sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9c8431a4241b103e58b15a278a687d5008778324816c23ccb718da15ccbce586 | Java | 8,401 | 289 | /*
* BrowserBean.java
*
* Created on November 12, 2003, 2:47 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.Iterator;
import java.util.List;
import java.util.Date;
/**
*
* @author wangqion
*/
public class ComparisonBrowserBean {
private static final int DEFAULT_DEPTH = 0;
... |
b033b3c9ca14b1f7fe40cc00271a75e1b53a2776a5ae7787439ca34279823466 | Java | 8,424 | 220 | 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.util.GrabBag;
import arcade.core.util.MiniBox;
import arcade.core.util.Parameters;
import arcade.patch.agent.module.PatchModule;... |
5e7b57cf89aa86d5e047529c4b599b3a5a400b367845ec055d4f32f896e9e31a | Java | 8,453 | 234 | package arcade.patch.env.component;
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 source sites.
*
* <p>Each index in the lattice can be assigned as a source, depending... |
6eda2d74d48f8ebe21707485cf73df3e728861d32d8d725efc36a804541e7333 | Java | 8,501 | 172 | /*
* Created on June 24, 2002, 2:11 PM
*
* Copyright 2006 Michigan State University Board of Trustees
*
* ClassifierTraineeMaker is used to create training files to be used by the classifier
*
*/
package edu.msu.cme.rdp.classifier.train;
import java.io.*;
import org.apache.commons.cli.CommandLine;
import org... |
22e275faeb6fdb2e186999092b91401e52c26b0a5f2a9bb7a827caa9972cedc4 | Java | 8,520 | 270 | /*
* 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... |
7f20ac345d50c9c90455e9dd1dd326de02d60fe95ff417a58ef7399105173fa4 | Java | 8,521 | 200 | /*
* 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... |
bba0351ae0f1f7f4f40a13d72a1f9fdb5ed7461df8d28f0250aa31697adac3aa | Java | 8,558 | 185 | /*
* 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... |
f4d51728ff7ade626e855e367e76900a5506138625e2770bc2aeda90a8af76b4 | Java | 8,560 | 246 | /*
* 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... |
0408479495c637141ddb199a98ff69cfe06dd2764b07f80359ce5959da7eaf39 | Java | 8,605 | 220 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
import picard.annotation.LocusFunction;
import java.util.Collections;
import java.util.List;
import jav... |
caab0de281ef60ca1f59cee87d6f9c98129adc78073fe33dbf87f8d3b3a07f72 | Java | 8,613 | 229 | package arcade.patch.agent.cell;
import java.lang.reflect.Field;
import java.util.ArrayList;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import sim.engine.SimState;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.... |
5e1034e1f0d46230e1688a9c75fc3a869d5481502b738d3a0702d151fff3c5f0 | Java | 8,615 | 194 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
5891bb84dded9a7ee1a654366fac38480a27357c9c8bc782aeb4e4ef755ae697 | Java | 8,742 | 230 | 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 arcade.potts.env.location.PottsLocations;
import arcade.potts.sim.Potts;
import arcade.pot... |
b4177d2a61e8eaf3c073c58e416c84937deae65633a217476b27c939521f4a1a | Java | 8,754 | 235 | /*
* 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... |
757f0fc1002cd2462e2c9a516ec463bd4e70a729628848968cb98d37b8dd4933 | Java | 8,763 | 241 | package arcade.core.sim.input;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import arcade.core.util.Box;
import static org.junit.jupiter.api.... |
957a658a65579003565641d7fea2c83c848ba6a50173b8458a5619bb38e2ee67 | Java | 8,788 | 184 | /*
* 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... |
ded783f910471b1ea3acd23c2fd89fd084011c1297b1d085c55d1493e1bafc01 | Java | 8,796 | 237 | package arcade.patch.sim.input;
import java.util.ArrayList;
import java.util.HashMap;
import org.xml.sax.Attributes;
import arcade.core.sim.input.InputBuilder;
import arcade.core.util.Box;
import arcade.core.util.MiniBox;
import arcade.patch.env.location.CoordinateUVWZ;
import arcade.patch.env.location.CoordinateXYZ;
... |
fc498c2e30dbc28155650f9f15fdf7e0b43ae32c7c175ef1ffec3aebf807d6cc | Java | 8,812 | 177 | /*
* 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... |
4a7d8865650d2f652b22a336191eb785d02d29436d21cb699990349a4150c58e | Java | 8,929 | 288 | package arcade.env.comp;
import sim.engine.SimState;
import arcade.sim.Simulation;
import arcade.env.loc.Location;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.comp.Sites} for source sites.
* <p>
* Each index in the lattice can be assigned as a site, depending on the initial
* spacings in the... |
b2355797424f36d0560748968b3a56e5756fc2ea947999809961a6cf265576e4 | Java | 8,935 | 176 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
90af6ff05d4f5d43493a0b1436325c130e20b7122f449b05019bc55b81e891ab | Java | 8,969 | 275 | package arcade;
import java.util.logging.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Date;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import org.xml.sax.Attributes;
import org.xml.sax.ContentHandler;
import org.xml.sax.Locator;
import org.xml.sax.XMLRea... |
4c7d890cc1af250c29e7f0828c5c73c59b25e5601a39530e62153f8a89e82d8d | Java | 8,975 | 216 | /*
* 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... |
fcdb4aba389461a311110f5e04176f6e58d2b3b71a7830590d576f4ef3952587 | Java | 8,997 | 199 | package arcade.potts.agent.module;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.potts.agent.cell.PottsCellFlyGMC;
import arcade.potts.env.location.PottsLocation2D;
import static org.junit.jupiter.api.Assertio... |
50726fa10c4661d5ed3b237cad90e86da4986ccc9aa6353a462afcf4bc249d33 | Java | 9,000 | 210 | /*
* 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... |
2c33efb90dc089820c51ab0b8d9cceec8ea2430cd1cf9c91eef81467ed31c3f1 | Java | 9,024 | 222 | package org.broadinstitute.dropseqrna.utils;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
/**
* This compresses and decompresses DNA sequences into a byte array.
* Each sequence is compressed into a byte array, where each base is represented by 2 bits.
* ... |
88c20e28d55ea954bc7ad5cc7c376ef0afd5d65fb11552c59908aae0b05a2835 | Java | 9,146 | 205 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
658aadd311d116bd044eda956643fdc1fba0895f9e32db8eea48cc0ffd612ced | Java | 9,155 | 312 | package arcade.core.util;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import org.junit.jupiter.api.Test;
import sim.util.Bag;
import ec.util.MersenneTwisterFast;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilit... |
e5f6585c740d145eb88f585a2488455fc552f835ac987c1e38aac6d526e45f5b | Java | 9,250 | 234 | package de.uol.neuropsy.recorda.recorder;
import java.util.Deque;
import java.util.LinkedList;
import edu.ucsd.sccn.LSL;
public class QualityMetrics {
// Quality parameters:
/**
* Default value for {@link #millisTimeoutNotResponding}
*/
private static final long DEFAULT_MILLIS_NOT_RESPONDING ... |
f43181e7ec68bde03a30555d17238b85bff6023a3a4a8ae17fdf67f55b1fd800 | Java | 9,266 | 279 | package arcade.core.sim.output;
import java.io.IOException;
import java.lang.reflect.Field;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import com.google.gson.Gson;
import sim.engine.Schedule;
import sim.... |
ebdb7cb9758cd35c2b9aa81bbb6a3f26b12de44ecc2d91df48a43da94ce90155 | Java | 9,300 | 202 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import com.google.api.gax.rpc.UnimplementedException;
import org.broadinstitute.dropseqrna.annotation.functionaldata.DataProcessorUtils;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
import org.broadinstitute... |
679d8517a7320a06378eed68eb6760ea33bea2f5b877975238d4fc81c6617803 | Java | 9,314 | 198 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
988c59edad5bb8297d0c72487841053f6efc132ce1df0327671766a1a3355c5d | Java | 9,363 | 222 | package org.broadinstitute.dropseqrna.metagene;
import org.broadinstitute.dropseqrna.barnyard.DigitalExpression;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.nio.PicardHtsPath;
import java.io.File;
import java.io.IOException;
import ... |
635cb0abad087682703e730088411352dc44a4f7d0b05a550f8062dac4e1ab4e | Java | 9,448 | 236 | /*
* 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... |
a02d7af4b9eedea7535222474a3153b9a2ee817f938cb1d5f47f3326cc8840a5 | Java | 9,469 | 270 | /*
* 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... |
b362a8b1943ecccbd1fa69e5e418abaa87a26b70d06250477194636a6805a96e | Java | 9,502 | 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... |
f274fef274fbbb3b070a0c9f517318a2c9b7399c8942bfc2d53d907c102cc8c4 | Java | 9,542 | 199 | /*
* Created on Feb 20, 2006
*
*/
/**
* This is a simple command line class to do classification.
*/
package edu.msu.cme.rdp.classifier;
import edu.msu.cme.rdp.classifier.cli.CmdOptions;
import edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter;
import edu.msu.cme.rdp.classifier.utils.ClassifierFactory;
... |
8ce67563359379d9f2579f262e3453b370ef6fc9abc28d63e22d04a834079a73 | Java | 9,566 | 223 | package org.broadinstitute.dropseqrna.utils;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
import htsjdk.samtools.util.Log;
import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import picard.nio.PicardHtsPath;
import java.io.File;
i... |
519e35fbf54eeca87d634f95a1e1674730bc2423e73159eb0536b0462e423c7d | Java | 9,573 | 274 | /*
* 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... |
20ee714d5df51f2aea28d788b43fa29140cc45833987ea010af7f27134d9e1c5 | Java | 9,663 | 198 | package org.broadinstitute.dropseqrna.eqtl;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.PeekableIterator;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;
import org.broadinstitute.dropseqrna.barnyard.ParseBarcodeFile;
import org.broadinstitute.drops... |
68811df204b73aeec095866490ca60d40d09b647bf51f9b1fcc8fd79196e9531 | Java | 9,664 | 226 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.dropseqrna.barnyard.Digi... |
493c98220d34e0f76adccb64920ed01b80659ce6fae54065a053fe4f8b67f13d | Java | 9,674 | 214 | /*
* Copyright (C) 2013 wangqion
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distribut... |
1de2651722563aaa897e3a04e685648a15dae9ad1a39c1f1a1db3dfdad84e973 | Java | 9,710 | 190 | /*
* Created on June 24, 2002, 2:11 PM
* LeaveOneOutTesterMain.java is the main program for leave-one-out testing.
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation.leaveoneout;
/**
* This is the Main class to do leave-one-out testing
*/
import edu.msu.cme.rdp.cla... |
39734df0c8f1f7e7fd166d45c1c7559c7f01813868b88f640c2abda2f5f5c127 | Java | 9,721 | 255 | 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... |
0b530ea9c66f42de498b43f80733760f78dbedab7d49a1f300de8e7c684e9e01 | Java | 9,723 | 224 | /*
* 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... |
82a789f86adc4170e3340fa697314b223524c2094d8f5470a2f543cec9925367 | Java | 9,737 | 227 | package org.broadinstitute.dropseqrna.spermseq.metrics.spermalleles;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.broadinstitute.barclay.argparser.Arg... |
69dbacba80f9850cd3457900f391063fa0d30c75b993c45239b71eededafb5b7 | Java | 9,768 | 278 | package arcade.potts.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
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.JsonSerializationContext;
import c... |
0684aabda0d385a2e90544c44cfb207420b1778128149fea67a821ee90fe31f3 | Java | 9,823 | 280 | package arcade.patch.env.location;
import java.util.ArrayList;
import arcade.core.env.location.Location;
import arcade.core.env.location.LocationContainer;
import arcade.patch.sim.PatchSeries;
/**
* Concrete implementation of {@link PatchLocation} for rectangular {@link
* arcade.core.env.grid.Grid} to a rectangular... |
23093c8cd0d7090f2fb9958c06cc91176e2d35ff414839e9e0f64feb7ea47bb7 | Java | 9,834 | 239 | package arcade.patch.agent.cell;
import java.util.HashMap;
import java.util.HashSet;
import org.junit.jupiter.api.Test;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
import arcade.patch.sim.PatchSeries;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import stat... |
890a7ccab5fca6cc84c1bd4cc7e28bfb8039116e470c1a121446b6abd3a9e5c9 | Java | 9,914 | 277 | package arcade.agent.module;
import java.io.Serializable;
import java.util.ArrayList;
import arcade.agent.cell.Cell;
import arcade.sim.Simulation;
import arcade.util.Solver;
import arcade.util.Solver.Equations;
/**
* Extension of {@link arcade.agent.module.Signaling} for complex EGFR signaling.
* <p>
* {@code Sig... |
e2866ac95d990871c710e779c807b5bc4bc73bd95d5ddf0ebc3d5114c6a5a170 | Java | 9,934 | 248 | /*
* 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... |
d84930e211e73b1f468c898d780565c5f91c85f5cbe0b68963c4d9f39beb1b04 | Java | 9,994 | 226 | /*
* 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... |
a810a4a6a96242ba86d9348f9ca23341c3aac893ed7a376226f51394bdc085db | Java | 10,003 | 267 | /*
* 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... |
c52686387b6508dc35fd850160bf5e3ca4c6aca4bb639aad3c42536005315041 | Java | 10,032 | 226 | package arcade.patch.agent.process;
import java.util.Arrays;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.process.Process;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCell;
/**
* Extension of {@link PatchProcessMetabolism} for complex met... |
cb5e4140a2ebac593bef708f09888dfc2369efeb2b64aa8997533b3764be4898 | Java | 10,067 | 210 | /*
* 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... |
71fb4861694ebb91fc0fcc2204838e58706aee7ef6b0ddf4bcbde9b76f83f92a | Java | 10,074 | 332 | package arcade.env.loc;
import arcade.sim.Series;
import sim.util.Bag;
/**
* Implementation of {@link arcade.env.loc.Location} for rectangular
* {@link arcade.env.grid.Grid} to a rectangular {@link arcade.env.lat.Lattice}.
* <p>
* {@link arcade.env.grid.Grid} coordinates are in terms of (x, y) and the
* {@link ... |
ef17182514ef4d9393ed714c067bcd7c645a8501196a883bdf61afec37e681c1 | Java | 10,080 | 266 | /*
* 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... |
dafa31d79173ab7e99ad4b3b89a93a5fbc9653b09f84025ec4d3fab216b89fc4 | Java | 10,099 | 229 | /*
* 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... |
195d9f23ac8dd75ebea724c577b8bdac55fb880d78f2b0ee36d0ea2da4cfe7e5 | Java | 10,104 | 204 | /*
* 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... |
aefd78e51efa84348d596d0540bd743a64a8353a26322e81c3220c5c79e565e2 | Java | 10,185 | 367 | package arcade.util;
import java.util.ArrayList;
import java.util.logging.Logger;
import static arcade.util.Matrix.*;
/**
* Static utility class implementing various numerical solvers.
* <p>
* Implemented solvers include:
* <ul>
* <li><em>forward Euler</em>: first-order method for ODEs</li>
* <li><em>cl... |
26033fc2cc4f7a837503104bd85569301c42eb230d8ed3540d2f397015994184 | Java | 10,242 | 236 | /*
* 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... |
6cf880cbc6b27517716800be498c5885249090df1d36c85c6e16b91763c4d2df | Java | 10,263 | 334 | /*
* 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... |
449312e5d68b3c818da48e1fdc70c2302b17db2e299d5dd75bfaae9d67340742 | Java | 10,281 | 251 | 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.env.grid.Grid;
import arcade.core.util.MiniBox;
import arcade.core.util.Parameters;
import arcade.potts.agent.cell.P... |
822e2745cb0091e30d7f41508b698cc64dfe5f37d566afb72a4069565cdee378 | Java | 10,282 | 255 | package arcade.potts.agent.module;
import java.util.EnumMap;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.mockito.MockedConstruction;
import sim.engine.Schedule;
import ec.util.MersenneTwisterFast;
import arcade.core.env.grid.Grid;
impor... |
bbdeed701d0e4d1ad5a322182452c706fbe05273018652ef28fd247ad2f43d3a | Java | 10,295 | 297 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.EnumMap;
import java.util.EnumSet;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.core.env.location.LocationContainer;
import arcade.core.util.Vector;
import arcade.potts.util.PottsEnums.Region;... |
a2992c7aa86c28a9a209db1155e86aa37c2360b732e13c5c09818c0418c7fcf6 | Java | 10,345 | 361 | package arcade.gui;
import java.awt.*;
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.*;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorde... |
3b4b8eefcf7f62febb509efbff34c0e46b167af27707f53df7f7ecb5c9b2129a | Java | 10,467 | 297 | package arcade.core.sim.output;
import java.lang.reflect.Field;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;... |
2aa0921390a2cf88cf8c9413a86f631b16aba896837cc27ab0fb2c1a97b4b5d1 | Java | 10,478 | 269 | /*
* 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... |
960d3a673a64c9eaad3214b3a057f09838c92f3332d724de2295daf5f27f871d | Java | 10,481 | 293 | package arcade.patch.env.location;
import java.util.ArrayList;
import arcade.core.env.location.Location;
import arcade.core.env.location.LocationContainer;
import arcade.patch.sim.PatchSeries;
/**
* Concrete implementation of {@link PatchLocation} for hexagonal {@link arcade.core.env.grid.Grid}
* to a triangular {@... |
2faa81183378109be283b13cda9d9d7cc8cba1ca04e06cc0ede1608da8d2739e | Java | 10,509 | 302 | package arcade.sim;
import java.util.*;
import java.lang.reflect.Constructor;
import sim.engine.*;
import sim.util.distribution.*;
import arcade.sim.profiler.Profiler;
import arcade.sim.checkpoint.Checkpoint;
import arcade.agent.cell.Cell;
import arcade.agent.helper.Helper;
import arcade.env.grid.Grid;
import arcade.e... |
4b393cbfd60db66a79a1aaf2e8f0be4bbe9aa2abf0248cb4e44256e79dcd5d60 | Java | 10,535 | 244 | /*
* 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... |
cd4a49c4b5ae0351add5d8b0ca24e8620d513bc85f6ee2de022d171ecd22e83e | Java | 10,558 | 214 | package arcade.vis;
import sim.engine.*;
import arcade.sim.Simulation;
import arcade.sim.Series;
import static arcade.vis.AgentDrawer2D.*;
import static arcade.vis.ColorMaps.*;
/**
* Extension of {@link arcade.vis.Visualization} for 2D simulations.
* <p>
* {@code GrowthVisualization2D} creates three panels:
* <ul... |
92095dacaf3b084b23fedb68ff5629d2d29976dd058362cc5f97aca68aa90fa7 | Java | 10,582 | 276 | package org.broadinstitute.dropseqrna.utils;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Function;
import java.util.stream.IntStream;
public class ... |
7a055d993e856a814402a8999d371cd871bfcfcc4cb664c972c1aac0a2b94e98 | Java | 10,622 | 240 | /*
* 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... |
195f1fd7ab691ba38fac89bf317c8718253bc8d217b75a35050c274e4c734499 | Java | 10,666 | 312 | /*
* 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... |
2e2405e7373cb5e737335ab024d1907ebf79834f5f52143292baa73323290144 | Java | 10,737 | 315 | /*
* 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... |
2d3168cc847155cf7a5c4d216c349a16139687b96caf98c9ad6b37ad520f7db2 | Java | 10,776 | 242 | /*
* 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... |
e3203a35a8bddeaf12cd93017526465fd36b1327e7984885092bdaa229fa5894 | Java | 10,799 | 351 | package arcade.env.loc;
import arcade.sim.Series;
import sim.util.Bag;
/**
* Implementation of {@link arcade.env.loc.Location} for hexagonal
* {@link arcade.env.grid.Grid} to a triangular {@link arcade.env.lat.Lattice}.
* <p>
* {@link arcade.env.grid.Grid} coordinates are in terms of (u, v, w) and the
* {@link a... |
c47c4b538d82621a9c7448fa2563968b3734ff3dd59eda3942fd9e8bc20c430b | Java | 10,883 | 290 | /*
* TrainingInfo.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 18, 2002, 5:01 PM
*/
package edu.msu.cme.rdp.classifier;
import edu.msu.cme.rdp.classifier.io.ProbIndexFileParser;
import edu.msu.cme.rdp.classifier.io.GenusWordProbFileParser;
import edu.msu.cme.rdp.cl... |
d1e25c767522cd7bba6e4f7e83007811070e8371f9c1c6bf338ac33f58b59718 | Java | 10,886 | 252 | /*
* TrainingInfoTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 19, 2003, 10:23 AM
*/
package edu.msu.cme.rdp.classifier.rrnaclassifier;
import edu.msu.cme.rdp.classifier.ClassificationResult;
import edu.msu.cme.rdp.classifier.Classifier;
import edu.msu.cme.rd... |
47880bae52170aa1523ec238a60267a9bd9adc1dbacfa06f54aa5ef654fc84a6 | Java | 10,901 | 346 | package arcade.env.comp;
import sim.engine.SimState;
import arcade.sim.Simulation;
import arcade.env.loc.Location;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.comp.Sites} for pattern sites.
* <p>
* A repeating pattern of lattice indices are assigned as sites, defined by
* tesselating the "uni... |
5623ed7687d7736b29eba6d7ce83cfa614f7de96fc301a2f2418311ea11fda99 | Java | 10,908 | 255 | /*
* 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... |
449285f8f5fa1fcac10e0ba6a974c461ae20eec61e2cab0eabe5e49a6ffd26ee | Java | 10,958 | 286 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
eece4d5687248f26b94bc83309e53b8e5ac06c831c07f45b91b874303fa4a663 | Java | 10,973 | 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... |
c58c0dc67baf87ede72fb7d0e903f12fc843681e8938bab5f941f855de785f1a | Java | 11,068 | 284 | package arcade.core.util;
import org.junit.jupiter.api.Test;
import sim.util.Double3D;
import static org.junit.jupiter.api.Assertions.*;
public class VectorTest {
static final double EPSILON = 0.0001;
@Test
public void constructor_givenXYZdoubles_returnsVector() {
double x = 1.01;
double ... |
ad8bc857c2fdac30ad6a75818559eadbaa9bc7d5afe3697e0b2a77b3ccd0dbd0 | Java | 11,093 | 311 | package arcade.patch.vis;
import java.awt.Color;
import arcade.core.sim.Series;
import arcade.core.util.Colors;
import arcade.core.util.MiniBox;
/**
* Container class for commonly used color maps.
*
* <p>Uses {@link arcade.core.util.Colors} to define mappings.
*/
class PatchColorMaps {
/** BurgYl colormap fro... |
1769c73019fde1680ca3ee928a7c6a75ee91b30e5c10666ecaa153a4e54ca7a9 | Java | 11,146 | 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... |
e28b27abff8558bd05f9beb623a8a5fd866101403d629a344fa125ceb4a2ef1f | Java | 11,160 | 272 | /*
* TreeFactory.java
*
* Created on June 24, 2002, 5:01 PM
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.classifier.train.LineageSequence;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator;
import java.io.BufferedReader;
... |
f2cc155e12d378a8dd9ace869b30cea6c75b827ab6a28375d0e595c54b846487 | Java | 11,262 | 234 | /*
* 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... |
dc134b8c47dbf14fe8b23f178ccbcc42bc292208d7f34cfb983de06313f3f06f | Java | 11,287 | 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... |
6acc01bf2b8b30d2245ca0080469711c3d552a5f5c2a3ca03ed3075d0688fb34 | Java | 11,368 | 390 | /*
* HierarchyTree.java
*
* Created on June 24, 2002, 2:36 PM
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.classifier.train.LineageSequence;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator;
import java.io.IOException;
i... |
81146e29df0a40d0dff0d6cd1bbaadbd97f0933c3dd6e4e7488616287dc866a5 | Java | 11,368 | 339 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.OptionalInt;
import static arcade.potts.sim.Potts3D.*;
import static arcade.potts.util.PottsEnums.Direction;
/**
* Static location methods for 3D.
*
* <p>Interface defines generalized 3D voxel methods that can... |
dc3c31358382b481e9e10291b89ef316ae6ce49c66310dd45676d4e0c0084539 | Java | 11,426 | 281 | package org.broadinstitute.dropseqrna.annotation;
import java.io.File;
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 org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk... |
87d2959d28dc651ddadcb8269b1aaa3bc446e4ca9dfcb1afbf273e84a05b5f3d | Java | 11,434 | 301 | package arcade.potts.sim.hamiltonian;
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.junit.jupiter.api.Assertions.*;
i... |
469e5914461450a232376380d4d7206aa5e7b8d8f4921be2ec5c179b402cb682 | Java | 11,486 | 250 | /*
* 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... |
34eb09b07ccba0797aec5ad924a7392e5df92657edaaf6a9a727ec6441e8b842 | Java | 11,504 | 254 | /*
* 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... |
81fa19417d11175c93ac9caa9fc63325c92ad83d97a468069c91c4236f9165b0 | Java | 11,531 | 296 | 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.PottsSeries;
import static org.junit.jupiter.api.Assertions.*;
... |
854d9ccb0b3ad4b98cd51e15d99fa65569b8979ef3dcf8846997120979b57b94 | Java | 11,591 | 385 | /*-
* #%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... |
d5a814259e9cf643a08d8cdc26b5d7704c730d370924b163236c152d67671edc | Java | 11,618 | 313 | /*
* 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... |
4ac3e5e20771485e4531fe27a1d2ccd48edcac480443d814cd0cbb153f017a4b | Java | 11,664 | 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... |
a91d06f7b0fb3e487084ad4a388052d69e8915b50b8762c790ce949579cb543a | Java | 11,690 | 298 | package arcade.potts.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;
import static arcade.potts.util.PottsEnums.Term;
/** Simulation m... |
5d0e58628d8c4c420d535b796b4742e876039906f59d52344a1091bb8f1734d5 | Java | 11,695 | 335 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.*;
import arcade.core.sim.Series;
import arcade.core.util.MiniBox;
import arcade.... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.