sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a21493b2e8c7f0676bdf067a59c98375fb8ee15b05e6f54b83c7f95464f7fefa | Java | 1,646 | 58 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Collections;
import java.util.Iterator;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
pu... |
b8cd670b264fd3748bbf8b668390a3685ead70b652102ee9ce9bdbeb66efab80 | Java | 1,657 | 40 | /*
* 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... |
eb93277e5bc6a280912f3a6862d153836b97688d2af701a6e6e19692033d500c | Java | 1,657 | 52 | package org.broadinstitute.dropseqrna.eqtl;
import java.io.File;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import org.broadinstitute.dropseqrna.eqtl.ParseContigGroups;
import org.testng.Assert;
import org.testng.annotations.Test;
public c... |
dcb21eb8923f254f6654af3edaeb9656c5df50d7d6868679eef30a4233ce492c | Java | 1,661 | 44 | /*
* 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... |
604d300605be29c8f555b32d930f5936ad1dfe1d3705d8050194a9f0a3b94032 | Java | 1,669 | 55 | package arcade.patch.agent.process;
import java.util.List;
import arcade.patch.agent.cell.PatchCell;
/**
* Abstract implementation of {@link Process} for cell signaling.
*
* <p>The {@code PatchProcessSignaling} process can be used for networks comprising a system of
* ODEs.
*/
public abstract class PatchProcessS... |
62fbe9a35332777acb3f4d16d980c4ac53e919bbc7ee0d09ac91dec8b0a1dc4b | Java | 1,686 | 41 | /*
* 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... |
500ffa4a0897af0ce1709acc5ba525cb694110dcd502971ae0df304ff0e295e4 | Java | 1,687 | 45 | /*
* 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... |
54bacbb03d6302269e6e60fc14b362af20c7709cac6b670c15609c20f4a48c55 | Java | 1,692 | 57 | /*
* 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... |
eeaf37711586dd1d49c9504b7101facb6b11f89d2d2fb333f804d9db0b74aab9 | Java | 1,704 | 65 | /*
* ClassificationResult.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on October 29, 2003, 4:51 PM
*/
package edu.msu.cme.rdp.classifier;
import edu.msu.cme.rdp.classifier.utils.HierarchyVersion;
import edu.msu.cme.rdp.readseq.readers.Sequence;
import java.util.List;
/**
* ... |
2035867789d3b65336e38676521688dff595f48fa10621b74aa7cccb80fcb026 | Java | 1,713 | 40 | /*
* 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... |
4c047f7d02d03e00ed38d21dfd3693e26de5d115605cd3a96549238d44fb1a75 | Java | 1,714 | 51 | /*
* 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... |
13440cec1ce0ab95bf8f711036e480e360ba0f21d0b48be3647de84ce61bf3bc | Java | 1,716 | 75 | package arcade.env.comp;
import sim.engine.Steppable;
import arcade.sim.Simulation;
import arcade.env.loc.Location;
/**
* A {@code Component} object is a steppable that interacts with the environment.
* <p>
* {@code Component} objects can be used for:
* <ul>
* <li>changing {@link arcade.env.lat.Lattice} arr... |
504b6819398f582cc329f01207a684aa0997fadb7f31e9a0c7bf77172fbc5a82 | Java | 1,717 | 41 | /*
* 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... |
2ee1e11d4ca8c7ab220cb6fdcf4eee50d7754f01d921847b85f7a5a3be5b0740 | Java | 1,733 | 50 | package arcade.patch.agent.process;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.process.Process;
import arcade.core.sim.Simulation;
import arcade.patch.agent.cell.PatchCell;
/**
* Extension of {@link PatchProcessSensing} for hypoxic sensing.
*
* <p>The {@code PatchProcessSensingHypoxic} process ad... |
d2d2aa719449949dc59ef7bd9801ed3dcc628ccf327d212c04e464d49261b4c5 | Java | 1,740 | 48 | package org.broadinstitute.dropseqrna.barnyard;
import java.io.File;
import java.io.IOException;
import java.util.Collections;
import org.apache.commons.io.FileUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.nio.PicardHtsPath;
public class GatherMolecularBarcodeDistributionByGeneTe... |
256118ab789da2ee00906eae27906f529d3fad9d82c69fe02e5d7c9c93a6a604 | Java | 1,748 | 66 | package arcade.core.util.distributions;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
/**
* A {@code Distribution} object represents a parameter distribution.
*
* <p>When created, the object immediately draws an initial value from the distribution. All getters
* should return this initial v... |
ea67f266e3edc09eedfc52b064a82dfac4e9b306a452219dea33d8b23cec205a | Java | 1,749 | 52 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Iterator;
import org.broadinstitute.dropseqrna.utils.FilteredIterator;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.OverlapDetector;
public class OverlapFilteringIterator<OD_TYPE> extends Fi... |
6052e1451014909b6ba24f8bb43995bb938027b769acc66e4b8cf7d33aa4cea5 | Java | 1,762 | 40 | /*
* 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... |
9073402d15d6415045a73b3cce11505e5496a7a00f1202259a5fdd00414b7720 | Java | 1,765 | 59 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import java.io.PrintStream;
import java.io.PrintStream;
import java.io.PrintStream;
public class ConfusionMatrix<T extends Enum<T>> {
private Class<T> enumClass;
private int[][] matrix;
public ConfusionMatrix(Class<T> enumC... |
65ef97f4a6c5ff124928aaca246103fdef1d1b8846518732fad0fd381a4f1204 | Java | 1,766 | 49 | package org.broadinstitute.dropseqrna.vcftools.filters;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import org.broadinstitute.dropseqrna.vcftools.filters.GenotypeGQFilter;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.variant.... |
28abacec34f39e3f2394fd60d2a3113ede22dc4bff9286705efaeadecf00db4c | Java | 1,770 | 50 | /*
* 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... |
21bc64e1451802dd8c9dd79fe483461371e1353e791007ba39794151b6dd721e | Java | 1,780 | 44 | /*
* 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... |
f7825e2d179e44addf1b6a9bb7bdf7b622c372d3191a21bb8333622972304ce3 | Java | 1,792 | 71 | /*
* GoodWordIteratorTest.java
* NetBeans JUnit based test
*
* Created on June 28, 2002, 12:10 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator;
import junit.framework.*;
import java.io.*;
/**
*
* @author wangqion
*/
public class Goo... |
800c178921111f5d5e03abb9fa69b5ec48686441414f61fe73c3f260b6134feb | Java | 1,798 | 54 | package org.broadinstitute.dropseqrna.metrics;
import java.io.File;
import java.io.IOException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collections;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.annotations.Test;
import org.testng.Assert;
import picard.nio.Pi... |
d8ddbe47f804fde83209fa84c07d6d168220ccb57274120175eaba3521c490fe | Java | 1,798 | 50 | package arcade.patch.sim.output;
import java.lang.reflect.Field;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import arcade.core.env.location.Location;
import arcade.core.sim.output.OutputSaver;
import arcade.patch.sim.PatchSeries;
import arcade.patch.sim.PatchSimulation;
i... |
800a322baf70befeda4dff29016571ede57f9c4fab974823d21283364360606b | Java | 1,799 | 44 | /*
* 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... |
c2a7852e256bb5e214b1d0f004694f995474dedb6d2fab2ff101e8563dd3cca8 | Java | 1,803 | 45 | /*
* 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... |
ee242e3111cc70e2f214be7565124bd44d0cc48a06af92685fb7bd0ce91c5a45 | Java | 1,809 | 67 | /*-
* #%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... |
2fa173f3bc77ec4cfa229231a26167dc834c745cbc7bf8e56ab80a4c089b7c60 | Java | 1,810 | 55 | package org.broadinstitute.dropseqrna.utils;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
public class OrderAssertingIteratorTest {
@Test
public void testNext() {
List<Integer> xs = Arrays.asList(1,2,3,4,5,... |
b644a80956bf99f94dc6dd83ded4b2869f3643432bc86d2583d411d33f86e788 | Java | 1,812 | 52 | /*
* 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... |
2c06db6c1305fd18018e7e5fcf0ec3c3c4958e54f3d2932727b25e767bf0bb8f | Java | 1,818 | 55 | package arcade.patch.env.operation;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
import arcade.core.util.MiniBox;
import arcade.patch.env.lattice.PatchLattice;
/**
* Extension of {@link PatchOperation} for natural decay to support including the half-life of
* certain biomolecules.
*
* <p... |
07556b573836b7871d6edcb5e0bda0fd27188db476c8d664092a88d37ee7b892 | Java | 1,832 | 46 | /*
* 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... |
d4be1098558e8cf304a226e10a0a272e756a6525e5242f60784473402e6542bc | Java | 1,838 | 40 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import org.broadinstitute.dropseqrna.utils.readiterators.StrandStrategy;
import picard.annotation.LocusFunction;
import java.util.Collection;
import java.util.List;
public interface FunctionalDataProcessorI {
/**
* Return the set of functiona... |
6344979c641ff86408db2df4c726314456980e4f43542926b5b5a11c918ce775 | Java | 1,842 | 49 | package org.broadinstitute.dropseqrna.censusseq;
import java.io.File;
import java.util.List;
import org.broadinstitute.dropseqrna.censusseq.SNPSampleRecord;
import org.testng.Assert;
import org.testng.annotations.Test;
public class SNPSampleRecordTest {
File ROLL_CALL_VERBOSE_FILE = new File ("testdata/org/broadin... |
04ae872f520fe4f13f19d8fd820d28165afca01f51e9a8883aabf22e30f71a9a | Java | 1,843 | 48 | package org.broadinstitute.dropseqrna.vcftools.filters;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import org.broadinstitute.dropseqrna.vcftools.filters.GenotypeGQFilter;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.variant.... |
ae107437a6c4efd03e107181c8b89ce81d246c438d4302b6490ee693c0052fae | Java | 1,858 | 59 | /*-
* #%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... |
234da67a5acb8d52a165a8efb1a0b76063120f9f55588910fc07db65789de5aa | Java | 1,873 | 49 | /*
* 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... |
84c66b6e10f212130ef37358274656c75f199e8057494fab112c607e7bf0c1a8 | Java | 1,878 | 48 | /*
* 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... |
31266ecaa430ffafa4564f96b7af6172240aa33e9793e64bbcb6887a68bc9ecf | Java | 1,889 | 57 | package arcade.potts.env.location;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
import static arcade.core.ARCADETestUtilities.*;
public class VoxelTest {
@Test
public void hashCode_validObject_returnCode() {
int x = randomIntBetween(0, 100);
int y = rand... |
9e9ee528de033d072af127ee3655b85ddd189217a1936832149af3310769f473 | Java | 1,897 | 63 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import arcade.potts.agent.cell.PottsCell;
import static arcade.potts.util.PottsEnums.Region;
/** Configuration for {@link VolumeHamiltonian} parameters. */
class VolumeHamiltonianConfig {
/** Associated {@link PottsCell} instance. */
final PottsC... |
c17b72a0809d6c59089ef109e543e3dcb2dc3440d27780e6678805071a1b080d | Java | 1,898 | 79 | package arcade.env.grid;
import sim.util.Bag;
import arcade.env.loc.Location;
/**
* A {@code Grid} represents the environment for agents.
* <p>
* Calculations for geometry, bounds, size, etc. can be handled either by the
* {@link arcade.env.loc.Location} object that is passed in with the agent (using
* the {@co... |
73e7f66d4cf541d991459d9e1d9fb748370c725cb99a80437d68849102f8f085 | Java | 1,901 | 63 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import arcade.potts.agent.cell.PottsCell;
import static arcade.potts.util.PottsEnums.Region;
/** Configuration for {@link SurfaceHamiltonian} parameters. */
class SurfaceHamiltonianConfig {
/** Associated {@link PottsCell} instance. */
final Pott... |
2ada4ba2d8b66d7347729cb8617952f617cfd036bd383bc9ee0003de82fab78a | Java | 1,905 | 74 | package arcade.potts.env.location;
import java.util.Comparator;
/**
* Representation of a voxel for locations.
*
* <p>Each voxel is defined by (x, y, z) coordinates. Two voxels objects are considered equal if
* they have matching (x, y, z) coordinates.
*/
public final class Voxel {
/** Comparator for voxels.... |
4f058126263e39bfde7aba3c35edd81518b6a5e732145eb15ba6ae8fe47739aa | Java | 1,906 | 45 | /*
* 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... |
55d2cf66bb635d07e2b07af5262134ca4bf2872718ff1c5abcea92782ef4fd54 | Java | 1,911 | 47 | /*
* 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... |
ae30542d3428b01970e25d5c1d259728a6759953edcea309d509d7e65f5b6dae | Java | 1,912 | 50 | /*
* 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... |
8d3c9a49471f7a629131ab5d69160e0354a48dbd4bbf829d3febcbabc6d86408 | Java | 1,923 | 59 | /*
* 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... |
d722dc353a7bc815db1d5dfe5ccd7594ce48e397215a8325ba355499e6a506fb | Java | 1,924 | 58 | package arcade.env.comp;
import arcade.sim.Simulation;
import arcade.env.lat.Lattice;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.comp.Diffuser} for rectangular lattice.
*
* @version 2.3.5
* @since 2.3
*/
public class RectDiffuser extends Diffuser {
/** Serialization version identifier ... |
2a32a84e27d5f26b6c6a133c58e85da5fa8ae494fd4a1e59522b2064c757918f | Java | 1,927 | 60 | package org.broadinstitute.dropseqrna.utils;
import org.testng.annotations.Test;
import static org.testng.Assert.*;
public class ByteArrayWrapperTest {
@Test
public void testEquals() {
byte[] data1 = {1, 2, 3};
byte[] data2 = {1, 2, 3};
byte[] data3 = {4, 5, 6};
ByteArrayWrap... |
07c8a0e5bebc3e17a904c25ea18ff3ac93e3dd3299c0517f53ba7d167c3ebe3a | Java | 1,932 | 72 | package org.broadinstitute.dropseqrna.metrics;
import java.io.File;
import java.io.IOException;
import java.util.Collections;
import org.apache.commons.io.FileUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.nio.PicardHtsPath;
public class BamTagOfTagCountsTest {
private static fi... |
912dd478d04ad8e4c65422bd4cf7039160689ba95621a2fffb672d882a50bcbe | Java | 1,936 | 63 | /*
* 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... |
a728d588e9d05325196c2b0c952676cc15609d92a893270bd8a486591eb4b32a | Java | 1,936 | 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... |
04e17842fc53dd04c7def4dd62538e85418ab3b34693f0e122e4cce0b84cca75 | Java | 1,937 | 54 | package arcade.potts.env.location;
import java.util.ArrayList;
/** Concrete implementation of {@link PottsLocationFactory} for 3D. */
public final class PottsLocationFactory3D extends PottsLocationFactory {
/** Creates a factory for making 3D {@link PottsLocation} instances. */
public PottsLocationFactory3D()... |
82e65317fbf7273fd18f87983a2fba71729b25070ea109b3defb647db767ac74 | Java | 1,954 | 70 | package arcade.potts.agent.module;
import sim.util.distribution.Poisson;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.module.Module;
import arcade.potts.agent.cell.PottsCell;
import static arcade.potts.util.PottsEnums.Phase;
/**
* Abstract implementation of {@link Module} for {@link PottsCell} agents... |
2f40d808c0a79df371fe43334d82927a5dcb9778c40664df72e7745b36c54ef5 | Java | 1,956 | 73 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.HashMap;
import static arcade.potts.util.PottsEnums.Direction;
import static arcade.potts.util.PottsEnums.Region;
/** Concrete implementation of {@link PottsLocations} for 3D. */
public final class PottsLocations3D extends PottsLocations ... |
79387f1acafbca0f3a584d11162ced3896cfc193304c4727ef06b42dc4c37f86 | Java | 1,960 | 68 | /*
* 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... |
b83c224980fce9f0b8eabbd30e16c9b164d49c2035d2487647f861aea89d3ec2 | Java | 1,965 | 45 | /*
* 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... |
5d8e9d4600285bb88f2f61554372d501126ef3e902cc7cc9a551fb204491b264 | Java | 1,969 | 64 | 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.util.PatchEnums.State... |
802e72e7e9826f9756ae0bf71e98b7e0351a1af0e8950b3e278638d5dcb73448 | Java | 1,981 | 53 | package org.broadinstitute.dropseqrna.censusseq;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.annotations.BeforeClass;
import org.testng... |
bffcf143ac3e88f398a15687030dc434199e6c95ae4977c6bc6af5d5f0c2469c | Java | 1,984 | 57 | /*
* 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... |
87daba54751517b0304e8d8f9976bf93bee19ac21c8c533ed7b62510f91a5f2b | Java | 1,993 | 60 | /*-
* #%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... |
ef5504aa2d51642be9fdb0973b326ae164f64cff13fa68f6564e339e563b73a9 | Java | 2,000 | 69 | /*
* 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... |
09aa3b11df31fc2ac5d237888d75d78203f29a34d46561be8b3b3c4431a61ad7 | Java | 2,020 | 50 | /*
* 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... |
e3d3fa7a5487e5e3c41682144bc10507712bff29d0dfbf74d5147c7d9a63e79d | Java | 2,021 | 42 | /*
* 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... |
2cea387b6698a185ed33aa2bb08db0b248bb1a698e5690aa701b3404369c2ac2 | Java | 2,030 | 77 | package arcade.core.vis;
import java.awt.geom.Rectangle2D;
import sim.engine.Steppable;
import sim.portrayal.Portrayal;
import sim.util.gui.ColorMap;
/**
* Visualization for simulation objects.
*
* <p>{@code Drawer} objects convert simulation objects into <a
* href="https://cs.gmu.edu/~eclab/projects/mason/">MASO... |
cf05703dbe0a9859958e3ddf3b0c5f52999297b5106eb8138f69a997924969f5 | Java | 2,031 | 57 | package org.broadinstitute.dropseqrna.vcftools.filters;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFFileReader;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
public cla... |
5fc214d8c0ea2faccc7e481dea850037ef430b7f73a4ea6825f90e40ac1c3729 | Java | 2,058 | 57 | package arcade.patch.util;
import java.util.HashMap;
import java.util.Map;
import arcade.core.util.EventLog;
/**
* Concrete implementation of {@link EventLog} for proliferation events.
*
* <p>{@code ProliferationEventLog} objects are created when a cell successfully completes its cell
* cycle and divides, capturi... |
843bf68828229c4f5774e005bc369e6158735715cd360dbfaa249850478eb607 | Java | 2,058 | 75 | package arcade.potts.env.location;
import java.util.ArrayList;
import java.util.HashMap;
import arcade.core.util.Vector;
import arcade.potts.util.PottsEnums.Direction;
import static arcade.potts.util.PottsEnums.Direction;
/** Concrete implementation of {@link PottsLocation} for 3D. */
public final class PottsLocation... |
3c7dbea517ccd453a3367081f13409cb788598fa09663d32cc4db93053be4e1f | Java | 2,059 | 49 | package arcade.patch.env.operation;
import arcade.patch.env.lattice.PatchLattice;
/** Extension of {@link PatchOperationDiffuser} for rectangular lattices. */
public class PatchOperationDiffuserRect extends PatchOperationDiffuser {
/**
* Creates a {@link PatchOperationDiffuser} for rectangular lattices.
... |
ddf3c674d511f0448df5753ae26935ed10a32b364ae961ccc134b816bbff38ce | Java | 2,073 | 59 | /*
* 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... |
bbdb08a1cd4e6844a43476effcb0e60d175fcaf9e697bd67afb3e47a4212d2ec | Java | 2,085 | 55 | /*
* 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... |
553dfa7d9d92efab0338142026fb9c9b10f8186d6c63598d67a1492c1c0a3663 | Java | 2,087 | 73 | /*
* FindWindowFrame.java
*
* Created on November 15, 2006, 10:53 AM
*/
package edu.msu.cme.rdp.classifier.train.validation.movingwindow;
import java.util.ArrayList;
import java.io.StringReader;
import java.io.IOException;
/**
*
* @author wangqion
*/
public class FindWindowFrame {
public static final int... |
14fe361b545f80d067c869400759b181c9d598e3bbd3b95d729beb37990e949e | Java | 2,091 | 61 | package org.broadinstitute.dropseqrna.vcftools.filters;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.stream.Collectors;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.variant.variantc... |
1e111132a36745d9306c4225b205762759b610c84c80860df9a199e6fde69898 | Java | 2,093 | 75 | package arcade.env.comp;
import java.util.ArrayList;
import sim.engine.SimState;
import arcade.sim.Simulation;
import arcade.env.lat.Lattice;
import arcade.util.MiniBox;
/**
* Implementation of {@link arcade.env.comp.Component} for generator sites.
* <p>
* A {@code Sites} object defines the locations of sites fro... |
0a8c63cdb5ee57b680a1bdcdeac58666111ee7f8c336fa8a5554464fed7b812f | Java | 2,094 | 68 | package arcade.potts.sim.hamiltonian;
import java.util.EnumMap;
import arcade.potts.agent.cell.PottsCell;
import arcade.potts.env.location.PottsLocation;
import static arcade.potts.util.PottsEnums.Region;
/** Configuration for {@link HeightHamiltonian} parameters. */
class HeightHamiltonianConfig {
/** Associated... |
a3c5a36387b91ef69215238798dfde59274581ec3afc817ceb0630657f2f0461 | Java | 2,094 | 64 | package arcade.patch.env.operation;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
import arcade.patch.env.lattice.PatchLattice;
import arcade.patch.sim.PatchSimulation;
import static org.junit.jupiter.api.Assertions.*;
im... |
88dd8c6309c14eebbf0c444f9cd88512d5ccf4b0d16479c7a9bb1a19d24e7449 | Java | 2,095 | 56 | /*
* 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... |
49b0e0fe342ecdfbed6f5d1f54f1a1b24af4aa069dc2a9e87b7fa39de69a0006 | Java | 2,098 | 42 | package examples;
import edu.ucsd.sccn.LSL;
public class HandleMetaData {
public static void main(String[] args) throws Exception {
// create a new StreamInfo and declare some meta-data (in accordance with XDF format)
LSL.StreamInfo info = new LSL.StreamInfo("MetaTester","EEG",8,100,LSL.ChannelFor... |
905bf109c9b62e08018e5b91cae8289bbc73c854ed8bfbf758d91e36b42c1cd4 | Java | 2,103 | 59 | /*
* 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... |
4a2958e06f84ac6dd86b7a420d42e3e2a7445c0f7bbcd1b5b6fbf7b96500c2f8 | Java | 2,109 | 83 | /*
* RankAssignment.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 25, 2002, 11:35 AM
*/
package edu.msu.cme.rdp.classifier;
/**
* A RankAssignment holds the classification result of a sequence at one rank level.
* @author wangqion
* @version
*/
public class RankAs... |
a88ce5cdb7e2e20c56384cbdb2de0eb50ea5ab38f0cde03235e0fdb51f275dac | Java | 2,119 | 70 | /*
* HierarchyVersion.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on November 13, 2003, 11:26 AM
*/
package edu.msu.cme.rdp.classifier.utils;
import edu.msu.cme.rdp.classifier.TrainingDataException;
import java.util.regex.*;
/**
* A HierarchyVersion holds the training set n... |
8787f0f0b916cc42edde04628fd2937d7ac0cba37a39ac6dbc5a1500affb4734 | Java | 2,120 | 52 | /*
* 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... |
9de37d276e9ac1c639e66f745fa9dd0a7ae7d4c523a946fa60b91b4060a12899 | Java | 2,120 | 50 | /*
* 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... |
3f04954179d6537b39d0df0f5430d163071559483e9eadc5cb8ec1a1b112939c | Java | 2,124 | 95 | /*
* Copyright (C) 2012 Michigan State University <rdpstaff at msu.edu>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 2 of the License, or
* (at your option) any later v... |
a7e0d9d1828d08356b3e388d1ef11ee9c46e328a2cf631aef578dec035c8a46a | Java | 2,128 | 58 | /*
* 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... |
04ef83b1e0e84f0b83d13b727309e4e0841e66fd5bf65c803808069925f5d934 | Java | 2,130 | 58 | /*
* 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... |
6361de61d3761a3d67804d9683f4124745321206d2c9ff0568ee73217a4f8cc3 | Java | 2,137 | 65 | package arcade.potts.sim.hamiltonian;
import org.junit.jupiter.api.Test;
import arcade.potts.sim.Potts;
import arcade.potts.sim.PottsSeries;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import static arcade.potts.util.PottsEnums.Region;
public class SurfaceHamiltonian2DTest {... |
d6dbc6607dc23c5602ee3bb2c49dc98a5a57f7f7c7b8d84586e261d29f5a2dbd | Java | 2,142 | 60 | /*
* 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... |
123daffe665f0e6eccf9eabe825b536a9daa1e3b3d556e409331637b10ac2cfe | Java | 2,152 | 65 | /*
* 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... |
d6c0076474e323cf2ba40c6ce3061d9b096035d37b1ed1159b386d45565d4b6d | Java | 2,152 | 63 | /*
* 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... |
1949329120237f7068eb64e105eb90a452e3f70d9068616d1ba73f69dd9d6ece | Java | 2,158 | 74 | /*
* RawSequenceParserTest.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 27, 2002, 6:48 PM
*/
package edu.msu.cme.rdp.classifier.train;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import junit.framework.Test;
import juni... |
1491ff4ef8b8ad064b4cf57a32a5f37ec593e3b677acecf893e024c5e918ec61 | Java | 2,161 | 62 | package org.broadinstitute.dropseqrna.barnyard.digitalallelecounts.sampleassignment;
import java.io.File;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import ht... |
a8e3ed5d9e7334a54eeb47760be249cb8d2352061ede110dd3eac319fafe7ac9 | Java | 2,170 | 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... |
fd7b4f434cb8ba5782c50e577d03127b0690a38f0d6945ca627b2d3842ad133a | Java | 2,173 | 77 | package arcade.core.util.distributions;
import sim.util.distribution.Binomial;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
/** Container class for Bernoulli distribution. */
public class BernoulliDistribution implements Distribution {
/** Probability of success for the distribution. */
... |
437e181b772f40e6f01c37259ea3cdc82b96d7031d5a32ddb1474c99caabc228 | Java | 2,177 | 56 | /*
* 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... |
ca0e36747d4803442f97243ead553f33f214bcfdf05cf81e6018e01bce5b9b7a | Java | 2,184 | 69 | /*
* 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... |
7fb01a267150be6a3f6a930d30b57e33d5473abb6afb726bcc5e7d9e6d32691c | Java | 2,190 | 65 | package org.broadinstitute.dropseqrna.annotation;
import org.testng.Assert;
import org.testng.annotations.Test;
public class RefFlatRecordTest {
@SuppressWarnings("unlikely-arg-type")
@Test
public void testEquals() {
RefFlatRecord r1 = new RefFlatRecord("foo", "trans1", "1", false, 1, 10, 2, 9);
RefFlatRecord... |
2ecca8b0d2b8aeb2d99e5a80c73e84b06e2d7c3b26fd4188bbae9d6926656f7e | Java | 2,198 | 66 | /*-
* #%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... |
f0c6acb8cc317665a040617a1e1490d40ffafaed74359b10a69d57e71f51e0f6 | Java | 2,211 | 78 | package arcade.agent.helper;
import sim.engine.*;
import sim.util.Bag;
import arcade.sim.Simulation;
import arcade.agent.cell.Cell;
import arcade.agent.cell.TissueCell;
/**
* Extension of {@link arcade.agent.helper.TissueHelper} for cell death.
* <p>
* {@code RemoveTissueHelper} is stepped once after the number of... |
759b77ba1655b2b22afc4242a3481b1666f0fc8823a120698b4a739a5fe5a185 | Java | 2,213 | 42 | package org.broadinstitute.dropseqrna.annotation.functionaldata;
import org.testng.Assert;
import org.testng.annotations.Test;
import picard.annotation.LocusFunction;
public class FunctionalDataTest {
@Test public void testType() {
FunctionalData senseCoding = new FunctionalData("A", "+", LocusFunction.C... |
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