sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
aa31ee91df8ce45b0820323b7d01862e892d0a530cc95efa695041b363bdd996 | Java | 6,616 | 172 | 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 arcade.patch.util.PatchEnums... |
3a52008acea260e91cf35008f5542fde01576f0fea70b4906868f2a80b7f03a6 | Java | 6,635 | 137 | /*
* 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... |
ccdb9d067e737b0cd5ec73367331663c5451b720631cd5af16949646a8f171c1 | Java | 6,647 | 195 | /*
* 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... |
54faa27603a73811e529dfd37d031a138b720ae8e6248996ea668239bf8ff247 | Java | 6,695 | 174 | /*
* 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... |
98fa82603e993a2dc23a9555e89740eeb4a5eb86fbab3290ee1bccd44f85f501 | Java | 6,699 | 179 |
/*
* HierarchyTreeTest.java
*
* 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.orientation.GoodWordIterator;
impor... |
3c1939112c695323f699f05a752db3cd189bd3ca941d6715916ee6db932c3417 | Java | 6,710 | 170 | /*
* NBClassifier.java
*
* Created on June 24, 2002, 5:52 PM
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation;
import static edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator.PERCENT_SELECTION;
import java.io.IOException;
import java.util.ArrayList;
import ... |
0ea72049f8ad3a43a2858f3d9ff068289f29c7e266c74d15ef466e28ee5e6f7a | Java | 6,720 | 153 | /*
* 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... |
fe1a6cd84df064a39efce1ce0a4626386f53ea5913504a0220f95e4be93f194a | Java | 6,755 | 206 | /*
* 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... |
4ba812b7e5752fac9ae53da0897237ea2f1c85813c1340d54dc2789193a03922 | Java | 6,776 | 125 | /*
* 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... |
84f94baf6f47b3fbc2fc5695e0c44df7f759f139696b7fd00a298618b322375e | Java | 6,779 | 189 | 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... |
b0326175f0fa2fd483ea2ca6d4d77feda278d4fad64b5b56ebe5ccdfbaa2f761 | Java | 6,784 | 188 | package arcade.patch.env.component;
import java.util.ArrayList;
import sim.engine.Schedule;
import sim.engine.SimState;
import arcade.core.env.component.Component;
import arcade.core.env.lattice.Lattice;
import arcade.core.env.operation.Operation;
import arcade.core.sim.Series;
import arcade.core.sim.Simulation;
impor... |
e13514cef552c641d3db842cebc17ad0d351e43183f16aed06c69cc7c3f3b92b | Java | 6,798 | 256 | package arcade.sim;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.ListIterator;
import java.util.Map;
import ec.util.MersenneTwisterFast;
import arcade.env.lat.Lattice;
import arcade.env.loc.Location;
import arcade.util.Parameter;
import arcade.env.grid.Grid;
import arcade.util.MiniBox;
/**
... |
fc054babb2fd74ee12777aecdfa13c9d0fb40d7adaa325cf1b441d053eaba88b | Java | 6,800 | 146 | /*
* 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... |
5de890a11a88e0331214cfcc769d539cc2ec7b7cc75a93f07f1ae8d652d1f644 | Java | 6,804 | 199 | 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 medium EGFR signaling.
* <p>
* {@code Sign... |
2f974c260558480c2c82d241ba419b612d56188b75869a6c9280e85deb6c7966 | Java | 6,845 | 206 | package arcade.potts.sim.hamiltonian;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.M... |
a3bf122dcfd53dc219178fdf3407da51d394fbb15af442ed74b81fc3f5faa76f | Java | 6,863 | 184 | package arcade.potts.sim.hamiltonian;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.Set;
import java.util.stream.Collectors;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.Location3D;
import arcade.potts.env... |
67274ec695ff118f8b251dcf2a8b45aa49a234429bb218372c3d756053ece757 | Java | 6,893 | 223 | package arcade.patch.env.component;
import java.util.EnumMap;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
/**
* Extension of {@link PatchComponentSitesPattern} for triangular geometry.
*
* <p>The pattern unit cell is given by:
*
* <pre>
* -----------------------------
* \ / \ / \ ... |
68e72c8d43db0cc713b72844805b10780aab5806e577ae9d0016309a11dff354 | Java | 6,907 | 141 | /*
* 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... |
e744175a5a433dcc321c29de12ca7f313e96515ab7846f85c96b26efd1f5a129 | Java | 6,907 | 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... |
de9b87f6062f6357bc2bcd144accfff60c6f11854d7923f20e5089a1fca14eb8 | Java | 6,909 | 204 | /*
* 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... |
6b8ab192fae071f7a34a4fa50c2674feaa9616bb6f8c2afc4e98320d1d3ec1b5 | Java | 6,922 | 176 | /*
* 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... |
907ac8b5a699aead7f365fc9ef051800085c557d61bc1bc6f68a23852056c616 | Java | 6,947 | 187 | /*
* 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... |
1ed4836fc0a55344109f3f93757bbc74dad259ca49dc9388458540f7c2a9b353 | Java | 6,949 | 286 | /*
* 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... |
4a8b525461dac971eb1c57c87d8813cfeedfc4258575838d0529bbb81f0dc1fc | Java | 6,957 | 155 | /*
* 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... |
c85513aa487f52586324a7b145e744fa7425d13dd96f27ba40e14a5096af8dd5 | Java | 6,975 | 228 | /*
* 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... |
5be92ccdccec2421c6a1b1d6fd9eff463a08eb4eb06b79e232316ec5605505af | Java | 6,980 | 194 | /*
* 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... |
1b653946a35f0bd274040bf67e21e76c5843fe5c724841312b0d7a6860704caa | Java | 6,988 | 167 | /*
* 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... |
76b6f883eaf640b41761950d936674e018b8e5734e843716ea740311b48d0c21 | Java | 6,988 | 151 | /*
* 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... |
4f305f360f7ed79d7e5d2c78f7da4a7f7a75021786274b4fd665355100b57913 | Java | 6,992 | 223 | package arcade.patch.env.lattice;
import java.util.HashMap;
import java.util.Map;
import sim.engine.Schedule;
import sim.engine.SimState;
import arcade.core.env.lattice.Lattice;
import arcade.core.env.location.Location;
import arcade.core.env.operation.Operation;
import arcade.core.env.operation.OperationCategory;
imp... |
e286a32d8af73b59ef58b4e6dc8cab4ef401a9e2e85f6e1a96c91b2a0fd77492 | Java | 6,998 | 205 | package arcade.core.sim.output;
import java.io.IOException;
import java.lang.reflect.Field;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import com.google.gson.Gson;
import arcade.core.agent.cell.CellConta... |
5af0ceea682f77a12c34fbc4874e649e346064acaecff5c7e24d64733ce32275 | Java | 7,007 | 252 | package arcade.util;
import java.util.logging.Logger;
import java.util.ArrayList;
import java.util.HashMap;
/**
* Command line parser built from XML defining the possible commands.
* <p>
* {@code} Parser is built using the {@link arcade.util.Box} created by
* {@link arcade.util.Loader} when parsing {@code command... |
9965f46d0d293d292cb9a975dc0d4add24de6611547eed56321cb25ed54d44b8 | Java | 7,014 | 194 | package arcade.potts.sim.hamiltonian;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.Set;
import arcade.core.util.Matrix;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import arcade.potts.sim.... |
2476e65923c71fe58fd26614ab7a00cb42488d9398cf7c8df97967de2f8c271f | Java | 7,018 | 175 | /*
* 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... |
eb95e70146590c9321545c2ffd9ca554480420090722ebb3c13753b9e1711f03 | Java | 7,035 | 217 | 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 NormalTruncatedDistributionTest {
private stati... |
ba72f298f391bd96399580f3458f570ac9efa22d15c3818c64abdcd693505a2e | Java | 7,076 | 163 | /*
* 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... |
eaf2715ff7868a051ec23a5deca4ec42331546ee0367250e1d57c01d6f3a00c5 | Java | 7,083 | 194 | package arcade.potts.sim.hamiltonian;
import java.util.ArrayList;
import java.util.EnumMap;
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.Potts... |
9bae759b15e30f264d3942318a481387444a254b95146ab96bdf8394967d0eea | Java | 7,089 | 170 | /*
* 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... |
2465a3e1df4d0214e03153443bc5268e8fc61365a01b44f484ec62597ba1972e | Java | 7,106 | 170 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import org.broadinstitute.dropseqrna.barnyard.GeneFunctionCommandLineBase;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.... |
a8954f2c7da9db4d64872d3a74093cdbff5172fb35276e8d13aab3e3cc5d0ee9 | Java | 7,114 | 172 | /*
* 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... |
043dc2b6c9e988af04e880fe4941fa8eee62f0e7986692628d03b898b975a4bf | Java | 7,134 | 219 | package arcade.core.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonSeriali... |
3bb4f663761b799fb21f76600f0338c66ee3c3d5f3eb7464e0df66596bb51bec | Java | 7,172 | 208 | package de.uol.neuropsy.recorda.recorder;
import android.util.Log;
import de.uol.neuropsy.recorda.xdf.XdfWriter;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import edu.ucsd.sccn.LSL;
/**
* An ongoing asynchronous recording of one LSL stream into ... |
fe522daf11b6ecbab35a4a0027fc3ba095413e660e54aa4666a7e76ed8f3a9ac | Java | 7,176 | 230 | package arcade.patch.env.component;
import java.util.EnumMap;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
/**
* Extension of {@link PatchComponentSitesPattern} for rectangular geometry.
*
* <p>The pattern unit cell is given by:
*
* <pre>
* -------------------------
* | | | | |... |
d27be892e172c5119e9ebbf1b58d9ef959c4d654f6c0c2f860792c9ec41b5c70 | Java | 7,189 | 271 | package arcade.core.util;
import java.util.ArrayList;
import java.util.HashSet;
/**
* Container that maps a key to a tag category and a series of attributes.
*
* <p>{@code Box} objects use two {@link arcade.core.util.MiniBox} objects to map between key, tags,
* and attributes. Rather than nesting the key to attri... |
70db989a761f2b439cd671170eb234b58efb1d4debdf802054ab44383b25a8ab | Java | 7,195 | 187 | /*
* 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... |
83237f909033084e91efdedd592c69d06b03b6fdc7ee60516712d212b891ad73 | Java | 7,223 | 194 | /*
* 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... |
53b1b66c1999e28a19d52b3c0579e8f3b83363df55862a5e26cd94de4f032e56 | Java | 7,258 | 218 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.StringUtil;
import htsjdk.... |
3409a6518a17bc9a3d7fb59efccd271e011a0b9791e52ee9feabe4f36dc270f3 | Java | 7,270 | 237 | package arcade.patch.env.location;
import java.util.ArrayList;
import arcade.core.env.location.Location;
/**
* Abstract implementation of {@link Location} for patch models.
*
* <p>{@code PatchLocation} objects define where agents are within the {@link
* arcade.core.env.grid.Grid} (relative to other agents) and re... |
cfe691f0ee3e52ebb64ccda45b694f2f1b6822c5d008922162bcdac394819c75 | Java | 7,286 | 243 | 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... |
4d42627d9ac130c02d63dbcce8d8f12d8c6789da21ed0021908b1c28daea8ea8 | Java | 7,287 | 214 | /*
* 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... |
e09c80261d5170901f912bf0c555e5b179402ff3c968c2c7950ce4ab7c1cb2b4 | Java | 7,294 | 168 | /*
* 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... |
3cdeec9dbac0437c996cd50d5708f8242c4ee9ef3785de86cef9250c96bec620 | Java | 7,347 | 186 | /*
* 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... |
f4da8bfd4155b1cb5dfd9f3410afece3001e53b81d00a4e371f3190a4d96050d | Java | 7,393 | 169 | /*
* 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... |
f8a9c760f59b5e569fba0cf9392999920a71c12522c6fa3e64541fe20f012803 | Java | 7,393 | 179 | /*
* 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... |
623944588b7cb0ae89cc234eebe2aa2c71cf9680daa21e527e7b5a176069fe20 | Java | 7,396 | 179 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import org.broadinstitute.dropseqrna.utils.CountChangingIteratorWrapper;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.... |
502de95eedb09e9619a7531157edf5728c1b42bde5e96a6909c43cb6bb4cbcfb | Java | 7,405 | 210 | package arcade.patch.agent.cell;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
import java.util.logging.Logger;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.*;
import arcade.core.sim.Series;
import arcade.core.util.G... |
8c13632cd7f0fd9d273920578af7e0c84ead0565e9e01bc9d7e821723032c8c4 | Java | 7,475 | 197 | /*
* 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... |
31a48e00f713b535ef70156536a0a5c18e94ddace86eb92e7b91b478d7c0330d | Java | 7,525 | 171 | /*
* 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... |
a5fb55b2955b12a142fe7b60f56e9e602fa859dd20d20cccf09ac76d1aaf3835 | Java | 7,545 | 158 | /*
* 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... |
c467d26e8a0eac837a753b993d1a37d4ee6151ef56ee3c806db48dfb3e6dfcf1 | Java | 7,546 | 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... |
26ec6dfc26028149f4e08fe6d809308e0e6d3b1ba5ae0de69d5a1922aee13456 | Java | 7,608 | 239 | package arcade.core.util;
import org.junit.jupiter.api.Test;
import arcade.core.util.Solver.Equations;
import arcade.core.util.Solver.Function;
import static org.junit.jupiter.api.Assertions.*;
public class SolverTest {
@Test
public void testConstructor__returnsException() {
assertThrows(UnsupportedOp... |
5413707d21576b318f75fd3ff4c2a978745f7e2834e263395e6d18a0565802cd | Java | 7,625 | 192 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.dropseqrna.annotation.functionaldata.*;
import org.broadinstitute.dropseqrna.barnyard.Utils;
import picard.annotation.LocusFunction;
import java.util.*;
import java.util.stream.Collectors;
/**
* Th... |
a05f4d746b99537b5f5d9cb75e7a31d7e4e19464c3b8c8ce57aff6a60195f07c | Java | 7,632 | 201 | package arcade.potts.agent.module;
import org.junit.jupiter.api.Test;
import sim.engine.Schedule;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellFactory;
import arcade.core.env.grid.Grid;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.potts.agent.cell.PottsC... |
4dceb6f3bb679dc9735cb797cd28cf4e93fde354e33b8b2554cc12e7206cf80e | Java | 7,639 | 295 | /*
* TaxonTree.java
*
* Created on November 7, 2003, 5:22 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.Iterator;
import java.util.NoSuchElementException;
/**
*
* @author wangqion
*/
public class TaxonTree extends AbstractNode{
private int taxid;
private String name;
privat... |
6f3ea7db410710a698fdc2ec8acf0c516934a7eb701207342575054668f9c8b0 | Java | 7,650 | 209 | package arcade.potts.sim.hamiltonian;
import java.lang.reflect.Field;
import java.util.Arrays;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static org.ju... |
6df0e1150dd800d534409e0c40f668d8541999b2582d02f185d3b6bade970d24 | Java | 7,657 | 155 | /*
* 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... |
db78e7735d0945d47bcdf9a69688e38b7f815a46278715bab0370366cc677773 | Java | 7,671 | 245 | /*
* 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... |
77aaa12012eab4a40e37ce3af3d9fad8acb9f76b6e6ce92fbca86a6852dd7ff1 | Java | 7,750 | 207 | /*
* 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... |
e4d146034ba54ba1c67a3ce81a9f5f938ec8e2b5e72f622b289ca4af858f4d7f | Java | 7,763 | 202 | /*
* 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... |
7748e6aa3280bfb46a57201ca4e0103f59580d83848d161060a34dfcb8d6c6c1 | Java | 7,784 | 207 | /*
* 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... |
399d86277b3584763802a0f0dc235dda7e6fcba0d38108e84956d4f24379b8b7 | Java | 7,795 | 171 | /*
* 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... |
bc403f67722ec45dcd1741ebf64b1a1c1d89666383c04c6c9f4eafdb8b58a778 | Java | 7,835 | 284 | package arcade.potts.sim;
import java.util.ArrayList;
import java.util.HashSet;
import sim.engine.Schedule;
import sim.engine.SimState;
import arcade.core.agent.action.Action;
import arcade.core.agent.cell.Cell;
import arcade.core.agent.cell.CellContainer;
import arcade.core.agent.cell.CellFactory;
import arcade.core.... |
1567a1b278e8a8d6da41be0addba1107ddaa34ff56291448974a327860f4709b | Java | 7,849 | 204 | package de.uol.neuropsy.recorda;
import android.annotation.SuppressLint;
import android.content.ContentUris;
import android.content.Context;
import android.content.Intent;
import android.database.Cursor;
import android.net.Uri;
import android.os.Bundle;
import android.os.Environment;
import android.provider.DocumentsC... |
d3107b4ebc54cdf7caa34efed3b35d7e775b4a531857c38f3d9be108070fb4dc | Java | 7,869 | 257 | package arcade.env.comp;
import java.util.logging.Logger;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.sim.Simulation;
import arcade.env.loc.Location;
import arcade.env.comp.GraphSites.*;
import arcade.util.Graph;
import arcade.util.MiniBox;
import static arcade.env.comp.GraphSitesUtilities.*;
/**
... |
5886de6190744e4f34083632c58e21b97430285b2371ced14db3387ce1928d3a | Java | 7,935 | 191 | package arcade.patch.agent.process;
import java.util.Arrays;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.process.Process;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCell;
/**
* Extension of {@link PatchProcessMetabolism} for medium meta... |
e0abb515523f730241fa7c3fa1bc3a08fe425fc2f5d5fd4c5b125450d9b40cef | Java | 7,950 | 185 | /*
* 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... |
27978058048794425e1447e1e488e26c074c677d1c6827bef4b1344fa31d62aa | Java | 7,953 | 197 | /*
* 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... |
93ab2e1eaccbf4c98886a15d881d63e92ff4f76567e6c916a47d4418a8ce4f3d | Java | 7,970 | 193 | /*
* 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... |
0c4ef3f283358ff1c8082c46344da6ff28f1e02b83e5dd6e6803e3c229a6cbc9 | Java | 7,985 | 212 | 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 complex metabolism.
* <p>
* {@code MetabolismComplex} explicitly includes pyruvate intermediate between
* glyc... |
6d5f5a04593aa07e0427765fc3b6d1ad755589f0d3c18ddea8da2381dd67c987 | Java | 7,989 | 198 | /*
* 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... |
2ed0b22bc41011840dadd39713e301158d6d789c707b5f578b11ffa8d6820d08 | Java | 8,000 | 226 | package arcade.patch.agent.process;
import java.util.List;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCell;
import arcade.patch.env.grid.PatchGrid;
import static arcade.patch.util.PatchEnums.State;
... |
74b2239f5743300ebc93cfd6c15a6ef930f1a12e669c300d30df8303aadc8b91 | Java | 8,011 | 180 | 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.*;
p... |
4874fbae9b1107fd686ec3756e99aa79e4117dd9252ee05167f3066ebf28ab47 | Java | 8,022 | 233 | package arcade.potts.agent.cell;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.*;
import arcade.core.sim.Series;
import arcade.core.util.GrabBag;
import arcade.core.util.M... |
0b0986639650badcb203f23a112e9657c1e3fe72f630cd1cecf9b69675c8ac8d | Java | 8,052 | 219 | package arcade.potts.sim.hamiltonian;
import java.lang.reflect.Field;
import org.junit.jupiter.api.Test;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arc... |
25f4e6ed9b5cbe4972660391d25292d61a3d233ffb1119f48e88e96689f17932 | Java | 8,090 | 225 | /*
* 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... |
cb996b51b441b707b90601e131ca6f2a5230b97c6301c1813fc9f4d79a9b08df | Java | 8,116 | 190 | package arcade.potts.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.EnumMap;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonDeserializationContext;
import com.google.gson.JsonDeserializer;
import com... |
66e077e3257e93b7e500a2734d88af4b347627be73bca8ea7ee6c1088c11b6c7 | Java | 8,154 | 160 | /*
* 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... |
c2534142a8c870e2b599cb58a84540f4ad03fdd71563ea44f7ba493ca4e5de27 | Java | 8,154 | 168 | /*
* 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... |
b46fed0c093b7f46a4d638479f605adb977c2ef04e508797ce3125697d4d3182 | Java | 8,158 | 200 | package org.broadinstitute.dropseqrna.eqtl;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.*;
public class CreateMetaCellsTest {
private ... |
900e6e79e8cd0683eed688029f534c6449bb07839c831b8d9d09dd3b1eb64526 | Java | 8,168 | 209 | /*
* 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... |
3157b9c5b43a6b60036fc52e230322371a2bb7d5a09d164032e20b4a8ef16c9b | Java | 8,169 | 224 | 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.CoordinateUVWZ;
import arcade.patch.env.location.Coo... |
6840800e981bebbfe10e9d50c29d2ed0640e834187fb3055c9f2f3c763d41eb8 | Java | 8,184 | 175 | /*
* 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... |
4986454b2bbab0226be55bbbd2f66545ad582dfff47bcc5174c089a98797e16e | Java | 8,233 | 221 | package arcade.patch.agent.process;
import java.util.ArrayList;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.process.Process;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.core.util.Solver;
import arcade.core.util.Solver.Equations;
import arcade.patch.agent.cell.P... |
288aab1a23ba634ddd86445719c6fed0599ee3f03ce7b6b2f2b320dfd3e962e9 | Java | 8,235 | 181 | package arcade.core.util;
import java.awt.Color;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
public class ColorsTest {
@Test
public void getColor_calledWithIndices_returnsColors() {
Color[] colorArray = new Color[] {new Color(1, 1, 1, 1), new Color(255, 255, 2... |
30f603cebfea7480b3b10ab2067e22c8861d4344b38b09d173861c7d7c31e34a | Java | 8,239 | 241 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Queue;
import org.a... |
bffd73dcf5adc4f8dd9e227c10869512d637b81de3ade5b1cf5d7cf65afc8d52 | Java | 8,247 | 271 | /*
* RawHierarchyTree.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 24, 2002, 2:36 PM
*/
package edu.msu.cme.rdp.classifier.train;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator;
import java.io.IOException;
import java.util.ArrayList;
import java.uti... |
3e9729c5074a66de07742329980832ae3a34c77f60b30d3a7d6157103a6c6e52 | Java | 8,258 | 217 | package arcade.patch.agent.cell;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.GrabBag;
import arcade.core.util.MiniBox;
import arcade.core.util.Parameters;
import arcade.patch.agent.module.PatchModule;
import arcade.patch.agent.p... |
62a6be6a4b88146840ab9e81d2a33afc24c948993e3092c70e96f9f8f152c020 | Java | 8,291 | 205 | /*
* 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... |
38705ca1c801ebead2d4528acb5b4c6b17ed6ff77015a392788db3192b2de839 | Java | 8,325 | 208 | /*
* 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... |
1cb2e4c1b79ed40e955eb351561a708fb0f2adfd4e2198227203c0cee747fb52 | Java | 8,364 | 263 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.HashMap;
import static arcade.potts.sim.Potts2D.*;
import static arcade.potts.util.PottsEnums.Direction;
/**
* Static location methods for 2D.
*
* <p>Interface defines generalized 2D voxel methods that can be applied for both {@link
*... |
1d9e088bacb4c5469c915c8e66cfdb26d2499247e80765d2b59c906638bdaf75 | Java | 8,371 | 211 | package arcade.patch.env.component;
import sim.engine.Schedule;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.core.env.component.Component;
import arcade.core.sim.Series;
import arcade.core.sim.Simulation;
import arcade.core.util.Graph;
import arcade.core.util.MiniBox;
import arcade.patch.env.location... |
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