulation;
import arcade.sim.Series;
import static arcade.vis.ColorMaps.*;
/**
* Extension of {@link arcade.vis.Visualization} for 3D simulations.
* <p>
* {@code GrowthVisualization3D} creates two panels:
* <ul>
* <li><em>agents</em> shows cell den... |
b176cbfb34543f9ebb714a7ed6c03598a01aa71add015ed550c2b1a47f657645 | Java | 5,103 | 133 | /*
* 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... |
b20849fe2cfc1e9ea3241b594b907f70eee42fb71e200d3a84d82a31c1d96b1c | Java | 5,114 | 135 | package org.broadinstitute.dropseqrna.sbarro;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
import org.broadinstitu... |
f0f82c1dacffa9e3759086e8d8ecd2afedbe2a50a4a499bc9bce192fae7f913c | Java | 5,120 | 144 | /*
* 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... |
19eb5cd43b35cd02920da2b9ab98ae7ff67df3e68a4e824b574f6ac65e5c8c62 | Java | 5,130 | 153 | package arcade.patch.env.component;
import java.util.ArrayList;
import sim.engine.SimState;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
import arcade.patch.env.location.CoordinateXYZ;
import arcade.patch.env.location.Patc... |
86e86814e6fdd59d3c2da380ea1690bd198d9a5b5f41b2885fa82bd4a6713077 | Java | 5,130 | 196 | package arcade.util;
import java.awt.Color;
import sim.util.gui.ColorMap;
/**
* Implementation of {@code ColorMap} for discrete and continuous color selection.
* <p>
* Custom color map management for use with visualization classes in
* <a href="https://cs.gmu.edu/~eclab/projects/mason/">MASON</a> library.
*
* ... |
d8f6135def6d4cf442aa7389dba833da7890206a9fcdf90d992cfe225ce99ac4 | Java | 5,131 | 246 | package arcade.agent.cell;
import java.util.Map;
import sim.engine.*;
import sim.util.Bag;
import arcade.env.loc.Location;
import arcade.util.Parameter;
import arcade.agent.helper.Helper;
import arcade.agent.module.Module;
/**
* A {@code Cell} object represents a cell agent.
* <p>
* <em>Types</em> (identifying ce... |
e7055e2faa16399105bcf3c6d599a6b082de62f664fc97320a456abdd4706e16 | Java | 5,143 | 135 | package org.broadinstitute.dropseqrna.barnyard;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.dropseqrna.beadsynthesis.GenerateRandomUMIs;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arr... |
72680cecaee6843eac98b05f6e83991aac354ed1069d694ae9455729e57ec579 | Java | 5,171 | 150 | /*
* 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... |
abffca0da2a4502c51064c4525baf5516d88deb4846de9d5447f1104daa0f7a7 | Java | 5,177 | 167 | /*
* 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... |
7f592b692584a32881dad9b4ec6c98eb974e999d488fa6f8361bc764c60cba86 | Java | 5,181 | 129 | /*
* 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... |
2970ee4c8c8fc5ca652360a05c449dbe83ef266c55141516da7e5a3625f37547 | Java | 5,182 | 188 | package arcade.env.grid;
import sim.util.Bag;
import java.util.Map;
import java.util.HashMap;
import arcade.env.loc.Location;
/**
* Implementation of {@link arcade.env.grid.Grid} using {@link arcade.env.loc.Location}
* object as hash.
* <p>
* {@code AgentGrid} uses the Location object to map to objects at the loc... |
0216a016b5d0754c778a40626b7e00d91a231e7bcbc3fdaea97781841bed5f52 | Java | 5,183 | 188 | /*
* UncNode.java
*
* Created on December 3, 2003, 4:00 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.Iterator;
import java.util.NoSuchElementException;
/**
*
* @author wangqion
*/
public class UncNode extends AbstractNode{
/** Creates a new instance of UncNode */
UncNode(... |
bbcb454b7f65c8bb9adc6ceca1f9d18a0f7a3e5e16254c3decaa17ba189a6363 | Java | 5,187 | 157 | /*
* 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... |
76a4ec37cafda9b8332abd7c5a198dc0f396cece7de42016f969e81f84f7be06 | Java | 5,198 | 114 | /*
* 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... |
4cc5bab8a233a7387da52b7d29021978dd8a88719f2288ac2daa1a9f19d4c632 | Java | 5,203 | 93 | package de.uol.neuropsy.recorda.xdf;
import de.uol.neuropsy.recorda.recorder.TimingOffsetMeasurement;
import java.nio.file.Path;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.List;
import java.util.Locale;
public class XdfWriter {
static {
System.loadLibrary(... |
8e9212636455af3921bf6f3465b461c67633bdf27cd38f06e9676c23233739e9 | Java | 5,206 | 165 | /*
* 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... |
043bc252eef00f396ce1b79fa2a84884fb694176eff44012a82813a22df176ce | Java | 5,215 | 136 | package arcade.patch.env.component;
import java.util.ArrayList;
import java.util.HashSet;
import sim.engine.Schedule;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.core.agent.cell.Cell;
import arcade.core.env.component.Component;
import arcade.core.env.location.Location;
import arcade.core.sim.Series;... |
96afe83683783d09f3cd56fc591af850f052780785907abb71f3d42ad8d154fc | Java | 5,219 | 158 | package arcade.agent.module;
import java.io.Serializable;
import java.util.ArrayList;
import arcade.agent.cell.Cell;
import arcade.sim.Simulation;
import arcade.util.Solver;
import arcade.util.Solver.Equations;
/**
* Extension of {@link arcade.agent.module.Signaling} for simple EGFR signaling.
* <p>
* {@code Signa... |
08a000ef817086f7c5c5e2bd7c25ce119d54e65c09ef255aa3d6f488017ef90d | Java | 5,232 | 157 | /*
* 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... |
eecddfd1b02c668dd65efc59372ff5b5a70cbdc13117432cf7fd68b6c9fd0389 | Java | 5,245 | 126 | /*
* 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... |
5062425f85bab975e7850fb6264cfb8f3de60aaeabf141863693aff6d0cd09b6 | Java | 5,246 | 150 | /*
* 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... |
71f5cd100629a7e6e32d91b46d3b0f3789d389de32d85b09445ba913f41a806f | Java | 5,253 | 97 | /*
* 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... |
c88fbd02f73aa65ff13e4ab1a6ab3deeccad0eb34a65ac2dadff0665194d8959 | Java | 5,262 | 114 | /*
* 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... |
21ab73684a3fe70d71f500362132ea99d59d0bff02f3eb29c9e315d274107ab6 | Java | 5,268 | 165 | /*
* 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... |
16ac889665d8827e1f63451446c081c66ab2512ad8d6b86589a415c66d21d900 | Java | 5,290 | 129 | /*
* 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... |
2f99e82852f0890cf666d15ad05ae519f1a4d93ceed86f0f9b47c87402c3315f | Java | 5,297 | 128 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.broadinstitute.dropseqrna.barnyard.GeneFunctionCommandLineBase;
import org.broadinstitute.drop... |
12d2011289701d556ed4756b6fb4ba67b8b3591eb1d03d26f76aab7f4436e567 | Java | 5,311 | 122 | package arcade.patch.env.location;
import java.util.ArrayList;
import org.junit.jupiter.api.Test;
import arcade.core.env.location.Location;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.*;
public class PatchLocationHexTest {
@Test
public void getNeighbors_call... |
70b355107abbb5ccc23b6b3694ebefe5923d2cf524fff5a6391479665fe6a0cb | Java | 5,312 | 151 | /*
* 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... |
ef95b44c9df636ea91eefe1234745954cfb0e644d449737def846178c4606f01 | Java | 5,322 | 116 | /*
* 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... |
24924b0731484037220e6f0cce9cc3f672e7e37561e50d3e53b99590b7732e37 | Java | 5,327 | 136 | /*
* 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... |
7d4e312370aeb34576faf640890c7a528846d72b87b5db87c8ccf250d28ed0d9 | Java | 5,335 | 132 | /*
* 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... |
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