sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e8e0802fd172efdfca045c2f280fc0250e085545379502280598f0143d1e3752 | Java | 11,732 | 248 | /*
* 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... |
efb8e357a23abc73f8f0a2692c7da2069425733b2de36d02664adf6d7dee9a3a | Java | 11,743 | 278 | /*
* ClassifierFactory.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on November 6, 2003, 10:56 AM
*/
package edu.msu.cme.rdp.classifier.utils;
import edu.msu.cme.rdp.classifier.Classifier;
import edu.msu.cme.rdp.classifier.HierarchyTree;
import edu.msu.cme.rdp.classifier.Traini... |
58a19437595ab3338ed59ddc4b62adc70552741bb14ba4536f301b927745781e | Java | 11,816 | 317 | package arcade.patch.env.component;
import java.util.EnumMap;
import sim.engine.SimState;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
import arcade.patch.util.PatchEnums.ComponentType;
/**
* Extension of {@link PatchComponentSites} for pattern sites.
*
* <p>A repeating pattern of lattice indice... |
20d3ca37addb1089df9151f6dd93b6ba8caeee662438e55d570a1c69bd2b20f8 | Java | 11,854 | 384 | /*
* 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... |
17cc4934ee6ecf182b1746cef124f56e47018d606d5ee5dcb5053253c4b1f4c9 | Java | 11,967 | 378 | package arcade.core;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.logging.Logger;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import org.xml.sax.SAXException;
impor... |
1153df49da03f8c67b43c9ecaf671ff71bf8952f96c686277262f5f2ba7cffb1 | Java | 11,974 | 274 | /*
* 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... |
60ef05af4bfbe3296b8fac7f90fe7a9ff8b298045fe30e0bfe80a96598800994 | Java | 12,126 | 292 | /*
* 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... |
28401e3034ad969e689430814ac477023a8da453a37eb1b08dfe5c11da142c31 | Java | 12,227 | 386 | package arcade.core.sim.input;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.logging.Logger;
import java.util.stream.Collectors;
import arcade.core.util.Box;
import arcade.core.util.MiniBox;
/**
* Command line parser built from XML defining the possible commands.
*
* <p>{@code InputParser}... |
08ed4f5565848514dd8b91711ab76626d649aeb6c4ed6dbaa5a3df8a0c110217 | Java | 12,236 | 253 | /*
* 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... |
9645a921600692fe08780267ea8ab07163c4149e3cae61f2e86d192eefacc124 | Java | 12,248 | 273 | package arcade.patch.agent.process;
import java.lang.reflect.Field;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.process.Process;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.... |
75915601a0a21bab7defd537b9164d02c5f81c8d3a14704706a7c663dce620bf | Java | 12,305 | 312 | 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 arcade.core.util.Vector;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.potts... |
df889fa9447ef155e13c52d34d2e33c77fd79a4e91fc941791d42d479dae133d | Java | 12,410 | 319 | package arcade.patch.agent.process;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.core.util.Solver;
import arcade.core.uti... |
c9971b075df5a35bc7dbc1ef0375070a7293c83a2086184bd9a220ff1ca6eec9 | Java | 12,482 | 364 | /*
* 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... |
9f3a1b5fe1a89af05a46b0ea8afd0248fd6ed283433ecb7bad57da54ebf77e84 | Java | 12,528 | 300 | /*
* 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... |
acbd5da8ed2973a3dbeac03c1401fe8fbf6491c148501551dc67c357eceb7145 | Java | 12,539 | 327 | 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... |
77db35ac8a8b1ab216c2d4e39f34ef1d08f51cc1399ae8eade5a9d0e3e09f78b | Java | 12,635 | 322 | package arcade.potts.agent.cell;
import java.util.EnumMap;
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.potts.agent.module.PottsModuleApo... |
2557b9f7242d78b54918db8341e2430ed7fbe151442b83aa1f03585767561fda | Java | 12,760 | 232 | /*
* 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... |
c48745cdd152d0e12dad1fc9abbda70d6f46c5e3f5f71bed53f6acd680bf28e8 | Java | 12,832 | 357 | /*
* 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... |
1a56c75f46b02fe8297fb7e38d9850b8ebe026b2c55367ad586f9e15a845042e | Java | 12,836 | 290 | /*
* 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... |
447979a39a91f5f23e019b198b18c7a18972bf0efd97c1ae7bd03e9d41fc3d78 | Java | 12,943 | 357 | package arcade.core;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.security.InvalidParameterException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.Objects;
import java.util.Scanner;
import java.util.jar.Attributes;
import java.... |
f0d7b5028e60738ab2ff915cd4ea29304881f69f7208b4f05d1c04c1bfa97ab0 | Java | 13,017 | 394 | package de.uol.neuropsy.recorda.recorder;
import de.uol.neuropsy.recorda.util.ListToPrimitiveArray;
import de.uol.neuropsy.recorda.xdf.XdfWriter;
import java.io.Closeable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.function.IntFunction;
import edu.ucsd.... |
dd0eb2983929669d2dee74a54b860caed8c64baedcc72522dcf7c07143d6746a | Java | 13,037 | 346 | /*
* 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... |
15825d373ba83127356670419a9aef619e1d06756d4dcd98f6f5c0e17f33d636 | Java | 13,083 | 336 | 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.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static org.j... |
3449b146ef7a018bbb7533eea0a030a980fd510aae783b319464042532d6b6c7 | Java | 13,087 | 329 | /*
* 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... |
0c774b7a76a58f9ceb3c287c42268e1f74e97a5bea31797f064478a32540f620 | Java | 13,116 | 327 | /*
* 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... |
c27607aab879fbaca851b830615b024a5f820e7d94096c3367cd9aa462dc2ea5 | Java | 13,182 | 506 | package arcade.util;
import java.util.ArrayList;
import java.util.Collections;
/**
* 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.u... |
a6474b35a1d9e129fab6f0b1a170afa0fce949a6480cc25413cce0d409759adb | Java | 13,235 | 305 | /*
* 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... |
768c8314eb5a1c6774d8df217e093c80d8b69e334a5b6c44b5bfefa85cc605b0 | Java | 13,256 | 379 | /*
* 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... |
1118b4bf3d08ecadb2cb8ced27a3db97fb97739cdbf2d5e1728ddcc0d187a128 | Java | 13,310 | 288 | 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;
import arcade.patch.agent.cell.PatchCellCART;
import arcade.patch.u... |
402db9ce5b0a899ecf5426ce7596b1ce0abc8a730b3ea5933092fe3398783039 | Java | 13,350 | 313 | /*
* 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... |
6e7c886b3972e57f642af1285eecaca9462860057723b5b2f6d1a6ef7d5dc1c2 | Java | 13,564 | 364 | /*
* 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... |
cd7c76a72a3e38986e6851c89bfea47cc75c1659a88321c500da367934ffc72a | Java | 13,568 | 456 | package arcade.patch.sim;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import com.google.gson.reflect.TypeToken;
import sim.engine.Schedule;
import sim.engine.SimState;
import arcade.cor... |
f1d977b1e6c9858c03f3cd19f927e281b2cc9742018524b62b0509c5cdcd4fc5 | Java | 13,674 | 274 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalDataProcessorStrategy;
import org.broadinstitute.dropseqrna.barnyard.GeneFunctionCommandL... |
b8a8543a90726d2ea11a1c92f650c57b1b9327a46f377c8eeb0c2a2d5d9213e3 | Java | 13,727 | 370 | 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 arcade.core.util.Vector;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.potts... |
7775c8a5e714196584e07c532a37789132173968e01b962ca91793afb433f953 | Java | 13,729 | 280 | /*
* 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... |
2829b7b049ca3cd0ea437ac15cec8bf2abea564fac4c811c9529ba8b68cca0cb | Java | 13,751 | 412 | package arcade.potts.sim;
import java.util.ArrayList;
import java.util.HashSet;
import sim.engine.SimState;
import sim.engine.Steppable;
import ec.util.MersenneTwisterFast;
import arcade.core.env.grid.Grid;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import arcade.potts.si... |
d9c4745e8262b0a490a0efbdbe1cf9d7048d6a33697830e4390ac05f5c93bbf3 | Java | 13,903 | 264 | /*
* 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... |
c411a050785d785f127aef03f2efe09c40e9f9df034987a31fc53385a8aa85bb | Java | 13,972 | 396 | /*
%
% ImageDecorrelationAnalysis GUI and input manager
%
% ---------------------------------------
%
% A detailled description of the method can be found in :
% "Descloux, A., K. S. Grußmayer, and A. Radenovic. "Parameter-free image
% resolution estimation based on decorrelation analysis."
% Nature methods (2019... |
8222985cce02d470b7d3d6fdbac4ddec6886aafc24acc4418b6f95b1f3823016 | Java | 13,982 | 297 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import org.broadinstitute.dropseqrna.annotation.functionaldata.DropSeqFunctionalDataProcessor;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalDataPro... |
7dd93c4af056f733a1513743050d7d5e13028b3ed8cb2d925c9d161f3de330d8 | Java | 14,043 | 308 | /*
* 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... |
118e546b1b65719b2d2638e587618c951e61d0471639fd601ba05731943f8dd9 | Java | 14,091 | 349 | package arcade.patch.sim;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import arcade.core.sim.Series;
import arcade.core.util.Box;
import arcade.core.util.MiniBox;
import static arcade.core.util.MiniBox.TAG_SEPARATOR;
/** Simulation manager for {@link PatchSimulation} instances. */
... |
c8f294dbe0091f9627a0822d66a35ec7e10ff2d688e52809c4b04c47557e74ef | Java | 14,094 | 305 | /*
* 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... |
05ff51326af5060e6bc5aea2c8b286b6dcc2003f487044f1f1ce8a468df1f1a4 | Java | 14,114 | 355 | package arcade.potts.sim.hamiltonian;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import arca... |
dfea911db16c2a83aef880c9a140dad6c66347336fe156525301ed19f7a0e02e | Java | 14,191 | 320 | /*
* 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... |
071b792c4955143fce2d736710e80c3d7c5fe0fea9a0b02273499fad90584d01 | Java | 14,212 | 387 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import org.junit.jupiter.api.Test;
import arcade.potts.env.location.PottsLocation;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.core.ARCADETestUtilities.*;
import static arcade.potts.util.Pott... |
07ae2d55aba2c28b2b3ff1a5ea18d61c4991c5e8572b155185b60d506ac98f8a | Java | 14,298 | 334 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.Collections;
import java.util.EnumMap;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.potts.agent.cell.PottsCellContain... |
5db02c3a7fd538fc9170064d5ff486f43bbba0ae7701034d4d6bb049fa965987 | Java | 14,377 | 414 | package arcade.patch.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.HashMap;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonSeri... |
e3929e0c456e6ef8749f6673ca5b8eae559a714ea0c316424173d5a45c2b4c0f | Java | 14,390 | 590 | package arcade.util;
import java.io.Serializable;
import java.util.List;
import java.util.Collections;
import java.util.ArrayList;
import java.util.Map;
import java.util.HashMap;
import java.util.Set;
import java.util.LinkedHashSet;
import sim.util.Bag;
/**
* Container class for directed graph using nodes as hashes.... |
e8970c26c2fec5ada399932197d3faf1ca239ab1528a301f3c217a609b038d6b | Java | 14,399 | 302 | /*
* 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... |
5e066a6ae53af1901b49094f1d9fc755958021cbe861ddb9cd18e4bee561f15c | Java | 14,425 | 415 | package arcade.core.util;
import java.util.ArrayList;
import java.util.Comparator;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.util.Matrix.*;
public class MatrixTest {
private static final double EPSILON = 1... |
9fdfac567aee7e6f74e1eec6924b32c10e417ecc23b2a7b417fd10fc7ea52dcd | Java | 14,494 | 321 | /*
* ComparisonCmd.java
*
* This is a command line comparison class
* Created on November 7, 2003, 5:14 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
/**
*
* @author wangqion
*/
import edu.msu.cme.rdp.classifier.ClassificationResult;
import edu.msu.cme.rdp.classifier.Classifier;
import edu.msu.cme.rdp.... |
220c84240e12b3b1ac5eaceaf33b1c34f4c90d0f2d1a3f4e881a3ef65ca7c295 | Java | 14,596 | 316 | /*
* 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... |
90fc302ca1b5e1055119291319fe6d119b8b8c7e75edf050e1f7ce61d4e54a3d | Java | 14,620 | 345 | /*
* 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... |
8bf50de3ff39d6eb4e85d3bbdbe8c8926ddab1b160fee003ccaf04d9ebea0926 | Java | 14,760 | 359 | /*
* 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... |
2f47bd6d35015c7c466d79f6d658ca16a6281ff4c01821779b2d1d4c851f67a1 | Java | 14,846 | 406 | /*
* 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... |
eb78452e0316b3ce765fd75765d46babb4598e7e37014edd1aa71b83c5c4f807 | Java | 14,943 | 377 | /*
* 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... |
a73b8f9496137765e38936e14a898a9bccefba33e2f5e753adb7bf54fcf24623 | Java | 14,963 | 342 | /*
* 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... |
65a390814910bdb4d5eaf7a356e53a6c81ef8fbc3d839126f0378aca767c8057 | Java | 14,992 | 323 | /*
* 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... |
41ccfdabd621b90ff2a72682408fbafe1e2ed4a719e044807185d160fbb878c1 | Java | 15,072 | 386 | /*
* 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... |
7601694066746606bdd9d4d2c196b32320a8f92f0b7d0511679c6764cff536e1 | Java | 15,075 | 424 | package arcade.core.util;
import java.security.InvalidParameterException;
import java.util.ArrayList;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.distributions.Distribution;
import arcade.core.util.distributions.NormalDistribution;
import sta... |
074c23fb7b3ff4461f8cc498b43269b4e1bee378996b7345e63672a9c087c15e | Java | 15,252 | 353 | /*
* Classifier.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 18, 2003, 6:05 PM
*/
package edu.msu.cme.rdp.classifier;
import edu.msu.cme.rdp.classifier.utils.ClassifierSequence;
import edu.msu.cme.rdp.readseq.readers.Sequence;
import edu.msu.cme.rdp.readseq.utils.o... |
23ec93e71c3eb7413e5a2d42c76b6980ac7dfca162a3df4f67af1ce7963cf03b | Java | 15,282 | 323 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.annotation.LocusFunction;
import java.util.List;
public class StarSoloFunctionalDataProcessorTest {
... |
2a78ebe441a56e03e3ac84cf8e029c01252177dbfd67480db15ffdc27ae8d7da | Java | 15,348 | 418 | /*
* 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... |
d7ab84b3b42ee25c836bde76981063d23a17932e686097124b8caea5c6820ff0 | Java | 15,373 | 411 | /*
* 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... |
e43f9e8b04eb9c0b09dc11e4734dbde294a14fbc1a1e5503f47222c4ccd0667b | Java | 15,416 | 376 | package arcade.potts.sim.input;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.stream.IntStream;
import org.junit.jupiter.api.Test;
import org.xml.sax.Attributes;
import arcade.core.util.Box;
import arcade.core.util.MiniBox;
import static org.junit.jupiter.api.Assertions.*;
import static org.mo... |
9aa4a57e124d60728e1e18cf084d0c1dd5af551b9d0677d6b26454f6c01884b6 | Java | 15,530 | 323 | /*
* 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... |
add8c84afca98b77d79dbb4c4638e7445a6e4b8965245bbeb5f6680dd4c278a0 | Java | 15,610 | 297 | package org.broadinstitute.dropseqrna.barnyard;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import org.apache.commons.math3.stat.regression.SimpleRegression;
import org.broadinstitute.dropseqrna.barnyard.digitalexpression.BarcodeSimulator;
import org.broadinstitute.dropseqrna.barnyard.d... |
1be536a7a6c618e8dd914edf07361bc5136caa236394ae8135894a89a5bd1771 | Java | 15,679 | 458 | 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... |
a6a533208867a2ba0a663edc2054e595e725646f7ec34f42db44a9a9ee46490e | Java | 15,700 | 471 | package arcade.agent.cell;
import java.util.Map;
import java.util.HashMap;
import sim.engine.*;
import sim.util.Bag;
import arcade.sim.Simulation;
import arcade.util.Parameter;
import arcade.env.loc.Location;
import arcade.agent.module.Module;
import arcade.agent.helper.*;
/**
* Implementation of {@link arcade.agen... |
92fd0fab9ff7132f6eec92bacd6d79181cd669da560961aa98f9487997f5f531 | Java | 15,764 | 401 | /*
* 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... |
d9513add453c665f7dea7c075744bd2a5e38852374cf5438d8d889ca38634227 | Java | 15,842 | 386 | package de.uol.neuropsy.recorda;
import android.app.Notification;
import android.app.NotificationChannel;
import android.app.NotificationManager;
import android.app.PendingIntent;
import android.app.Service;
import android.content.Context;
import android.content.Intent;
import android.content.pm.ServiceInfo;
import an... |
c1ac70503688b917cbc01738dddb12727336dca244182210cf1a006254f87291 | Java | 15,963 | 485 | package arcade.core.util;
import java.util.ArrayList;
import java.util.logging.Logger;
import arcade.core.util.Matrix.Value;
import static arcade.core.util.Matrix.*;
/**
* Static utility class implementing various numerical solvers.
*
* <p>Implemented solvers include:
*
* <ul>
* <li><em>forward Euler</em>: fi... |
17fec6a90be5de0f6f1da42c6c5962b6b7a21b8b9cece77f033618721bbc9a60 | Java | 16,144 | 370 | /*
* 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... |
2b64e103abb1e354c76490649f00f886397234e9aed08dfefaf3c86030b73b2a | Java | 16,357 | 406 | /*
* 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... |
26dd94142a26483356e033add44ccacb1af4e3865bc3cc76fa19713c806107fd | Java | 16,398 | 348 | /*
* 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... |
75260d6d5576bc595904fdbe5af1b16d9d3b6f849e8d4a9eb5b9d07301493792 | Java | 16,428 | 357 | /*
* 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... |
0901fde0fdc7128d17278686e0500dc63ba878cd3a77aaf0295729beda6fa453 | Java | 16,493 | 454 | package arcade.patch.vis;
import java.awt.Color;
import java.awt.Font;
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.po... |
7ceb6e137cfaf5c1acede842efaadc1c0f46a1b93d85b9be882fcde16dc9a15f | Java | 16,511 | 421 | package arcade.patch.agent.cell;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.Cell;
import arcade.core.env.location.Location;
import arcade.core.sim.Simulation;
import arcade.core.util.GrabBag;
import arcade.core.util.Parameters;
import arcade.patch.env.grid.PatchGrid;
import ... |
a0158ef2814ebcaa2416263d129d0396730c3ad1163a0b3e4afb6100e3cb437d | Java | 16,535 | 415 | /*
* 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... |
ce1c8ed1360272eb084397bc903fbad225833ce416f03d9e533188235cd0a75d | Java | 16,586 | 392 | package org.broadinstitute.dropseqrna.metrics;
import htsjdk.samtools.*;
import htsjdk.samtools.util.*;
import org.apache.commons.lang3.StringUtils;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.dropseqrna.barny... |
ce6b12d89ac1c87f75b87c95eb8f4d6d8ee41ffec48d57d1a3f1795a8347c84f | Java | 16,611 | 451 | /*
* 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... |
87fe19d0b33f74902d177e5ffb230a780cc45297ff8cddd665ffa7b31b01f371 | Java | 16,695 | 317 | /*
* 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... |
0c42ce0123e1ad04c9edc9ca76e23228e789c495cf7f541f34e3b91bb1e1099b | Java | 16,748 | 402 | /*
* 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... |
728d0ab97c307f7b7ac57e9bd9769b7439117377ebde4ac9a9c7ac1397b7746f | Java | 16,752 | 492 | package arcade.core.sim;
import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import sim.display.GUIState;
import sim.engine.SimState;
import arcade.core.sim.output.*;
import arcade.c... |
f666587bf1c3a644e69d987af4a904a498a207bc5daa35e9597e1713a916dabb | Java | 16,808 | 597 | /*
%
% Main ImageDecorrelationAnalysis class
%
% ---------------------------------------
%
% A detailled description of the method can be found in :
% "Descloux, A., K. S. Grußmayer, and A. Radenovic. "Parameter-free image
% resolution estimation based on decorrelation analysis."
% Nature methods (2019): 1-7."
%
... |
d58d03a9a5d92e68550ac6a74d3b3264ed962f87b0667044b17e53dd74d6b727 | Java | 16,851 | 507 | package arcade.core.util;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.distributions.Distribution;
import arcade.core.util.distributions.NormalDistribution;
import arcade.core.util.distribu... |
690c3bfbb309cbeb23d69c193eb5db0a11e6b7c9a201fe622455bead4ce59ed2 | Java | 16,916 | 404 | /*
* 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... |
a5b23b009266fc0d1d3a0b22f2b77f0be60fb728d891edead04dd44a920daf95 | Java | 16,947 | 388 | package arcade.potts.agent.cell;
import java.util.Arrays;
import java.util.EnumMap;
import java.util.EnumSet;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.core.util.MiniBox;
import arcade.core.util.Parameters;
import arcade.potts.env.loc... |
cea3301bb465fd70a0879c5ed712eacae9abdeda8486fdf3cea71023baa43765 | Java | 17,083 | 595 | package arcade.potts.agent.cell;
import java.util.EnumMap;
import sim.engine.Schedule;
import sim.engine.SimState;
import sim.engine.Stoppable;
import arcade.core.agent.cell.Cell;
import arcade.core.agent.cell.CellContainer;
import arcade.core.agent.cell.CellState;
import arcade.core.agent.module.Module;
import arcade... |
bf0c33e89cc3ca7f3df45af2647a4fe4f502a0959cc7f2bd9ba2b89c076867ec | Java | 17,122 | 464 | 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... |
299ab3acd7f8393d041db605973d0cc956d3a06c6f6678171fc0b974be183abf | Java | 17,317 | 442 | 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.... |
37c7d3acb6fa39fd01a5798f354f882da57bee2204fed683f78a697f839f91c5 | Java | 17,333 | 463 | package arcade.potts.env.location;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.stream.IntStream;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.*;
import arcade.core.sim.Series;
import arcade.core.sim.out... |
491d53f8cf9c25f960780c595db9a2268169bd6e4c4ddd2e3fd47e0b6b08ddc8 | Java | 17,371 | 450 | package arcade.potts.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonDeserializationContext;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import ... |
e513ae071c01de77f2d9746902710f31ebbad9035d1b1ce47c80cb43dd04b936 | Java | 17,402 | 390 | /*
* 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... |
278968f57413a8f7fbb4fc3c91cde7b1a0500143bff7c9ea3a4742be0ab178bd | Java | 17,445 | 424 | /*
* Tester.java
*
* Created on June 24, 2002, 6:26 PM
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation.leaveoneout;
import java.util.*;
import java.io.*;
import java.text.*;
import edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult;
import... |
52262ccd1ca3e52e7f659ef0b4df2396c3ec69880990b4a4ce1aea9738f26862 | Java | 17,497 | 448 | package org.broadinstitute.dropseqrna.annotation;
import java.io.BufferedWriter;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
i... |
37d4d8af59d6b461514aaac8b5fc3f858c80f53fdb0a15b78e76cd5294b21f8f | Java | 17,558 | 375 | /*
* 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... |
6d3fc5c53c681e1d331309b8d2832ac186899eb7431d6df2aa265b674a699154 | Java | 17,582 | 524 | package arcade.core.sim.input;
import org.junit.jupiter.api.Test;
import arcade.core.util.Box;
import arcade.core.util.MiniBox;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.*;
import static arcade.core.sim.input.InputParser.*;
public class InputParserTest {
priva... |
de9a8078b83c1cad3d6b93901ec113d5f193229972782a5b852bd01b0abf00e3 | Java | 17,641 | 382 | /*
* 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... |
45f9205a740073160bf0812bc692955e16d6e2084a2697a759c6afd921077093 | Java | 17,661 | 196 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
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