sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
eafdecc573170938fd2a1e7ab60885fd0da977775e849aa1699c8cc4fb8cad3e | Java | 3,418 | 75 | /*
* 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... |
29eb2cd137844011e9cad922d89051c1ff645aa41120b8be547c3e2a87bfaa54 | Java | 3,420 | 82 | /*
* 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... |
a617fe572d477336e53b3342299f5d3b8db38172db3b596fd927bd37987aaa53 | Java | 3,420 | 130 | package arcade.agent.helper;
import java.util.ArrayList;
import sim.engine.SimState;
import sim.util.Bag;
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.helper.Helper} fo... |
e34c3f5cfdc74d419e8a6308efae9010ec2dbd8097be9a69f2f3ceb8b509f121 | Java | 3,424 | 95 | /*
* 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... |
97202367732a396f58e75a33c13e2d8352940e5374a8fcd5c0f2f57580a403e4 | Java | 3,430 | 101 | /*
* 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... |
b083fb07b33b28807935d3797f667858a1d9e6c9d00d85e57b2b7675166effd9 | Java | 3,433 | 89 | package arcade.patch.sim;
import arcade.core.agent.action.Action;
import arcade.core.env.component.Component;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
import arcade.patch.agent.action.PatchActionConvert;
import arcade.patch.agent.action.PatchActionInsert;
import arcade.patch.agent.action.PatchAc... |
8f1d08565f673d72ffdee1d6beb077a54940aaea6c8676f7d2c227355b6da0df | Java | 3,441 | 101 | /*
* 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... |
0f9be470cf2b24919371aa083289e0d496e47e609a750ac4b64b9e3fb8860a99 | Java | 3,448 | 75 | /*
* 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... |
a384d2f2e77da9206a9e0355a4aa07799963ba784480cfcccf4eecab343fe1fe | Java | 3,450 | 89 | package arcade.patch.sim;
import arcade.core.agent.action.Action;
import arcade.core.env.component.Component;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
import arcade.patch.agent.action.PatchActionConvert;
import arcade.patch.agent.action.PatchActionInsert;
import arcade.patch.agent.action.PatchAc... |
c56f71dc5aecbc3e2081f618b236fa83f393b63ad52ba9c723e464783cc7377f | Java | 3,450 | 80 | /*
* 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... |
dcf85f31db1dcae2065b8f1a0d40c84610c35c0a919326a5fdcfa8cf80d53590 | Java | 3,461 | 97 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.regex.... |
49288b8f799119c80f1d9d9fc963e673b5afb81bd481bc9eef43a8a00fcb01d5 | Java | 3,467 | 123 | /*
* 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... |
b5fa1554c75849f3fba0b0dfbd7ff495617d93a8d50beefcbdc5929fe8a89175 | Java | 3,470 | 107 | 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.assertAll;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static arcade.core.ARCADETestUtilities.randomStri... |
a557a8b2ae7950e147a1f21feb2a3cc04c3760f56e0b83c0db9e2fd2f3b7baf9 | Java | 3,471 | 83 | /*
* 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... |
edd3561fab5754646a160025480a86e7a07533f781887837283a73646558edfc | Java | 3,474 | 92 | /*
* 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... |
491cddd1a40bc303afcb12a30a9cd7b6cbe82121cd05255c0f0dfe0e50a4c890 | Java | 3,491 | 97 | package arcade.patch.env.location;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.LocationContainer;
import arcade.core.env.location.LocationFactory;
import arcade.core.sim.Series;
impo... |
43a2f7519f6fcda8b5a4f6f7fd513157bc8a0459c0615cf071a542a84bcc6744 | Java | 3,513 | 90 | /*
* DecisionMaker.java
*
* Created on June 24, 2002, 6:05 PM
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
imp... |
432412a5997b419eb3a8563e6a9f42f5cdaccff510c2cf1dcc0506879c610b51 | Java | 3,515 | 103 | package arcade.potts.agent.cell;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
import arcade.core.util.Parameters;
import arcade.potts.agent.module.PottsModuleQuiescence;
import arcade.potts.env.location.PottsLocation;
i... |
619f9f68a855ccb3c23b5ed58b37309d279f79bd4ec78155d6a4393db193d85b | Java | 3,521 | 72 | package org.broadinstitute.dropseqrna.sbarro;
import java.io.File;
import java.io.IOException;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
public class TagReadWithRabiesBarcodesTest {
/*
* Test data generation:
* gunzip -c /broad/mccarro... |
5557c332b0baac2226242cf163301c53fc34bf6b4116b0ba4225b14d1bbd9cec | Java | 3,532 | 74 | /*
* 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... |
b4518cf1381a93ca900ed8f8abdb876e1d98dad8fed98904044eee4b514feac2 | Java | 3,534 | 106 | package arcade.patch.env.component;
import java.util.ArrayList;
import sim.engine.Schedule;
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;
import arcade.patch.env.operation... |
55ea3013a259047e9aaa99dfa728181690f53f36303b9811c478ea8ac0446faa | Java | 3,537 | 115 | /*
* 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... |
2a9102cc5565bc2dd2575f67ff46e630c841394c03c5a1bd0291210b5f2cd4d2 | Java | 3,543 | 136 | package arcade.patch.env.grid;
import java.util.ArrayList;
import java.util.HashMap;
import sim.util.Bag;
import arcade.core.agent.cell.Cell;
import arcade.core.env.grid.Grid;
import arcade.core.env.location.Location;
import arcade.patch.env.location.PatchLocation;
/**
* Implementation of {@link Grid} for patch mode... |
97c29f2857d3f1664c14e0c75427731f1a991671c52b1274074404322e0921b3 | Java | 3,543 | 110 | package arcade.potts.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellContainer;
import arcade.core.env.location.Location;
import arcade.core.sim.Simulation;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import arcade.potts.sim.Potts;
impor... |
200201210bfbb0c7bf8a95306068be5e6d1a7e2c2ea6e6a582023c16015ee1a9 | Java | 3,547 | 81 | /*
* 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... |
a1f08de04c0b7ca47c79dbfb0894e286d2dd9669c4418bcbf14c34c833571318 | Java | 3,551 | 92 | package arcade.potts.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.util.PottsEnums.Phase;
/**
* Implementation of {@link PottsModule} for agents that divide upon reaching a volume ... |
e97bdc4fe171d987b59c8560673d144dd896bbcdcb9a3a74b349e4e2896d40b9 | Java | 3,556 | 104 | 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.core.util.exceptions.InvalidParameterValueException;
import arcade.potts.agent.modul... |
9f07d152b4ec31836a4c65e69810025e8dc1a5b5906eab35310e4462edb2406f | Java | 3,560 | 121 | /*
* 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... |
e21d8217bf9009bdecdad6d82d835924824ed0a274afe5f0c14c11308e8a21bd | Java | 3,571 | 133 | package arcade.vis;
import java.awt.geom.Rectangle2D;
import java.lang.reflect.Method;
import arcade.agent.cell.Cell;
import sim.engine.*;
import sim.portrayal.Portrayal;
import sim.util.gui.ColorMap;
/**
* Visualization for {@link arcade.env.grid.Grid} and {@link arcade.env.lat.Lattice}
* objects.
* <p>
* {@code... |
dd4bc86c394d98ffee81b4652bd077f001096605cd4f81e6542d5413a44beb20 | Java | 3,577 | 79 | /*
* 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... |
16e53d0a70acd6069dac4ef66ca862089ab5b1059988fd7c1def538672eb50b6 | Java | 3,615 | 108 | package arcade.patch.agent.action;
import java.util.ArrayList;
import sim.engine.Schedule;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.core.agent.action.Action;
import arcade.core.agent.cell.Cell;
import arcade.core.env.location.Location;
import arcade.core.sim.Series;
import arcade.core.sim.Simulat... |
db0429b3ebaf98cae4cc5a099bc760987a452128f02bc5072ab25c3d9ddbe51d | Java | 3,624 | 90 | /*
* 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... |
e6696c0885f576fb4d291cdc1e6203f227a23aa68e2c42be5aca7aeaecdd1011 | Java | 3,640 | 86 | /*
* 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... |
d28e9a1bdd1e7fcbbd73fbde5938e3cdeef510e5099fce980febb62e58bac21f | Java | 3,649 | 83 | /*
* 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... |
4fdc598dd2c8c7a7a4a6611e41c06f817f602a5c7a1981035dd422168c7a56e5 | Java | 3,667 | 94 | /*
* 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... |
b9d0b792140d96fe35758bc4d21c8508691e967c29e531138c4c0d7d72c0a541 | Java | 3,680 | 97 | /*
* 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... |
9e1fb48e8e8a38c5ae68d3de75854a9592c29d6d300e6425d9391e74c044e845 | Java | 3,705 | 118 | package arcade.core.sim.input;
import java.io.IOException;
import java.util.logging.Logger;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.XMLReader;
import org.xml.sax.helpers.DefaultHandler;
import arca... |
2029247e0bf946734eed367eb7d0523a4d0058dd623b7adde4bdfb893587082f | Java | 3,706 | 111 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Iterator;
import java.util.regex.Pattern;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.dropseqrna.utils.TransformingIterator;
public class BAMTagCleanupIterator extends TransformingIterator<SAMRecord, SAMRecord> {
private ... |
aed77adaa68755f3982bb3e0e962738d022bfeced733b386d7c97fa632b35706 | Java | 3,707 | 125 | /*
* 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... |
4237773186b0784d113298786f24c1c534b57ed8c7af2d4cf9f5cb78e7123fab | Java | 3,725 | 104 | package org.broadinstitute.dropseqrna.utils;
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.Allele;
imp... |
8c6810c0b381fd7305fd6586223ff0ba38aea9b6d43d554966d6dcdbd3bd8569 | Java | 3,732 | 120 | /*
* 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... |
0ffa5c6348d12e6b868f604a686d59325be21b6dbd0828bef9e3c515af7fcec5 | Java | 3,738 | 106 | package arcade.patch.sim;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import org.junit.jupiter.api.Test;
import sim.util.Bag;
import arcade.core.agent.cell.Cell;
import arcade.core.agent.cell.CellContainer;
import arcade.core.env.grid.Grid;
import arc... |
1b3f70edfa5f6073b43511ce9061da994dd36b1beeaa9a81add42ed7cd6e3d58 | Java | 3,744 | 89 | /*
* 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... |
76c5709af56d8019646df7e81f4284761503352e5e60d4b1895bf3d81a229c33 | Java | 3,765 | 108 | package arcade.patch.agent.module;
import java.lang.reflect.Field;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import sim.engine.Schedule;
import ec.util.MersenneTwisterFast;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCellCART;
import arcade.patch.agent.cell... |
98e88aea8427d066b67ec9db3e12f0590a43b23d4c0a4e2c0cdc6906be96be6c | Java | 3,792 | 108 | package arcade.potts.env.location;
import java.util.ArrayList;
import org.junit.jupiter.api.BeforeAll;
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.Region;
public... |
65cdb273c5ce29a352369bb26f6f57ea5412233493553266725c82032ad26f08 | Java | 3,799 | 129 | /*-
* #%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... |
aad1bba524c521a9315f40d2aecea4594445a5c362c38136c671e9545bd4ea1a | Java | 3,812 | 131 | package arcade.agent.helper;
import java.lang.reflect.Constructor;
import java.util.Map;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.sim.Simulation;
import arcade.util.Parameter;
import arcade.agent.cell.Cell;
import arcade.env.loc.Location;
import arcade.util.MiniBox;
/**
* Implementation of {@l... |
22540e2b8048806a8974e66f3906ab9e8610e35e63c32bdb764a1042b027f894 | Java | 3,821 | 105 | package arcade.potts;
import java.io.File;
import java.nio.file.Files;
import java.nio.file.Path;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import arcade.core.ARCADE;
import arcade.core.sim.Series;
import arcade.potts.sim.input.PottsInputBuilder;
import arcade.potts.sim.output.PottsOu... |
2a716fd1640ec91742df6bdac1dcdb2fb615a87e9d12241d3a96e5a1a5d8ce7b | Java | 3,827 | 126 | package arcade.patch.agent.cell;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.Cell;
import arcade.core.agent.cell.CellContainer;
import arcade.core.agent.cell.CellFactory;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.Location;
import arcade.core.util.GrabBag;
import arc... |
64ad1d455e56cff299f1c2265779f018c7a64c7a627731dafe9866b1ed6600f0 | Java | 3,835 | 105 | package arcade.patch;
import java.io.File;
import java.nio.file.Files;
import java.nio.file.Path;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import arcade.core.ARCADE;
import arcade.core.sim.Series;
import arcade.patch.sim.input.PatchInputBuilder;
import arcade.patch.sim.output.PatchOu... |
c29f97ba1e93b7757ea6d6266b1896074b4e4212c9ee531d34bffd5ea4ff9735 | Java | 3,851 | 117 | /*
* 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... |
c61f24634715a44961f4f484188535f3d4c24482c4a01c76e0aa9cfdef8c9744 | Java | 3,858 | 101 | package org.broadinstitute.dropseqrna.censusseq;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.annotations.BeforeClass;
import org.testng... |
ebc4da8d47e8d1ae79e9c427a22f5cb310b5732b0cec0692d2504a3a36f8966f | Java | 3,881 | 112 | /*
* 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... |
955775e38c139247b0018e7ac5a42857997afc060ef834ca7523fa41283b31e7 | Java | 3,882 | 107 | 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.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import htsjdk.samtools.util.In... |
e8101025276ba89b88a65bf1f9a9cfdbfd449eaa4333edb34736771e5b46e7c7 | Java | 3,892 | 122 | /*
* 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... |
6ea2089d50b4f7da3929c12536decbbff43b4473f2a26bee9e55ce0164b289a2 | Java | 3,894 | 79 | /*
* 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... |
c3092d4ba675a65b93f765013a3eb3855d21ff60be683f4e510b0b8f9f90bf7a | Java | 3,915 | 143 | package arcade.vis;
import java.awt.*;
import arcade.sim.Series;
import arcade.util.Colors;
/**
* Container class for commonly used color maps.
* <p>
* Uses {@link arcade.util.Colors} to define mappings.
*
* @version 2.3.6
* @since 2.3
*/
class ColorMaps {
/** Color map for cell state */
static final Col... |
a3df19fe3f4e009daa1620df94fd10136bbb2a1173c1258e272ca2f63a5e349d | Java | 3,929 | 94 | /*
* 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... |
af01a370801a43e2da739860fbf67c4078487427caef15259e2b3d68e70e44fd | Java | 3,942 | 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... |
96b286c4edf947230f12ed99a7791f75342578016b640db5e4951380b7532888 | Java | 3,945 | 120 | 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.assertAll;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTru... |
c7806bee38aac73b5a6057568a1f7f2548cefcf7b6ff4e0eddf9d865cef1beec | Java | 3,949 | 86 | /*
* 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... |
80d339dfb6da53a00892127f43c1cb29ceaa926d4d8cf9030ba7c1b150a58a75 | Java | 3,962 | 92 | /*
* 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... |
7184e6a32b4742d8185ab340a0aa0b53d20362dedbb910c2571e0398a865f2e3 | Java | 3,974 | 112 | package arcade.potts.env.location;
import java.util.ArrayList;
import org.junit.jupiter.api.BeforeAll;
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.Region;
public... |
16d9e043a5aa1a68828bc15e573e157f171caf273ffd6c67293e67805dc39998 | Java | 3,989 | 134 | package arcade.env.comp;
import sim.engine.SimState;
import arcade.sim.Simulation;
import arcade.env.lat.Lattice;
import arcade.env.loc.Location;
import arcade.util.MiniBox;
/**
* Implementation of {@link arcade.env.comp.Component} for generating concentrations.
* <p>
* A {@code Generator} is associated with each... |
3303f51829e8fb9565248c0ddd5185a2cac228452c675d64054b2549cc4f1656 | Java | 3,989 | 112 | /*
* 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... |
6014d9a3f1e205fe386d8366d4facc30960f44efbeb814a57bbb897db626d081 | Java | 3,992 | 135 | /*
* RawSequenceParser.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 24, 2002, 2:13 PM
*/
package edu.msu.cme.rdp.classifier.train;
import edu.msu.cme.rdp.readseq.readers.Sequence;
import edu.msu.cme.rdp.readseq.readers.SequenceReader;
import java.util.*;
import java.io... |
6b1c24de6e044b8459aa9348b0fbcb0f30bc5225270614578ffcad9ba0913e73 | Java | 4,005 | 127 | /*
* ParsedSequenceTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 8, 2004, 2:29 PM
*/
package edu.msu.cme.rdp.classifier.rrnaclassifier;
import edu.msu.cme.rdp.classifier.utils.ClassifierSequence;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterato... |
495c7f3df66df66360fe7df3876e30a3d44013fb4931f83b827462d97eca1e95 | Java | 4,010 | 82 | /*
* 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... |
8390495f2d381717a55434648eeb0af5911b52d0d7db58f5738257a3f6b77586 | Java | 4,010 | 90 | /*
* 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... |
384364b982b3e7e0c808a25d5b74e8de1edc5f6a6f37e29e0726d069bf0b215d | Java | 4,025 | 169 | package arcade.env.lat;
import arcade.sim.Simulation;
import arcade.env.loc.Location;
import arcade.env.comp.Component;
import arcade.util.MiniBox;
/**
* A {@code Lattice} represents the environment for molecules.
* <p>
* Each {@code Lattice} is a 3D array of doubles, where the values can represent
* molecular c... |
7400ed9026bd1220b1eb2597ed1873ce71677548e896750f3e32c74aab1e4e4b | Java | 4,041 | 95 | package arcade.patch.agent.process;
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.PatchCellCART;
/**
* Extension of {@link PatchProcessInflammation} for CD8 CAR T-cells
*
* <p>{@cod... |
a5e31f64df89114bf73a598f04fe4b6b671a1a08db635a0dd8374b751da4796f | Java | 4,063 | 85 | /*
* 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... |
df6577bfbfdd80ac819fa7290eccc83f8cce8573854823c108de5b0255c29f11 | Java | 4,066 | 100 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import org.junit.jupiter.api.Test;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.core.ARCADETestUtiliti... |
5869a0db904dbf50382557f9ff44be7e256375715db55b213cc37dc107c2d280 | Java | 4,094 | 99 | /*
* 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... |
c7236b94c5aa84792695f429e54a39e6b45078a4a8ec3f7b9a23424f2b908db1 | Java | 4,101 | 96 | /*
* 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... |
58776ac3ef3389541a33a0a3184a2c0c425eca6d05f769fca03c4ab043d93cbc | Java | 4,107 | 90 | /*
* 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... |
d302a6295808fa219739fd1b44411f1ef377ef173bcb55dc7fcba58b2cf71150 | Java | 4,112 | 97 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.annotation.functionaldata.*;
import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
import picard.annotation.LocusFunction;
import java.util.*;
import java.util.stream.Collectors;
publ... |
510b5661c5e78c99c8863038d5b4bdbc8cedfde5859bf4d27c0f70c96d130a5b | Java | 4,113 | 118 | package arcade.core.util;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.ListIterator;
import java.util.Set;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
/** Container class for utility methods. */
public final class Utilities {
... |
686292cdd5a0b9880f7b4198cad86580d2cd8a3715c6280dd8fc053b724fcc46 | Java | 4,124 | 112 | package arcade.potts.agent.module;
import sim.util.distribution.Poisson;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.potts.agent.cell.PottsCell;
import static arcade.potts.util.PottsEnums.Phase;
import static arcade.potts.util.PottsEnums.Regi... |
d52b22e04ab2d9fe8ed59b496190b3a90dd01e6e3de6f34dbc62f3f8b4b2381b | Java | 4,137 | 100 | package org.broadinstitute.dropseqrna.vcftools.filters;
import htsjdk.samtools.util.Log;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.dropseqrna.utils.FilteredIterator;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
import jav... |
a47fcacdbdab92c3f440a529f19fa1f354bede8293fe0581e9fcffcf9c2f916f | Java | 4,150 | 123 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import arcade.core.util.Vector;
import static arcade.potts.util.PottsEnums.Direction;
/** Concrete implementation of {@link PottsLocation} for 2D. */
public final class P... |
6ded328a62191c4d288479ee4cf7bf36068be32c512d6e748c2d8d62a09265ca | Java | 4,159 | 116 | /*
* 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... |
f851d304aae94d577986ffa5e348381cd94fa680e1c6404ed802b091b5b98d29 | Java | 4,168 | 98 | /*
* 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... |
a268467b9f760dea5f02afd0837f4c093732580e1349eeffbb2fb836c3c98d76 | Java | 4,195 | 112 | /*
* MainMovingWindow.java
*
* Created on November 15, 2006, 11:28 AM
*/
package edu.msu.cme.rdp.classifier.train.validation.movingwindow;
import edu.msu.cme.rdp.classifier.train.LineageSequence;
import edu.msu.cme.rdp.classifier.train.LineageSequenceParser;
import java.io.*;
import java.util.ArrayList;
import ja... |
5abd2f55cd7b5928decba78b77bea5ce307be81730e61f00a5301e7acad05f37 | Java | 4,200 | 115 | package arcade.patch.agent.action;
import java.util.ArrayList;
import sim.engine.Schedule;
import sim.engine.SimState;
import arcade.core.agent.action.Action;
import arcade.core.env.location.Location;
import arcade.core.sim.Series;
import arcade.core.sim.Simulation;
import arcade.core.util.MiniBox;
import arcade.core.... |
37e13e1b14761955a3c406a09fdc973942a66df03ea4ac1b5b47247bb32bb2f2 | Java | 4,220 | 92 | /*
* 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... |
8bb8cd69b4f82d7b0a6f16161f2bfa91c9c41cd31677c6e801c4b7a58994f904 | Java | 4,245 | 114 | 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... |
606110c13ea3bd075bc9e068f4da8633cc767b780d50bdce587482715ea1b340 | Java | 4,253 | 100 | package org.broadinstitute.dropseqrna.utils.editdistance;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
public class FindSimilar... |
ea7dcdff149d30175670a6727aaf3b67a9dc57f6b58f03d76e365a0ded8604ef | Java | 4,259 | 121 | package arcade.potts.sim.hamiltonian;
import org.junit.jupiter.api.Test;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.potts.util.PottsEnums.Region;
public class SurfaceHamiltonian3DTest {... |
6e375527e236adcedc51dd52e563abce5d92348c79dfd710764504fdf10fd92e | Java | 4,267 | 122 | /*
* 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... |
923c1b134f6fe4eaae2ea927bac042c6f0f45c07aa814fefa198c52c624641d0 | Java | 4,275 | 123 | /*
* 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... |
1a1d0b47c6128e74615c37f7d61f65d37a5ec1170633396345f699574d9dc513 | Java | 4,280 | 143 | /*
* 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... |
8095736d715a8c9360b8a5d4eb7d0c8f5bfd6f04e2eabed4f955cf1bad7a1231 | Java | 4,292 | 117 | /*
* 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... |
6f4a32b576c6e8f49df8e2f512864402febd71741c288c352e6f8abdbc34b403 | Java | 4,305 | 106 | package arcade.patch.agent.process;
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.PatchCellCART;
/**
* Extension of {@link arcade.patch.agent.process} for CD4 CAR T-cells
*
* <p>{@c... |
89437ded6f5d1899c18e8cb8ef4362df7b123c072883b6de7b9b4d863671f609 | Java | 4,313 | 112 | package org.broadinstitute.dropseqrna.utils.alignmentcomparison;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
public class CompareDropSeqAlign... |
e59e9585025dd5c02a811e1295c63ced96fd1c87b9e4da151d6c953ec8030dd7 | Java | 4,327 | 113 | /*
* 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... |
265f3fc4dfac4993399881a359c9be1173eeb4a570b195ab49a3efca183ae008 | Java | 4,344 | 90 | /*
* 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... |
aada2c8cf5b5f5b5027ae7745b60d77a74c348d8273c92dea8417ffbe76bbe2e | Java | 4,344 | 136 | package arcade.core.sim.output;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.logging.Logger;
import com.google.gson.Gson;
import arcade.core.agent.cell.CellContainer;
import... |
4bdff21bdcb46a63dfb44b89feccf6feaf9aa723ee6a05b5412602dd20c2cc3d | Java | 4,355 | 106 | /*
* 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... |
f133b854f160323a03eede65d9ce84bdf54a93e0e9dc17f17fe4767e71bd3d9a | Java | 4,371 | 154 | package arcade.env.lat;
import java.util.HashMap;
import java.util.Map;
import arcade.env.comp.Generator;
import arcade.env.comp.Component;
import arcade.env.loc.Location;
import arcade.sim.Simulation;
import arcade.util.MiniBox;
/**
* Implementation of {@link arcade.env.lat.Lattice} using for loop array iteration.... |
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