sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ff9d968ab7ac7a598cf9d423c3958b601ebe0c384d8e4b2dde140f809ecea17c | Java | 17,697 | 376 | package arcade.patch.vis;
import java.util.ArrayList;
import java.util.Arrays;
import sim.engine.SimState;
import arcade.core.sim.Series;
import arcade.core.sim.Simulation;
import arcade.core.vis.*;
import static arcade.patch.vis.PatchColorMaps.*;
/** Extension of {@link Visualization} for patch models. */
public fin... |
b5c0848e082072dca1db7923d169480ba2fcf1c5efaca14b33c0b45749b3dbe8 | Java | 17,840 | 451 | package arcade.potts.sim.hamiltonian;
import java.lang.reflect.Field;
import java.util.EnumMap;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import arcade.core.util.Matrix;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import ... |
2a149a2b04eb10074a64fab2ca04e9fda0669c0e4c0805a6604c0f00dea4db0a | Java | 17,961 | 585 | package arcade.patch.agent.cell;
import java.util.HashMap;
import java.util.Map;
import sim.engine.Schedule;
import sim.engine.Stoppable;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.Cell;
import arcade.core.agent.cell.CellContainer;
import arcade.core.agent.cell.CellState;
im... |
2f612ee8d41f74eeac7b4abd26b3c1be262dbf92714037038762f167560f6b20 | Java | 18,029 | 442 | /*
* 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... |
ca31ee67afc83d197b77f59dd2a65ab24bd89e953ebfe129a5be7ae18230942f | Java | 18,040 | 507 | /*
* Tester.java
*
* Created on June 24, 2002, 6:26 PM
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation.movingwindow;
import java.util.*;
import java.io.*;
import java.text.*;
import edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult;
impor... |
3787e8f85c97f0f4a9b83ba7305df005013b903dfcd23638ec17519a3711ed58 | Java | 18,052 | 506 | /*
* 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... |
6397cf9dab52a5d39108b03d3fe3c8f43d8735900c1ef29f08f72be76256da59 | Java | 18,115 | 618 | package arcade.core.util;
import java.util.ArrayList;
/**
* Container class for dense and sparse matrix representations.
*
* <p>Class provides a subset of matrix operations needed for solving a system of linear equations
* using the successive over-relaxation method in {@link arcade.core.util.Solver}.
*/
public ... |
21b50e79fd7be8fae9df8b327c5875a2e8dd23175a013a619760dc07f34efc61 | Java | 18,258 | 360 | /*
* 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... |
4dd467fd6bffc62e5d5da0a06e9ac0e8dcc9e5cd4bd97fd48801776d97ad18a3 | Java | 18,418 | 509 | package arcade.potts.sim;
import java.util.HashSet;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import arcade.potts.sim.hamiltonian.AdhesionHamiltonian2D;
import arcade.potts.sim.hamiltonian.Hamiltonian;
import arcade.potts.sim.hamiltonian.PersistenceHamiltonian;
import arcade.potts.sim.... |
5b3d8a20feaa9213123f463f7ac3e68a8eb448179658d53a92755f72be124140 | Java | 18,535 | 458 | /*
* 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... |
76662c0c1e3ee543e86ee5fdb11e2404ab7db57d439d8eff9c714ad26c96dd8a | Java | 18,566 | 432 | /*
* 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... |
23881603d3becb0d74593b2c94839625380772c3a3023f4571cd341e6169f2a5 | Java | 18,570 | 442 | /*
* 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... |
f16fa28e907bcfb3f043bf0cd5ead676fe2689dcba6dcfd462951e2cc2aa7124 | Java | 18,583 | 413 | /*
* 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... |
c615804fdc843ec3201819f0cc7e455a204fd4441ac26a8444a4b423afff48f2 | Java | 18,672 | 470 | package arcade.patch.sim;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import arcade.core.util.Box;
import arcade.core.util.MiniBox;
import arcade.patch.vis.PatchVisualization;
import static org.junit.jupiter.a... |
5f035b5fb767f8a36daa1748e41097bb8487756201c37309f2e59074f3661532 | Java | 18,815 | 518 | package arcade.core.gui;
import java.awt.BorderLayout;
import java.awt.Container;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
import java.io.OutputStream;
import java.io.PrintStream;
import java.util.logging.LogManager;
import javax.swing.BorderFa... |
ecac865ef6ab6924da8c1e49b7f0c670cb4ae17bd0b8431c5cf0b2488f5ac2f6 | Java | 18,844 | 389 | /*
* 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... |
6b2d95893f3e1a126c61d2d59c1a46fc6bcadf316725a2fb1ca503c3b6f35647 | Java | 18,908 | 386 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.IOUtil;
imp... |
b002de40d3f6133110dcca5b58654f2b18547c6fac2cffd496a91f48ec151765 | Java | 19,001 | 572 | package arcade.potts.vis;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.geom.Rectangle2D;
import sim.engine.SimState;
import sim.field.continuous.Continuous2D;
import sim.field.grid.DoubleGrid2D;
import sim.field.network.Network;
import sim.portrayal.DrawInfo2D;
import sim.portrayal.Portrayal;
imp... |
20f4f8b688bbf1828886ade0d199e44409f0fe2b3a36c738dc90da5a5e1ac3cf | Java | 19,094 | 516 | package arcade.potts.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.EnumMap;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonSeria... |
a7e7944199a27a3cb5b2494aa253939a2d3c071a7a1436031d903795f3d08d5d | Java | 19,110 | 608 | package arcade.env.comp;
import java.util.ArrayList;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.sim.Simulation;
import arcade.util.Graph;
import arcade.util.MiniBox;
import static arcade.util.Graph.*;
import static arcade.env.comp.GraphSitesUtilities.*;
/**
* Extension of {@link arcade.env.comp.... |
a589bc6b95500f5a6ae78ac056a0f276963f7f4f3b5c24ea9e6f1048d979f417 | Java | 19,149 | 410 | /*
* 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... |
167a58748e8912c081f696bd3c5a52353f85b246ae7bdf88334371889bf69683 | Java | 19,301 | 388 | /*
* 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... |
37bd1fa24134a429b95e9f5c08dfb5477fc68cd08993c42049949c70ff28e1d7 | Java | 19,411 | 450 | /*
* 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... |
a58b16c6b3226b6ed0dbeecbcb2c3cd2f5b6ceb0fb02e642c4992196468dce2b | Java | 19,416 | 380 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.annotation.Lo... |
26fb19c86633ecd7a68133b9f789bddff21d5e07bcbc70ac2a7e73449a33cc21 | Java | 19,443 | 395 | /*
* 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... |
7891b2c812c52cb057fc1f7e1e99a557afcb3b82dfb2e8354d384e1daa8e908a | Java | 19,500 | 501 | package arcade.potts.sim;
import java.util.HashSet;
import arcade.potts.sim.hamiltonian.AdhesionHamiltonian3D;
import arcade.potts.sim.hamiltonian.Hamiltonian;
import arcade.potts.sim.hamiltonian.HeightHamiltonian;
import arcade.potts.sim.hamiltonian.JunctionHamiltonian;
import arcade.potts.sim.hamiltonian.Persistence... |
179d69c6223ae4fc525732b85c2744733861af5c91d8f2d42a14dc241dfb78e2 | Java | 19,599 | 473 | /*
* 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... |
df162a8a113df4c60a2efd45a56aaa5f45c2305b914f3c0a1699ccf4a6c34d22 | Java | 19,619 | 509 | /*
* 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... |
25d050a7d1afb580ffe40ddf8b8bf541b3d58c2f0281b6a3e9e8b47fccac6f55 | Java | 19,629 | 628 | package arcade.env.comp;
import java.util.ArrayList;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.sim.Simulation;
import arcade.util.Graph;
import arcade.util.MiniBox;
import static arcade.util.Graph.*;
import static arcade.env.comp.GraphSitesUtilities.*;
/**
* Extension of {@link arcade.env.comp.G... |
9599340070ecce9f023d7fd107650fe3ac91655e2ae8ad367df91e2e8bfca638 | Java | 19,790 | 707 | package arcade.core.util;
import java.util.ArrayList;
import java.util.HashSet;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.*;
import static arcade.core.util.Box.*;
public class BoxTest {
private static final int NUMBER_KEYS = ... |
d13a47464c08b283fd7919507309e75a64b67d869bdb0b304ddfddd21ed7c713 | Java | 20,059 | 548 | /*
* 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... |
eb9616c81a92b425cceac3534f0edfb564e368ceed847faba46a2602e6dcf76e | Java | 20,243 | 519 | /*
* 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... |
6c8d8fc6d49fc3e334a80ff5b7aa7a87cd7d3da70d99ccf18a88f09d25b36031 | Java | 20,377 | 440 | package arcade.patch.agent.cell;
import java.lang.reflect.Field;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import sim.engine.Schedule;
import sim.engine.Steppable;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.MiniBox;
import arcade.cor... |
c0b5e447a4a993c4b2f6f5bd0e82ea3deff9d4bc202bc41d72feb7ed1316e134 | Java | 20,875 | 612 | package arcade.potts.vis;
import java.util.ArrayList;
import sim.engine.SimState;
import arcade.core.sim.Series;
import arcade.core.sim.Simulation;
import arcade.core.vis.*;
import static arcade.potts.vis.PottsColorMaps.*;
/** Extension of {@link Visualization} for potts models. */
public final class PottsVisualizati... |
efb102ee99b524a57da8f7fa256551c71efff15ec1a3ae24f134be3d4a26d6fe | Java | 21,004 | 541 | package arcade.patch.vis;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import java.util.HashMap;
import sim.engine.SimState;
import sim.util.gui.ColorMap;
import arcade.core.vis.Panel;
import arcade.patch.agent.cell.PatchCell;
import arcade.patch.env.component.PatchComponentSites;
import arcade.patch.... |
d0777a9a74b9b2048bd6e4281d75121509e6769440c0f9ca440d0231ef6850ec | Java | 21,139 | 473 | package org.broadinstitute.dropseqrna.censusseq;
import java.io.BufferedWriter;
import java.io.File;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.ut... |
8698e1a306c5b8795b492288dde6ab255c2221421c13f33f2bfd505859fba06f | Java | 21,152 | 535 | /*
* 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... |
381a20939babbecc6dd8870034c948610893f8fcec822002c96b314bef44782b | Java | 21,192 | 394 | /*
* 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... |
148e7fbf7fb11788f0146509c44ed728aeab5e81514cb7af353324c627315e5f | Java | 21,526 | 336 | /*
* 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... |
e7c00bf32ea5bf411fd2fca7efb04c13eaabcc055f87bd775e04f70316590200 | Java | 22,066 | 518 | /*
* 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... |
14d604ae142186e8ee724d44d4519fd5d4c433a5d3d85aeff17ace32548f910a | Java | 22,487 | 590 | package arcade.potts.agent.cell;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.stream.IntStream;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.*;
import ar... |
3c7b5f4ba77242fd149d29a10d1c90e457e824457b4628a3f831bf23dd14cf7c | Java | 22,537 | 460 | /*
* 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... |
f213e54d1ce42c5d557d0503081500fd3ca8065276342d1e70da81abbc4179da | Java | 22,553 | 600 | /*
* 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... |
e6b504731de3fbad7fb206ea5606033ac1d507c54a9a14afa386b803b8343e48 | Java | 22,672 | 528 | /*
* 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... |
61d073eaed25c22621c54af3b3114dc0c906d3034553d10223d2f8dad68a8d93 | Java | 22,735 | 442 | /*
* 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... |
ae69683f3121730e62ac324941302c20e21afa58651e43fd584e45597b00a62b | Java | 22,970 | 465 | /*
* 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... |
899950d7fee5d7e1a1a50ec773cebd18310cf0eee32f740cfd985ac19717d505 | Java | 23,038 | 469 | /*
* 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... |
c47163661598cfa0954020c5ec96586ec317411948d7ef8f3cd73d1b838225f1 | Java | 23,088 | 586 | /*
* 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... |
754a30d8218473e7868e64fe86e54792c07f3dda32ec7a8b484b733e4c6f9ede | Java | 23,658 | 670 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.HashSet;
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.core.ARCADETestUtilities.*;
import static arcade.po... |
9aea5e2d69caf431962f146aea54503c6e0795e5fd47130b82fce0b660fa9e05 | Java | 23,873 | 486 | /*
* 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... |
56f95edc24dc1e67da4e573c10df3b8d515b07b42ad4b2119e6850247372e3eb | Java | 24,072 | 757 | package arcade.vis;
import java.awt.*;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import sim.engine.*;
import sim.portrayal.FieldPortrayal2D;
import sim.portrayal.Portrayal;
import sim.portrayal.network.*;
import sim.portrayal.continuous.ContinuousPortrayal2D;
import sim.portrayal.DrawInfo2D;
import... |
0c05b5dbc12ea9a07520405aa628da9a5f554dd323ac87c00616480408b31104 | Java | 24,314 | 655 | package arcade.potts.sim;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import sim.engine.Schedule;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.ag... |
74e853d6e4e037c642a01808f10a32787b1a88cecb8126c68df4d3cdce415a6a | Java | 24,402 | 871 | package arcade.core.util;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Queue;
import java.util.Set;
import sim.util.Bag;
/**
* Container class for directed... |
6021d7aa8c1c15ed26e74f5fa6761b4540e640120c042fff7a5bb1b775fdf294 | Java | 24,598 | 559 | /*
* TreeFactory.java
*
* Copyright 2006 Michigan State University Board of Trustees
* Created on June 24, 2002, 5:01 PM
*/
package edu.msu.cme.rdp.classifier.train;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import jav... |
c68a2d56b8c0c8fae62a6747216c19dc9a27e0a03cacf5be54ee155e8c600b51 | Java | 24,861 | 541 | /*
* 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... |
1129123789c21c30d712a20edd9f2d38f4c0db47d5da451c90e5f14499c3dc7b | Java | 25,030 | 673 | package arcade.patch.env.component;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.EnumSet;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Series;
import arcade.core.util.Graph;
import arcade.core.util.Utilities;
import static arcade.core.util.Graph.Node;
import... |
3e600e0d2abd3296158aec498f4456226f984daf583455a5e776ddcb0d4e9c42 | Java | 25,082 | 627 | package arcade.patch.agent.cell;
import java.util.ArrayList;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.*;
import arcade.core.util.GrabBag;
import arcade.core.util.MiniBox;
impor... |
ce28b8752e8f5dfdce97ebde095747239b6cda372d5d59130d97c8eda86bd5b3 | Java | 25,537 | 519 | /*
* 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... |
719925ac7deac1d42bf43d8a10bfb5cae60f53b3de4ed6331041ad671dba6e43 | Java | 26,179 | 681 | /*-
* #%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... |
db840b8633aa44fc70dcdbeffa9123f5aee801ef5aebbad10ab3dbffd4024c1d | Java | 26,668 | 706 | package arcade.patch.env.component;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.EnumSet;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Series;
import arcade.core.util.Graph;
import arcade.core.util.Utilities;
import static arcade.core.util.Graph.Node;
import... |
4204fb3d1a3aacba1f1a087626f3e5f00cd62e3ee0934b8f3aa12df886be81aa | Java | 28,508 | 864 | package arcade.core.util;
import java.util.ArrayList;
import java.util.HashSet;
import org.junit.jupiter.api.Test;
import sim.util.Bag;
import arcade.core.util.Graph.Edge;
import arcade.core.util.Graph.Node;
import static org.junit.jupiter.api.Assertions.*;
public class GraphTest {
@Test
public void nodeConst... |
a330ffc2d471eed98b3a955c85d14b814fbffaa8d2c72c40208f4a3d7227d89b | Java | 28,765 | 591 | /*
* 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... |
5c23cfe6325cba5fe346043e8902bded513f73b7c304440e429c68cb593555c9 | Java | 28,954 | 867 | package arcade.patch.env.component;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashSet;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.core.sim.Series;
import arcade.core.util.Graph;
import arcade.core.util.Graph.Edge;
... |
e5519e7a0f1df782005cd568b720c8cb7dbc15cd133e95241535df87cf0e3100 | Java | 29,288 | 594 | /*
* 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... |
484b035ffe535841737f099c16747edea51f6a6f70f6d8c8463371ab21c85a9a | Java | 29,455 | 612 | package org.broadinstitute.dropseqrna.metrics;
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.annotation.GeneAnnotationReader;
import org.broadinstitute.dropseqrna.annotatio... |
49016221d2e33f1643e12fe0ab1df43a7d13ca85b72ee338d75572380751fa88 | Java | 30,045 | 676 | package org.broadinstitute.dropseqrna.metrics;
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.annotation.GeneAnnotationReader;
import org.broadinstitute.dropseqrna.annotatio... |
c56ab319fd5aa4d184e0069cd336c8676a37fc70b95bd468d3d0572201286091 | Java | 30,704 | 1,031 | /*-
* #%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... |
d9324b8a5ddc45165b948952453de907c2c0b89ce3193d018074c9dc4497cfb8 | Java | 30,746 | 999 | package arcade.env.comp;
import java.util.ArrayList;
import java.util.LinkedHashSet;
import java.util.HashSet;
import sim.util.Bag;
import arcade.util.Solver;
import arcade.util.Graph;
import arcade.util.Matrix;
import static arcade.env.comp.GraphSites.*;
import static arcade.util.Graph.*;
/**
* Container class for ... |
1ac6a7937725d458ebad7b86e11eb8750697c1965a85c82d5f4992e7ec53b917 | Java | 31,260 | 1,074 | /*-
* #%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... |
1460e638b6d8f6c32f7e76bc787a1db61f23f225861d2d9bd1f9fabe528c243c | Java | 31,449 | 722 | package arcade.potts.agent.module;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import sim.util.distribution.Poisson;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
import arcade.core.util.Parameters;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.... |
c26c5b1c6748199dade9a34a6887231be5144c224f6c78a4f2593c887ead5c91 | Java | 31,459 | 626 | /*
* 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... |
a9832d45c47efa80e6a5f2c0be33304e8519885d5a2b84d51dc6479ab93dbe6d | Java | 31,813 | 950 | package arcade.sim;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.logging.Logger;
import java.text.DecimalFormat;
import java.lang.reflect.Constructor;
import sim.engine.SimState;
import sim.display.GUIState;
import arcade.agent.helper.*;
import arcade.env.comp.*;
import arcade.sim.profiler.*;... |
d1a17c19a9c34a0247b08eaf70900d0cee0aa47070224fb159ea82e8d6058ab2 | Java | 32,659 | 937 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.LinkedHashSet;
import sim.util.Double3D;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.core.env.location.LocationContainer;
import arcade.cor... |
2381e99989b42be02e034215fe5db6647ea2235aa5f86553297d07932ecbc9fc | Java | 32,767 | 790 | /*
* 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... |
0fbfa79df8ada7118a1f67d19535a23de8adc79055d09b0f54a5a2b8b18ebe5c | Java | 33,042 | 714 | /*
* 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... |
364d25a453406e4560b6a1f8a4d2fc028c39307349008bfa5e1249779ebb64f5 | Java | 36,047 | 667 | /*
* 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... |
8eb26d697731dabe41c3dfc7f6c3f9c591221cee618af878ca30dec3d2e2fb98 | Java | 37,854 | 915 | /*
* 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... |
2eed181db4e8db68dc0f9591e1a6c8c06af5e3d7da6f8f19b6d7c16f30bafff5 | Java | 38,542 | 790 | /*
* 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... |
c7e798b27df0f62854f0aebd5caaece189f27641d3601b7ffbe6bb5e5f63f891 | Java | 38,592 | 704 | /*
* 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... |
1bdf989562c80aa1c5a5a94afd5bbc73daf322a70a85269a88e091c5d118e7bc | Java | 38,836 | 980 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.HashMap;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.Vector;
import arcade.potts.env.location.PottsLocationTest.PottsLocat... |
f134d9cb8bafa3873252d827f881d16b407e5831c8527cf458a5c1ed5fd5d8e7 | Java | 39,475 | 1,046 | package arcade.core.sim;
import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import sim.display.GUIState;
import sim.engine.Schedule;
import sim.engine.SimState;
import sim.e... |
84165ee3bac5e14f46a077c143d4f96525316e1769c0b5323f246e101f79d626 | Java | 39,806 | 1,031 | package arcade.potts.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.engine.SimState;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.Cell;
import arcade.core.env.grid.Grid;
import arcad... |
546bcfcc41d08e905c51a311da18866e5692d3db6ec1fdaea80b40b8875f6bdd | Java | 40,046 | 933 | /*
* 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... |
14616e3c0311b36f5d955a8ec212aafbde47d1a4824ea0f0401a19e1834568b4 | Java | 40,247 | 965 | package arcade.patch.agent.cell;
import java.util.ArrayList;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import sim.engine.Schedule;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.*;
import arcade.core.uti... |
9c1d29a24c1f1ba8a88d6c2d5dba7acb55b4ff91c5f1677e936f981399f86589 | Java | 41,895 | 1,234 | package arcade.patch.env.component;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Series;
import arcade.core.util.Graph;
import arcade.... |
ffa4bfecbbd83ddf307cd41f451cc9da8f88c1927edec836738232c826f93e46 | Java | 43,096 | 1,032 | package arcade.potts.sim;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Series;
import arcade.core.util.Box;
import arca... |
cd9cde31262f3e5b9234721621417ae8580756dd1084a75cec5d698c2dbd5dc8 | Java | 45,435 | 1,212 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.HashMap;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.*;
import static arcade.potts.env.location.Voxel.VOXEL_COMP... |
7a7d35cfee5a9a805a61e557fd726139d90d8f6e8cbb30e806f39d6ea1877ead | Java | 46,112 | 1,293 | package arcade.patch.env.component;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashSet;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.util.Graph;
import arcade.core.util.Graph.Strategy;
import arcade.core.util.Matrix;
import arcade.core.util.Solver;
impor... |
6002f48eec5f61358efecf8ffe59092cbf389915df56f6af7f3fd3e58a6b1f35 | Java | 52,117 | 1,808 | package arcade.env.comp;
import java.util.ArrayList;
import java.util.LinkedHashSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import ec.util.MersenneTwisterFast;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.sim.Simulation;
import arcade.env.loc.Location;
import arcade.util.Grap... |
82694c9c47b627044a6911552ef7925a155fb39fc9c43a877c39f58eed83e6fa | Java | 55,511 | 1,393 | package arcade.potts.agent.cell;
import java.util.Arrays;
import java.util.EnumMap;
import java.util.EnumSet;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.mockito.stubbing.Answer;
import sim.engine.Schedule;
import sim.engine.Stoppable;
import ec.util.MersenneTwisterFast;
impor... |
417d3fc1636ee4cad2ac45cc201d506c572ded6c151a82409213611a722318e8 | Java | 55,946 | 1,239 | /*
* 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... |
9e9db481c48cf4e62491b3d72fa1c7652241d67523b8080892a097540635f851 | Java | 60,528 | 1,666 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import sim.util.Double3D;
import ec.util.MersenneTwisterFast;
import arcade.core.util.Plane;
import arcade.core.util.Vector;
impor... |
b76d3400e4e78fb2a565ebbadf6f3e5f7764dee2896cee545dde7ee6c84e6aec | Java | 71,401 | 1,119 | package edu.ucsd.sccn;
import com.sun.jna.Library;
import com.sun.jna.Native;
import com.sun.jna.Platform;
import com.sun.jna.Pointer;
import java.io.IOException;
/**
* Java API for the lab streaming layer.
*
* The lab streaming layer provides a set of functions to make instrument data accessible
* in real time ... |
620397dae69aed42321135ac9e14c0c0cde774af784821aac11e40c3051d7bd4 | Java | 71,433 | 1,119 | package edu.ucsd.sccn;
import com.sun.jna.Library;
import com.sun.jna.Native;
import com.sun.jna.Platform;
import com.sun.jna.Pointer;
import java.io.IOException;
/**
* Java API for the lab streaming layer.
*
* The lab streaming layer provides a set of functions to make instrument data accessible
* in real time ... |
fd7212be12b50b54b717df794ca9fc3993aa5f1eb068963db162d3ef203c5449 | Java | 90,697 | 2,371 | package arcade.potts.sim;
import java.util.HashSet;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import arcade.potts.sim.hamiltonian.AdhesionHamiltonian3D;
import arcade.potts.sim.hamiltonian.Hamiltonian;
import arcade.potts.sim.hamiltonian.HeightHamiltonian;
import arcade.potts.sim.hamil... |
400d1b1a475143c6ad2d287362aeb26be91e3950f165748d6ea212cb10719c21 | JavaScript | 29 | 1 | var highlightActive = false;
|
2855b3c92f358b932eb9db631c3d2e983486e0cf4a6fc72a4abb678f6aeb92d7 | JavaScript | 72 | 4 | var searchData=
[
['real_2eh',['real.h',['../real_8h.html',1,'']]]
];
|
0d0dd26f93f7360dcf64ed97c5f7d4ed6740667ee27aa8ae2244313a3b98efd9 | JavaScript | 74 | 4 | var searchData=
[
['rqa_0',['RQA',['../namespace_r_q_a.html',1,'']]]
];
|
c045495a23bdfb440d0d3b36cf9e9415741b13a81d8bf20225b2858c0eec00c1 | JavaScript | 74 | 4 | var searchData=
[
['fnn_0',['FNN',['../namespace_f_n_n.html',1,'']]]
];
|
009f436eddb81a945b273e53831e90f4026760d1b4ed33ba179c97908ca4b62c | JavaScript | 77 | 4 | var searchData=
[
['fnn_2epy_0',['FNN.py',['../_f_n_n_8py.html',1,'']]]
];
|
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