sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
17a06a022ba2c03272c8d2f8cf657b741c9e204da2581d96c810b1c52e5bc260 | Java | 2,778 | 74 | /*
* 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... |
70e87b99f8b4b83058004b687418314b56e5e58a89a7252d7baf94dcc6c912d0 | Java | 2,782 | 97 | package arcade.sim.checkpoint;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.sim.Series;
import arcade.sim.Simulation;
import arcade.agent.cell.Cell;
import arcade.agent.helper.Helper;
import java.io.Serializable;
/**
* Extension of {@code Checkpoint} for cell agents.
*
* @version 2.3.2
* @sinc... |
8dea02a8429044508519b339817284181a08184d243174292c3a0904e6ec1844 | Java | 2,793 | 62 | /*
* 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... |
0814e6a601e9766e4690e3aa7522c74dbed891f6c0c23e33850693fa38bcbc04 | Java | 2,814 | 75 | /*
* 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... |
ecb21b2a989a2a345dfa77375309e08f9e19bffda5e58a8f553bdafdc51668fd | Java | 2,819 | 76 | /*
* 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... |
2747c7d204bd37aa01b0d19b4eb421a0a3949d0be7ae44059e9c9eb1932a4001 | Java | 2,823 | 102 | package arcade.util;
import java.io.Serializable;
import sim.util.distribution.Normal;
import ec.util.MersenneTwisterFast;
/**
* Container class for parameter with normal distribution and bound checks.
* <p>
* Each {@code Parameter} is associated with a random number generator to select
* additional parameter val... |
ab4cab1980afd9dfdc69a748b32fd33ca443668a5432b2002566988e15fed7c5 | Java | 2,827 | 55 | package org.broadinstitute.dropseqrna.utils;
import java.io.File;
import java.util.List;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.Log;
import org.testng.annotations.Test;
public class AssertSequenceDi... |
7429227b45705b3da4a9b49c8ed26ce4fa921f30b42d7e55e9ca0da7786a04ad | Java | 2,830 | 92 | package arcade.agent.cell;
import java.util.Map;
import sim.engine.SimState;
import arcade.sim.Simulation;
import arcade.agent.module.Module;
import arcade.env.loc.Location;
import arcade.util.Parameter;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.agent.cell.TissueHCell} for cancerous tissue cells.... |
09395628dc49635c785d71e0ff93ece1539cab13ccc51c7ff49a3ede0f3f0448 | Java | 2,833 | 101 | /*
* ParsedRawSequence.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 25, 2002, 10:28 AM
*/
package edu.msu.cme.rdp.classifier.train;
import edu.msu.cme.rdp.readseq.readers.Sequence;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator;
import java.io.IOExc... |
c09b1e995e06f0eb4468c14898caf19ae35d74a76b1cd582d40bf2df47014250 | Java | 2,843 | 71 | /*
* 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... |
d890a570bb8dae8ed32c1487ad42139b990b6bd6087e28c6b3ae315a77f0b1ef | Java | 2,851 | 122 | package arcade.vis;
import java.awt.geom.Rectangle2D;
import sim.engine.SimState;
import sim.portrayal.Inspector;
import sim.display.*;
import arcade.sim.Simulation;
/**
* Extension of {@code GUIState} wrapper of simulations for visualization.
* <p>
* {@code Visualization} organizes the visualization into {@link ... |
35a8cbdcfa69b0f4c0cd481671edfe80b532ec26b55fb8817916699594d81300 | Java | 2,860 | 91 | package arcade.patch.agent.cell;
import sim.engine.SimState;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.Location;
import arcade.core.sim.Simulation;
import arcade.core.util.GrabBag;
import arcade.core.util.Parameters;
import static arcade.patch.util.Pat... |
5504792cea393a3208b419b829a2dac6ca3f3189bc3ca7af2c989fe3bb3940cf | Java | 2,860 | 60 | package org.broadinstitute.dropseqrna.eqtl;
import java.io.File;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.dropseqrna.eqtl.CalculateXReactivationCovariate;
import org.broadinstitute.dropseqrna.eqtl.EqtlCovariate;
import org.testng.Assert;
import org.testng.annotations.Test;
public class ... |
040531cfd80774e5bf11175e7f96a0495a553c8bbf0c04aec279782683b7c1c6 | Java | 2,880 | 87 | package arcade.potts.sim.hamiltonian;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static arcade.potts.sim.Potts2D.MOVES_X;
import static arcade.potts.sim.Potts2D.MOVES_Y;
import static arcade.potts.sim.Potts2D.NUMBER_NEIGHBORS;
/** Extension of {@link SurfaceHamiltonian} for 2D. */
publ... |
1b6c7b0526a8472ade50a44e1ab3710c7c7439ab9aa4ef9fde33e159c9bf1df0 | Java | 2,881 | 91 | /*
* 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... |
2de57d08bdcc0dbc43ec6ee735386d251174fdce048841c9283d6e533d9dcfc3 | Java | 2,886 | 105 | /*
* 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... |
da3d7109b6b8a8e8d780af2cc88c6307b8d2713a35b283f7fb92dd2cb038ea7a | Java | 2,894 | 61 | /*
* 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... |
0e99ecf18ef40d6443b1db54acf2cd4afe63cddd94d72472f15d031c98a49054 | Java | 2,897 | 84 | /*
* 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... |
a8d167b4cf12b569505a09b3e97aae6629cc1e271fc1d8424b145c009d1696f1 | Java | 2,907 | 84 | package org.broadinstitute.dropseqrna.censusseq;
import org.apache.commons.math3.stat.descriptive.moment.Mean;
import org.broadinstitute.dropseqrna.utils.statistics.BinomialStatistics;
import htsjdk.samtools.metrics.MetricBase;
public class CsiMetrics extends MetricBase {
public int NUM_SNPS;
public int REF_COUNT;... |
639b457083ece966a500ff6a3ff13849c7791d38221d3ed334ffdcf5d20fc26f | Java | 2,909 | 54 | /*
* 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... |
e406250a89c4b6eb5379a30d93970f252b5d3a49bbba98663f7d7b66b643aa67 | Java | 2,910 | 69 | /*
* ProbIndexFileParser.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 19, 2003, 10:41 AM
*/
package edu.msu.cme.rdp.classifier.io;
import edu.msu.cme.rdp.classifier.TrainingDataException;
import edu.msu.cme.rdp.classifier.utils.HierarchyVersion;
import java.io.Buff... |
0532eab12f0018ede6695cc3c2d2bf37f48738da9daba98f00cd98caed5ac92e | Java | 2,912 | 70 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
32e92c1c7afe8f868ea68fa90929eab6f811d9164d1fe16fd33524fd53b9a048 | Java | 2,912 | 110 | package arcade.vis;
import java.awt.Color;
import java.awt.Point;
import java.awt.geom.Rectangle2D;
import javax.swing.JFrame;
import sim.display.Controller;
import sim.display.Display2D;
import sim.display3d.Display3D;
import sim.portrayal.FieldPortrayal2D;
import sim.portrayal3d.Portrayal3D;
/**
* Wrapper for JFr... |
80c47b3135fb4ea5b53d65ee4a6460b883d3c9905ce2968ba6bd832680e660a8 | Java | 2,913 | 102 | package arcade.potts.sim.hamiltonian;
import java.util.HashMap;
import java.util.Set;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static arcade.potts.sim.PottsSeries.TARGET_SEPARATOR;
/** Implementation of {@link... |
ba59e05bc68c6ea61c45637554411a8d19e27e7669d544460df557cf8d92677d | Java | 2,921 | 77 | /*
* 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... |
56b8bfa39b6b761832887b66885ea62894f8371a8d80ba78570f42a9a1c1e1da | Java | 2,941 | 81 | /*-
* #%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... |
245b04677915cf8ecfbbf8ffaa1a0a24031c6585fbf97a748654d7b0663e4671 | Java | 2,945 | 69 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
8ed203f144e45165aaa482bca789ba775698d7773b6f530a085b3d46d46b1d89 | Java | 2,954 | 85 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.GdacAlleleFrequency;
import org.broadinstitute.dropseqrna.barn... |
9d10010f5b730a28699f327c20b19f56f28951f752d23923b95d7ed23edec999 | Java | 2,954 | 72 | /*
* 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... |
b063a8ff1f616a1e3af588b8457eee209d1236387f302b32867f17c9dda597fc | Java | 2,959 | 71 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
75b3fbe3453d352b252f756967702b59655e01e8b784f5e2d8a78cc3d6e06363 | Java | 2,961 | 81 | /*
* 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... |
2b4e65b319437c8325e445168143089c88e7ed14bf0a4bf8c9a5001f59003b1e | Java | 2,964 | 87 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
import org.testng.Assert;
public... |
d1471b4fbaca32079d6c22a6661b0bdbf1e1c44ebdbd61511cde9c2b0662357f | Java | 2,967 | 88 | package arcade.potts.sim.hamiltonian;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static arcade.potts.sim.Potts3D.MOVES_X;
import static arcade.potts.sim.Potts3D.MOVES_Y;
import static arcade.potts.sim.Potts3D.MOVES_Z;
import static arcade.potts.sim.Potts3D.NUMBER_NEIGHBORS;
/** Extensi... |
243339d0222d98b8bc68f24cf0b3cc8db551701f8da257ede7d51a1611486478 | Java | 2,976 | 87 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.regex.... |
406b469ab1b2ede44e6afdf09ee16da0da304822fa1405429e092dbc22433601 | Java | 2,979 | 61 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import htsjdk.samtools.util.Log;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
import org.broadinstitute.dropseqrna.utils.readiterators.GeneFunctionProcessor;
import picard.annotation.LocusFunction;
import j... |
90ea35538d583bd85813562b1512d99c52befe3de6d753fbbad3ec4e55675aa3 | Java | 2,980 | 104 | package arcade.core.vis;
import java.awt.Color;
import java.awt.Point;
import java.awt.geom.Rectangle2D;
import javax.swing.JFrame;
import sim.display.Controller;
import sim.display.Display2D;
import sim.portrayal.FieldPortrayal2D;
/**
* Wrapper for JFrame windows containing visualizations.
*
* <p>Each JFrame obje... |
693c3559d142fbeb739be3f1b14b10dc95b70da7aa7c01f2403fec7665ff1d31 | Java | 2,982 | 74 | package arcade.patch.env.operation;
import arcade.patch.env.lattice.PatchLattice;
/**
* Extension of {@link PatchOperationDiffuser} for triangular lattices.
*
* <p>Operation also check if the triangle is pointed up or down based on the row and column, where
* the top left of the 2D array at coordinate (0,0) is a ... |
02d99c95ee6a5ce3382ec420903fb7f9b27a5c924df7c9e01689eec7de0bb999 | Java | 2,987 | 94 | /*
* 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... |
1b8360df9590e456e6e6a7655446d8ff47c98bb034bf9cceb1c48d5c0a1438dc | Java | 2,997 | 89 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment;
import java.io.File;
import java.util.Collection;
import java.util.Map;
import org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.GdacAlleleFrequencyReader;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.L... |
42b9b75a185541724a4ccaac82ac04f91fcf7eec442bf7e824d7519d4fc15918 | Java | 3,005 | 69 | /*
* GenusWordProbFileParser.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 19, 2003, 11:26 AM
*/
package edu.msu.cme.rdp.classifier.io;
import edu.msu.cme.rdp.classifier.GenusWordConditionalProb;
import edu.msu.cme.rdp.classifier.TrainingDataException;
import edu.ms... |
4f14c383bcdc0e84a22f17b93ca00c5849bcc4e30000b48784572df4ecff14c6 | Java | 3,011 | 75 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
a6064e68bce7810995c4e4e5a5331e7c858bebc22ef9da551460979277b0096a | Java | 3,014 | 86 | package org.broadinstitute.dropseqrna.utils;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
import static org.testng.Assert.*;
public class DNACompressorTest {
@Test(dataProvider = "dnaStringLists")
... |
8b8c3ae821d3a579d76adab22f14888bbfe524a7287d3e0a1893616751db1459 | Java | 3,015 | 79 | /*
* 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... |
00fc15f09f66059bf60f12f1b61cbdaca576897f6e0b1e462a9f6bb3f9ab1205 | Java | 3,016 | 82 | /*
* 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... |
34c04f68eedf47e7ce73c74281d3d25fb575b6f437cbbe516ae0cf33aa73674d | Java | 3,016 | 116 | /*
* PixelCalculatorBean.java
*
* Created on March 11, 2005, 12:01 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.Iterator;
/**
*
* @author wangqion
*/
public class PixelCalculatorBean {
private int s1Total = 0;
private int s2Total = 0;
private Taxon taxon = null;
... |
e0ee1f8aadd3ecf1c434a3039021d4f9c14b463f0747043fd48ff5dd491a294f | Java | 3,017 | 45 | package org.broadinstitute.dropseqrna.barnyard;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalDataProcessorStrategy;
import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
import picard.annotation.LocusFunction;
import p... |
82faa4f928ca6b0779548ed7f21b45984a8557b52913dddcfa6841949472c5ec | Java | 3,019 | 104 | /*
* 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... |
a619ccb61141987af7161cdc2077adfdaca262d0f50c00cd3378e40215555d16 | Java | 3,023 | 82 | /*
* 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... |
c19aa7ca9f437f345d44048545cb3b72b0b328f13ec38d84f36e358b144dadcc | Java | 3,034 | 90 |
/*
* TreeFactoryTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
* Created on June 25, 2002, 3:59 PM
*/
package edu.msu.cme.rdp.classifier.train;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.util.HashSet;
impo... |
347bd4ae5a54e052f2f242aed6508033a7b233af3c016574231dd92377c50d6e | Java | 3,037 | 88 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts;
import java.io.File;
import java.io.IOException;
import java.util.Collections;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMFileHeader;
import org.testng.Assert;
public class Fi... |
dbb684fda630597f17fdb5f9b496ad9f5353433a0c70cf3d4cc5fbd3cc9dbfc5 | Java | 3,079 | 74 | /*
* 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... |
8f415c8194de2aef646c6929e118cbbb8d09a9d2a07737ac52e771d96acecfcf | Java | 3,084 | 71 | package org.broadinstitute.dropseqrna.vcftools.filters;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.variant.variantcontext.... |
6331be169f91b3d5525475a5c74b12b5a33bbf7ea11378f175de0381082b1d26 | Java | 3,085 | 98 | /*
* 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... |
f8f32f6b501cf599541156fd665f19b38e04a0fe9c612bf28fcef5d5410811d7 | Java | 3,097 | 66 | /*
* 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... |
07a9a5c4913c66ff778c7842e5519001f767ece0bbd7db6d77abaec9a7d565ac | Java | 3,112 | 95 | /*
* 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... |
26734378dcc8b895de47591c535487e47be492a752c265eee0d9c51d6e403504 | Java | 3,119 | 99 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
7c76aba4a50308cdd724a90b3a552a1b25cea39370185d5529268304037146ab | Java | 3,126 | 94 | package arcade.patch.agent.module;
import java.lang.reflect.Field;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCellCART;
import arcade.patch.agent.cell.PatchCellTissue;
import arc... |
e9db56c7fd6c5a3169a2ef8e980687863c39d18112ee8a5ec72e916af5addb36 | Java | 3,130 | 115 | /*
* 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... |
5959639889e733c206d6341bc785c1a132954798ab45732d624075fb1ecaaca6 | Java | 3,141 | 89 | /*
* 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... |
f32192b8fb710dfa4708e89663286c4e0d1a0af6282c1c947c82f06d1d5fc0dd | Java | 3,142 | 93 | package arcade.potts.agent.cell;
import java.util.EnumMap;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.cell.CellState;
import arcade.core.env.location.Location;
import arcade.core.util.GrabBag;
import arcade.core.util.Parameters;
import arcade.potts.agent.module.PottsModuleApoptosisSimple;
import arca... |
1a7f4c96a74544c976b5b883aaa669bae318688705686c22d0cacaa8cfa30ae6 | Java | 3,166 | 77 | /*
* 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... |
e83759c0ad60e92f2ad6e9a3869172abea2da94bdc2c81766b1c544a8e9c549f | Java | 3,166 | 106 | /*
* 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... |
9818bd75611730358aa0cd76458997101b590321fc506e289589a32ce922e01c | Java | 3,167 | 93 | package arcade.agent.cell;
import java.util.Map;
import arcade.sim.Simulation;
import arcade.agent.module.Module;
import arcade.env.loc.Location;
import arcade.util.Parameter;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.agent.cell.TissueCCell} for cancerous stem cells.
* <p>
* {@code TissueSCell} ... |
52b6b63b0d7a34e23bc2dbc2776d821e1becb5ed880043bc163a4b55f431f980 | Java | 3,188 | 86 | package org.broadinstitute.dropseqrna.barnyard.digitalexpression;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.broadinstitute.dropseqrna.barnyard.digitalexpression.DgeIterator.DgeLine;
import org.testng.Asse... |
983aa366641b9664286ffa6991f39ca7c05b7d36bc96f7d5a4ee5b5f45915c9f | Java | 3,190 | 73 | /*
* 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... |
71922ac2a61b72fbc7b81eedc5b2a97afc4dd95fbab01d684cf688b8a219a395 | Java | 3,191 | 122 | /*
* HierarchyTree.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 24, 2002, 2:36 PM
*/
package edu.msu.cme.rdp.classifier;
import java.util.ArrayList;
import java.util.List;
/**
* A HierarchyTree holds the taxonomic information of a taxon.
* @author wangqion
* @ver... |
c6d06fd469b3dd6d8702b45b42a42bea87e891b06dcd55af987d81d03b5cfe74 | Java | 3,191 | 85 | package arcade.core.sim.output;
import java.lang.reflect.Type;
import java.util.ArrayList;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonDeserializationContext;
import com.google.gson.JsonDeserializer;
import com.google.gson.JsonElement;
import com.google.gson.JsonObj... |
24a11c7f01d2c3194cb4c3a49cb39319125755ab975dcd2c72c00ee8c1f5e90d | Java | 3,196 | 91 | /*
* 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... |
390519d1501ffa146283b25f8fd169f52cebb142bfd60924a78691b20329452d | Java | 3,201 | 86 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
206880bd88cb9e9261d34979522373e951482cf1c84bc68585ffc555c4745a01 | Java | 3,203 | 87 | package org.broadinstitute.dropseqrna.barnyard;
import java.util.Collections;
import java.util.Set;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
public class ChimericUmi {
private final String molecularBarcode;
private final Set<String> chimericGenes;
public enum CHIMERIC_STRATEGY {
REMOVE_... |
a757700d1e8a85367117bacd6986c8a2ab925398125d2351ae979392ceb6c270 | Java | 3,215 | 66 | /*
* 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... |
ab15873109f6805af28248f737566dcd8162ba51a8fbf1ec06c09b40f104376d | Java | 3,221 | 92 | /*
* 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... |
36703f33a53238cf479863e96146df2ae8028f099f05f46f869949fc4a8b0024 | Java | 3,225 | 68 | /*
* 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... |
154e5286c41f784f88b2d09d5858192fe395a01464dd3287834ce3c7df3adda0 | Java | 3,228 | 93 | /*
* 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... |
e19b6d4eadd956f4102fb52aaa953c9b793adb63ca8c37255770140bd5cb06fd | Java | 3,233 | 153 | package arcade.core.agent.cell;
import sim.engine.Schedule;
import sim.engine.Steppable;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.module.Module;
import arcade.core.agent.process.Process;
import arcade.core.agent.process.ProcessDomain;
import arcade.core.env.location.Location;
import arcade.core.uti... |
7be70e7d40e8a10199bf19f088b63478b9ff7ac31b510f75e226803c862dc204 | Java | 3,236 | 67 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
942ea78840f32e6b60c17b47d6d2f4cb1cdaa0f06eb033b06f1ce8727ab02bf0 | Java | 3,242 | 98 | /*
* 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... |
948a3948762b722d52a715bb41e86ba99c1eb103cc81e2636e9ca8a2ca3a8e39 | Java | 3,243 | 71 | /*
* 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... |
6eaa3addc71af7c64c9e365402c76a44496ff4816e2d435097bc0ff0739869e7 | Java | 3,247 | 84 | /*
* 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... |
f1679660bddee35ad949417417fb5fb7b948af11e9e910b3ea76a47fef3d2ed8 | Java | 3,250 | 102 | /*
* 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... |
f72656aab6fcb419a8f7ffd64cd24aaf47b71c6fb1d2de5ded59c3f559c7d71b | Java | 3,250 | 73 | /*
* 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... |
264e141bcb6adaf4fd6f4ff77710d31003baf18811004703b54406b1dc12a4ac | Java | 3,251 | 73 | /*
* 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... |
d73becc385c18f2ef36ecaa090910adc44b817ae952b7e382fbfbd8eb2c85e90 | Java | 3,259 | 86 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
3d9396a192bb619d487f5254766ee5febac42a83e10ce6f94fc6acd105046be3 | Java | 3,264 | 101 | package arcade.agent.cell;
import java.lang.reflect.Constructor;
import java.util.Map;
import arcade.sim.Simulation;
import arcade.agent.module.Module;
import arcade.agent.module.*;
import arcade.env.loc.Location;
import arcade.util.Parameter;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.agent.cell.... |
40cf6187e1d3c8872991dd4c3de82c7d1362d86eeaeaeb25a254935886e4d306 | Java | 3,265 | 99 | package arcade.patch.sim.output;
import java.util.List;
import java.util.Map;
import com.google.gson.Gson;
import arcade.core.env.component.Component;
import arcade.core.sim.Series;
import arcade.core.sim.output.OutputSaver;
import arcade.patch.env.component.PatchComponentSitesGraph;
import arcade.patch.sim.PatchSimul... |
e989463c179faa3dcd8a8d92fbc667023e111d8cf5f914f826a5a863556468ee | Java | 3,276 | 59 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.Collections;
import static org.testng.Assert.*;
public c... |
cd7e337e4840a1df87d147af7b9da2754fee57497d9e5fe4a9c57cdf42f28f92 | Java | 3,293 | 92 | /*
* MIT License
*
* Copyright 2017 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
b4ac97a84b1471bc0a096a1078729c6a56d1649ac7fb103ae01f32d0b27b5338 | Java | 3,325 | 99 | package arcade.sim.profiler;
import sim.engine.*;
import arcade.sim.*;
import arcade.env.comp.GraphSites;
import arcade.env.comp.GraphSites.*;
import arcade.util.Graph;
/**
* Extension of {@code Profiler} to output graph structure and hemodynamic
* properties.
* <p>
* The output JSON includes:
* <ul>
* <l... |
3a30f59b53c83c3729fbf60f4f6e1724c1e003c47231290daa047cd319fcd0db | Java | 3,326 | 132 | package arcade.core.vis;
import java.awt.geom.Rectangle2D;
import sim.display.Controller;
import sim.display.GUIState;
import sim.engine.SimState;
import sim.portrayal.Inspector;
/**
* Extension of {@code GUIState} wrapper of simulations for visualization.
*
* <p>{@code Visualization} organizes the visualization i... |
d3051df137c593afba7672ee210ecb87e47c1586c5d5278916f5473343d82fe0 | Java | 3,333 | 70 | /*
* 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... |
60f8ecbd363177e412deb2c82a2552d5a3fdcc4cd945bf98f8e5b685a535302d | Java | 3,343 | 95 | /*
* MIT License
*
* Copyright 2023 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modi... |
98d4eb0a04281278f9ec0d99108d13f250c5d945452fa2e3602c560ffe30bad8 | Java | 3,349 | 86 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import org.junit.jupiter.api.Test;
import arcade.potts.agent.cell.PottsCell;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.core.ARCADETestUtilities.*;
import static arcade.potts.util.PottsEnums... |
515be0f93c5b61416fb6f174558504fbb93c7c60b8ec7b4ae849f7843e4b9673 | Java | 3,350 | 140 | package arcade.util;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.regex.Pattern;
/**
* Container that maps a key to a value.
* <p>
* {@code MiniBox} objects are dictionaries that use a String to String hashmap.
* Utility methods are provided to return the contents as specific types.
*
... |
4d9056229bbea73305eb741dda6afe771ba09ea1be95168bc19beaf35307d741 | Java | 3,353 | 85 | /*
* 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... |
16ad4c19dcc71d5142e3db603558e800665745e8806d0cf2963712df332a83bf | Java | 3,362 | 100 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Iterator;
import java.util.regex.Pattern;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.dropseqrna.utils.TransformingIterator;
public class ReadNameCleanupIterator extends TransformingIterator<SAMRecord, SAMRecord> {
privat... |
77088fec0d6d9f0853dfaa50d17258651859f77c7dd8e01c725ac3cf407a4321 | Java | 3,364 | 86 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import org.junit.jupiter.api.Test;
import arcade.potts.agent.cell.PottsCell;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.core.ARCADETestUtilities.*;
import static arcade.potts.util.PottsEnums... |
70fc5cdab4116fe2d103497374a63f111d154859fca9bab6e47bfd23c51481e7 | Java | 3,367 | 64 | /*
* 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... |
89c78d90bdf0573c6795f2b59c23752febb194d3a3d44dd1ecc4ba45fd113bc3 | Java | 3,384 | 96 | package arcade.patch.agent.action;
import sim.engine.Schedule;
import sim.engine.SimState;
import sim.util.Bag;
import arcade.core.agent.action.Action;
import arcade.core.env.location.Location;
import arcade.core.sim.Series;
import arcade.core.sim.Simulation;
import arcade.core.util.MiniBox;
import arcade.patch.agent.... |
063e86e47d32770afd842c912e9b40ac2b58dd371e83d1c3545c7cb196d9c9c2 | Java | 3,399 | 95 | package arcade.patch.agent.module;
import ec.util.MersenneTwisterFast;
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.agent.cell.PatchCellTissue;
import arcade.patch.agent.process.PatchPr... |
705adc97d922b69e31a2fec80be9db9fa527a3255d1211f97c23c64e6a24e899 | Java | 3,410 | 130 | package arcade.core.env.lattice;
import sim.engine.Schedule;
import sim.engine.Steppable;
import arcade.core.env.location.Location;
import arcade.core.env.operation.Operation;
import arcade.core.env.operation.OperationCategory;
import arcade.core.util.MiniBox;
/**
* A {@code Lattice} represents an environment layer.... |
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