sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f338eb6cd99861934aadbfa9623787b559deb769c8a69e9df760836e18915def | Java | 1,078 | 43 | package arcade.env.grid;
import arcade.env.loc.*;
import sim.util.Bag;
/**
* Extension of {@link arcade.env.grid.AgentGrid} for rectangular grid.
* <p>
* Each rectangular location has four positions.
* Uses {@link arcade.env.loc.RectLocation} as {@link arcade.env.loc.Location} object.
*
* @version 2.3.2
* @si... |
f0be49023fa5e4861bf8019402a484608bce47d86aa202d8a718a6b92ec3f98e | Java | 1,085 | 31 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.io.File;
import java.util.Collections;
import java.util.List;
import org.broadinstitute.dropseqrna.barnyard.ParseBarcodeFile;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
public class UMIReadIte... |
55ca21ce16b8a5e7b69a0a320c033cfd1ec07991dea058a62f41d4da2bcf42fc | Java | 1,086 | 50 | /*
* ClassificationResult.java
*
* Created on June 25, 2002, 11:35 AM
*/
/**
*
* @author wangqion
* @version
*/
package edu.msu.cme.rdp.classifier.train.validation;
public class ValidationClassificationResult {
private HierarchyTree bestClass;
private double posteriorProb;
private float numOfVote... |
c1d8b5f8b01494f78e7bbeeea2428f77bf94901a152e2981e0ef19981263a04c | Java | 1,109 | 26 | package arcade.core.agent.module;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
/**
* A {@code Module} object is an exclusive subcellular steppable.
*
* <p>{@code Module} objects represent subcellular behaviors or mechanisms within a {@link
* arcade.core.agent.cell.Cell} object, such as t... |
c506692e7fd10fb14dc7e4ad39a0534fbdbed8237f25ef01d55916fa36c43cd0 | Java | 1,113 | 50 | /*
* AddLogsTest.java
* JUnit based test
*
* Created on June 28, 2002, 12:19 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
import edu.msu.cme.rdp.classifier.train.validation.AddLogsTest;
import edu.msu.cme.rdp.classifier.train.validation.AddLogs;
import junit.framework.*;
/**
*
* @author wangqion... |
ec9d4599261dcaa620b92ab3bfbf154d65411a782ee566913619f8d8657864b3 | Java | 1,120 | 40 | /*
* GenusWordConditionalProb.java
*
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on September 8, 2003, 1:47 PM
*/
package edu.msu.cme.rdp.classifier;
/**
* A GenusWordConditionalProb holds the index of the genus node,
* and the conditional probability that genus node contains the ... |
5809bc652d45e53dac41cda9ae93ffff96111149f912d32cb9dc4f45f934eda0 | Java | 1,128 | 36 | package arcade.patch.agent.process;
import arcade.patch.agent.cell.PatchCell;
/**
* Abstract implementation of {@link Process} for {@link PatchCell} sensing.
*
* <p>The {@code PatchProcessSensing} process can be used for adding molecules to the environment
* based on cell state or environmental conditions.
*/
pu... |
5ad1e2435cf3664c9f9f630a20522ffd068270dc64df1038a94fa099ac6083b9 | Java | 1,135 | 38 | 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.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
public... |
19e0da4a3ee1a0e8b6c473038d42d345bcdceb5c706423d6fe8a0b3af2863061 | Java | 1,140 | 29 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.OverlapDetector;
import java.util.function.Predicate;
public class IntervalListPredicate implements Predicate<SAMRec... |
0c810d28991ff3dba601d76bc1459d67444d3d2e5ae19d66c50f81f48473abb3 | Java | 1,146 | 40 | package arcade.core;
public final class ARCADETestUtilities {
protected ARCADETestUtilities() {
throw new UnsupportedOperationException();
}
public static int randomSeed() {
return randomIntBetween(1, 1000);
}
public static int randomIntBetween(int lower, int upper) {
retu... |
e0188d3a56f0cbd539a6a1fda2c65f3f98005e1626bb551ba4b6da04c4fc91ed | Java | 1,171 | 37 | package arcade.core.util;
import java.util.Map;
/**
* Abstract class representing a logged simulation event.
*
* <p>{@code EventLog} objects capture specific events that occur during a simulation, recording
* when the event happened and what type of event it was. Subclasses define the specific details of
* each ... |
6afe94289da0126730a2568e8e2609c5135201cdd7038b416d88615694b46f9f | Java | 1,174 | 69 | /*
* Taxonomy.java
*
* Created on August 21, 2002, 5:14 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
/**
*
* @author wangqion
*/
public class Taxonomy {
public static final String GENUS = "GENUS";
int taxID; // the taxonomy id
int parentID; // the parent taxonomy id
int depth; ... |
98afda2442576c7169106cf124dc8b61dc16beaf7acd2e91e23b13eeb57148cc | Java | 1,177 | 39 | 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... |
7b5ba9cff923e96c52a7e49b00d49959b07368276139293b733f3efaba892be0 | Java | 1,186 | 48 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Collections;
import java.util.Iterator;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBuilder;
public class GeneStrandFilteringIteratorTest {
@Test
publ... |
8f38a4cb01c480fe4061fbf056e013e1f339fee265c6acda751727fc031bd18b | Java | 1,204 | 40 | package arcade.patch;
import arcade.core.ARCADE;
import arcade.core.sim.Series;
import arcade.core.sim.input.InputBuilder;
import arcade.core.sim.output.OutputLoader;
import arcade.core.sim.output.OutputSaver;
import arcade.patch.sim.input.PatchInputBuilder;
import arcade.patch.sim.output.PatchOutputLoader;
import arc... |
112b41aa77ba694d4455a2cc8d88b54abc3fcccbbb79efa7de1f49b3cf43860a | Java | 1,219 | 23 | package org.broadinstitute.dropseqrna.utils.editdistance;
import java.util.List;
import org.broadinstitute.dropseqrna.utils.ObjectCounter;
/**
* Interface to plug in various collapse strategies for greedy collapse algorithm in MapBarcodesByEditDistance.collapseBarcodesGeneric
* @author nemesh
*
* @param <T> The ... |
133e35abfbc3cb3a083c5a2301cf193591f6e80b804754ceec4ce0a7ca433258 | Java | 1,225 | 40 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
import java.util.function.Predicate;
import htsjdk.samtools.SAMRecord;
/**
* Given a tag name and a collection of values, filters reads that do not have one of the values.
* @aut... |
d48a2925332d7eef9540f3a65a281eafbd8f7e1ad3258e0d4dc6397df6b59e95 | Java | 1,230 | 56 | package org.broadinstitute.dropseqrna.utils.editdistance;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
public class FindSimilarEntitiesResult <T,M> {
private final Map<T, List<T>> entity... |
61d0e752bc351a4f11e845a647be1a13d0525dbd3b4d7fca175b24bfc4be9534 | Java | 1,231 | 29 | package arcade.core.env.operation;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
/**
* An {@code Operation} object is a non-exclusive environmental layer steppable.
*
* <p>{@code Operation} objects represent environmental behaviors or mechanisms within a {@link
* arcade.core.env.lattice.L... |
c86d97a230b10f5091974dee728171943d0565de56f977b03bebce19576af974 | Java | 1,241 | 28 | /*
* 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... |
1acecd58556aa11b6eb85b4315578b214bf140730afd054991cbd75ef87d2298 | Java | 1,243 | 44 | package org.broadinstitute.dropseqrna.annotation.functionaldata.disambiguate;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalData;
public class ValidationStatus {
private final GeneWithFunction star;
private final GeneWithFunction dropseq;
public ValidationStatus (GeneWithFun... |
7d1ad795e898422673610f7224d708833cbbef20c1d58f4c60955561116c7290 | Java | 1,244 | 37 | package org.broadinstitute.dropseqrna.utils.readiterators;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
import java.util.function.Predicate;
import htsjdk.samtools.SAMRecord;
public class ChromosomeFilteringPredicate extends RequiredTagPredicate implements Predicate<SAMRecord> {
p... |
e279696aa120041ddc519c92032b37d73b75ab942ca85c61bb089f3bbd41f570 | Java | 1,247 | 42 | package arcade.env.comp;
/**
* Specification of molecular details for {@link arcade.env.comp.Sites}.
* <p>
* A {@code Site} contains the correct set of environment lattices for a given
* molecule.
* Molecule codes are defined in {@link arcade.sim.Simulation}.
*
* @version 2.3.0
* @since 2.3
*/
abstract clas... |
04466d0f357cd9b1d7699cb45af2d99fb6184fa33569d41284776e7af93d383f | Java | 1,248 | 43 | package arcade.env.lat;
import arcade.sim.Simulation;
import arcade.env.comp.*;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.lat.EnvLattice} for rectangular lattice.
* <p>
* {@code RectEnvLat} uses the {@link RectDiffuser} for diffusion on a rectangular
* grid.
*
* @version 2.3.12
* @since... |
e2cdf360c7b2ded0ec54190cd413a9855ab473918caafe6a61190aed6037e9af | Java | 1,256 | 34 | package arcade.patch.env.location;
import java.util.ArrayList;
/**
* Concrete implementation of {@link PatchLocationFactory} for rectangular geometry.
*
* <p>Cell agents exist on a rectangular grid and molecules in the environment diffuse on a smaller
* rectangular lattice, such that each grid rectangle correspon... |
bd247ed07e8033f67ca593e7cddd78375674caee94f706f5f47cf9413494393a | Java | 1,261 | 38 | package org.broadinstitute.dropseqrna.vcftools.filters;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.varia... |
6c1630a53d528cdc34ffac8544971806c35ca2d0f199afbe12dbecdb5a32963d | Java | 1,265 | 31 | /*
* 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... |
e647bec0de532f68226e090fb08f0f06bdda852e60611166b047e60230ccce9d | Java | 1,279 | 32 | /*
* 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... |
8876da8d669b11b48bdec045b658962924bf4608ec4fc91998de054901f40868 | Java | 1,282 | 75 | /*
* Score.java
*
* Created on November 10, 2003, 5:24 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
/**
*
* @author wangqion
*/
public class Score {
private float score;
private Taxon node;
private Score nextSeqScore; // the score of the next sequence at current rank
private Score nextAssig... |
2e74476885615bfdfa3f89d3f455f487e7f6cbdd5b31102213fe23dfef729494 | Java | 1,288 | 36 | package org.broadinstitute.dropseqrna.censusseq;
import java.util.HashMap;
import java.util.Map;
import org.testng.annotations.Test;
import org.testng.Assert;
public class OptimizeSampleRatiosCommonSNPsResultTest {
@Test
public void test() {
Map<String,Double> result = new HashMap<>();
result.put("Donor1", 0.... |
5e906bb98c2cbd5a06fc5e86da03f78e34023808cbb00b552a7a7a6c616c43e0 | Java | 1,289 | 30 | package arcade.core.agent.process;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Simulation;
/**
* A {@code Process} object is a non-exclusive subcellular steppable.
*
* <p>{@code Process} objects represent subcellular behaviors or mechanisms within a {@link
* arcade.core.agent.cell.Cell} object, suc... |
9ba3a9973eaf667fc99246b3b6bda9dd81baf05172ad65882bfcd45d4b1c949a | Java | 1,292 | 44 | package arcade.agent.module;
import java.io.Serializable;
import arcade.sim.Simulation;
/**
* A {@code Module} object is a subcellular steppable.
* <p>
* {@code Module} objects represent subcellular behaviors or mechanisms within
* a {@link arcade.agent.cell.Cell} agent, such as metabolism, signaling networks,
... |
e93009279cbea16b43fd7ff0f354649b79316f3ef515022c5673511eeef9b6f5 | Java | 1,296 | 36 | package arcade.patch.util;
import java.util.Map;
import org.junit.jupiter.api.Test;
import arcade.patch.env.location.Coordinate;
import arcade.patch.env.location.CoordinateXYZ;
import static org.junit.jupiter.api.Assertions.*;
public class LysisEventLogTest {
private static final Coordinate COORDINATE = (Coordin... |
a4e662d6bf6052f3a918b61a4e5b890a35e9f5409545a6154b439a2851f29c09 | Java | 1,300 | 34 | /*
* 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... |
4adb7029e4ec169dac477c7039ba6ad8ce596674b446064e43339f49c85909a0 | Java | 1,301 | 40 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.HashSet;
import java.util... |
d12475a36b45c1af009594c2dfd8f353663aee75dd1d6d93827a8d2b0200b6e2 | Java | 1,302 | 31 | /*
* 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... |
de3b7aab158fb9bb9971fa22b4405423d89fd545ed602b2a352f6d43db804de7 | Java | 1,304 | 42 | package edu.msu.cme.rdp.classifier.train.validation;
class AddLogs {
// an interval of 0.01 gives a maximum error ~ 3E-6
static final double interval = 0.01;
static final int xlateFactor = (int) Math.round( 1.0 / interval );
// -13 gives value of ~ 2.3E-6, acceptable error
static final int ... |
300fc80bee548b33dc8d2a6b50431c7b62c277ae9648e79d018aa9701cfb67f9 | Java | 1,311 | 46 | package org.broadinstitute.dropseqrna.utils;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.broadinstitute.dropseqrna.TranscriptomeException;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordSetBu... |
0e2448c172ca55ae66acce7416ce79de2e6f8793f1e06ef7ad2ef2111a1023c6 | Java | 1,328 | 39 | package arcade.core.env.component;
import sim.engine.Schedule;
import sim.engine.Steppable;
import arcade.core.sim.Simulation;
/**
* A {@code Component} object is a steppable that interacts with the environment.
*
* <p>{@code Component} objects represent any entity that interacts with the environment. They can
* ... |
39b7f79b4be9912dd5548b22b35f0389fbb2984f972b34cd389cfaf76365e2d2 | Java | 1,333 | 46 | package arcade.patch.env.location;
import arcade.core.agent.cell.CellContainer;
import arcade.core.env.location.Location;
import arcade.core.env.location.LocationContainer;
import arcade.core.env.location.LocationFactory;
/** Implementation of {@link LocationContainer} for {@link PatchLocation} objects. */
public fin... |
5707c6c1a2c7ebdbacba0d0c771c4cb259febe7db8b933f6bcfe683ec9427397 | Java | 1,335 | 31 | /*
* 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... |
2db9d3546250699e50dc6e6fbc1bdbcc323993ee22e568adc5b8f96872cd5f8c | Java | 1,336 | 39 | package arcade.core.agent.action;
import sim.engine.Schedule;
import sim.engine.Steppable;
import arcade.core.sim.Simulation;
/**
* An {@code Action} object is a steppable that interacts with agents.
*
* <p>{@code Action} objects represent any entity that interacts with agents. They can be used for:
*
* <ul>
* ... |
b571e649f6201c3095b58eef7152a4ef0580711cb1d7e46f60e52933923334ed | Java | 1,341 | 56 | package arcade.agent.module;
import java.util.List;
import arcade.sim.Simulation;
import arcade.agent.cell.Cell;
import arcade.env.loc.Location;
/**
* Implementation of {@link arcade.agent.module.Module} for cell signaling.
* <p>
* The {@code Signaling} module can be used for networks comprising a system of
* ODE... |
d6ecead30b83608311504b66412449e16e3944580de031853e0ac1cf729dc054 | Java | 1,342 | 74 | /**
* Taxonomy.java
*
* Copyright 2006 Michigan State University Board of Trustees
* Created on August 21, 2002, 5:14 PM
*/
package edu.msu.cme.rdp.classifier.train;
/**
* A Taxonomy holds the raw taxon information.
* @author wangqion
*/
public class Taxonomy {
int taxID; // the taxonomy id
String tax... |
2a46c7ab5e06aeee601e020dc5b3a18787cb3c324e0bcdd55f06b39c131dace9 | Java | 1,344 | 45 | package arcade.env.lat;
import arcade.sim.Simulation;
import arcade.env.comp.*;
import arcade.util.MiniBox;
/**
* Extension of {@link arcade.env.lat.EnvLattice} for triangular lattice.
* <p>
* {@code TriEnvLat} uses the {@link TriDiffuser} for diffusion on a triangular
* grid.
* Triangular grid locations have (... |
3b9a18e7f46e718a22b743579b356caebe1d55ec43e27a2051d068b8e0e6daa3 | Java | 1,348 | 31 | /*
* 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... |
30d92baf82273c2c5b7232b8b978d4219bccce6511bf7f4a2b8472cdbac24fd2 | Java | 1,370 | 30 | /*
* 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... |
7f1b6cdf49ed833f9ba94458d27e3c07621511320424e5734824b12893f13332 | Java | 1,376 | 46 |
/*
* ClassifierTestSuite.java
* NetBeans JUnit based test
*
* Created on June 25, 2002, 3:59 PM
*/
package edu.msu.cme.rdp.classifier.train.validation;
import junit.framework.*;
/**
*
* @author wangqion
*/
public class ClassifierTestSuite extends TestCase {
public ClassifierT... |
8e4c71f76c337435da6d3bf31e6a12df3ed46bc6cc4d5f264ec34cd887bf5823 | Java | 1,379 | 45 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalDataProcessorStrategy;
import org.broadinstitute.dropseqrna.utils.CountChangingIteratorWrapper;
import picard.annotation.LocusFunction;
import java.uti... |
8fd77cd90a7da7db89538444de3856f1dcd54d7cf2aa3c6fdcb9cf4a1e5ee918 | Java | 1,391 | 35 | /*
* 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... |
c821cdd75ae3b648f93c50eb57a1218776eb10ebff0d728bd0cc54866139ecc9 | Java | 1,393 | 46 | package arcade.core.agent.cell;
import ec.util.MersenneTwisterFast;
import arcade.core.env.location.Location;
import arcade.core.util.Parameters;
/**
* Container class for {@link Cell} objects.
*
* <p>The container implementation should contain the minimal set of information needed to
* initialize a {@link Cell} ... |
c11fa920f4177c254975520aad2c7db71a5ee42ba507549bb8d5a1afe9168532 | Java | 1,407 | 46 | package org.broadinstitute.dropseqrna.annotation;
import java.util.List;
import org.testng.Assert;
import org.testng.annotations.Test;
import htsjdk.samtools.util.Interval;
public class GQuadruplexTest {
@Test
public void f() {
// handy examples http://bsbe.iiti.ac.in/bsbe/ipdb/g4dna.php
// I trimmed a set o... |
af7bcb4ebf2e3ab13b115e2a43314de330e6495f324fcf48fb9a33a333fd0fe1 | Java | 1,414 | 56 | package arcade.core.agent.cell;
import ec.util.MersenneTwisterFast;
import arcade.core.sim.Series;
import arcade.core.util.GrabBag;
import arcade.core.util.MiniBox;
/**
* Factory class for {@link Cell} objects.
*
* <p>The factory manages the creation of {@link Cell} objects by either:
*
* <ul>
* <li>Loading e... |
513e146603a72e711428fe19948ca1cf9b6ae39af0169609ac3fe7b75500c6f0 | Java | 1,417 | 41 | package org.broadinstitute.dropseqrna.spermseq.metrics.spermalleles;
import java.io.File;
import java.io.IOException;
import org.apache.commons.io.FileUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
public class GenotypeSpermTest {
private static final File BAM_FILE = new File("testdata/org/b... |
1fb31f409b13fb5a484c037156ff1f1ce2b715df2dff3d5ac5c31ebe5fb423e2 | Java | 1,420 | 36 | package org.broadinstitute.dropseqrna.eqtl;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import org.broadinstitute.dropseqrna.eqtl.PrepareEqtlCovariates;
import org.broadinstitute.dropseqrna.utils.TestUtils;
import org.testng.Assert;
import org.testng.annotat... |
58d11d16928230432734904a10fe5da6c480742171ea449e4fc380dca0424bf8 | Java | 1,429 | 43 | package arcade.core.util.distributions;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
/** Container class for truncated normal distribution. */
public class NormalTruncatedDistribution extends NormalDistribution {
/**
* Creates a truncated normal {@code Distribution} from parameters di... |
442a1cd8e0cf2c7c3b59ce7ff100a1269c48125ab5136ae5e1926abcc28d337f | Java | 1,435 | 61 | package arcade.agent.helper;
import sim.engine.Steppable;
import arcade.sim.Simulation;
/**
* A {@code Helper} object is a steppable that interacts with agents.
* <p>
* {@code Helper} objects can be used for:
* <ul>
* <li>introducing outside perturbations to the cells in the system, such as
* the addin... |
1a4307b9c56026736921e8fb4ea655c933af68d8415fba4c674db3a76957a7b2 | Java | 1,444 | 34 | /*
* 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... |
373b2f78f1695d98641f3ef58cda33d1c520469dde11ab4c87071e745d026dbd | Java | 1,445 | 32 | /*
* 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... |
d942ec40775b8c02c865716b688949d04f0f6f27d9ae8ad7f781b821f6eebddc | Java | 1,447 | 40 | package arcade.patch.env.lattice;
import org.junit.jupiter.api.Test;
import arcade.core.util.MiniBox;
import arcade.patch.env.operation.PatchOperationDecayer;
import arcade.patch.env.operation.PatchOperationDiffuserTri;
import arcade.patch.env.operation.PatchOperationGenerator;
import arcade.patch.util.PatchEnums.Cate... |
420dcd698b618974541a0507c955c0bf0d8ac461901ab88898a6c74a7daa92b2 | Java | 1,448 | 51 | package org.broadinstitute.dropseqrna.utils;
import static org.testng.Assert.assertEquals;
import java.io.File;
import java.util.List;
import org.testng.annotations.Test;
import htsjdk.samtools.metrics.MetricsFile;
import htsjdk.samtools.util.IOUtil;
public class FilteredReadsMetricTest {
static final File ME... |
f10cd3617102d393f7e6d4264594319cdcec8028a661de12194355bc2fe4566a | Java | 1,451 | 61 | package arcade.patch.env.location;
/**
* Representation of (x, y, z) coordinates.
*
* <p>Each coordinate is defined by (x, y, z) values. Two coordinate objects are considered equal if
* they have matching (x, y, z) values.
*/
public final class CoordinateXYZ extends Coordinate {
/** Coordinate x value. */
... |
254863476433f9cfe51490327030d18417c648bec0b7d850d42a7c271a25fa3f | Java | 1,454 | 39 | /*
* 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... |
dbb6c7be6fe67a3b2c41f2dd2639983966e8f2cb97927b77dc4c2e7ee8d74cf7 | Java | 1,459 | 43 | /*-
* #%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... |
c9651e5041c8f4d62d3f3db89e7d5fcbc623df4a7aae0eeae4f06b55783fb441 | Java | 1,468 | 40 | package arcade.patch.env.lattice;
import org.junit.jupiter.api.Test;
import arcade.core.util.MiniBox;
import arcade.patch.env.operation.PatchOperationDecayer;
import arcade.patch.env.operation.PatchOperationDiffuserRect;
import arcade.patch.env.operation.PatchOperationGenerator;
import arcade.patch.util.PatchEnums.Cat... |
3cc447438d70d69c2718fa4b883310558b0c2f0f0a7ee57ee6c77bc7bd5a14db | Java | 1,475 | 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... |
2f27d57824046ed37a39ef955235230c6c183ff4e12503a6fc4039c0e8b3d4d2 | Java | 1,482 | 53 | package arcade.core.env.grid;
import sim.util.Bag;
import arcade.core.env.location.Location;
/**
* A {@code Grid} represents the environment for agents.
*
* <p>Calculations for geometry, bounds, size, etc. can be handled either by the {@link Location}
* object that is passed in with the agent (using the {@code Gr... |
848ed9669404f01b72b2f04f6dfe6dc0d22b992738e8f0800a072fd05e990b53 | Java | 1,486 | 40 | /*
* 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... |
f643d805a18160b73413ad424667ff0540c79d7f1c2b7101727e039774e9cf9a | Java | 1,489 | 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... |
d25e613d5c0b5dca3198d812e294b37d383ad6314e3513514783b610980c21b3 | Java | 1,492 | 38 | package org.broadinstitute.dropseqrna.utils.readiterators;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import org.broadinstitute.dropseqrna.annotation.functionaldata.FunctionalDataProcessorStrategy;
import org.testng.Assert;
import org.testng.annotations... |
49b8cde324972deeeefaea98910c97777ab436fc5fe958c9269111dff8daf17e | Java | 1,493 | 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... |
fe3a158c723901d22269c9d00e18ddfb8e1d146f2a6b9d3172cf2a98a3192562 | Java | 1,493 | 38 | /*
* 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... |
0fc2c0121b7b89702db894e07140cc25a509206b20b2b77e6c37a5a63cd455b2 | Java | 1,496 | 38 | /*
* 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... |
a3124aa6927092f12a6a99ba87f3333e8af4f3924915547488bbd593780319c3 | Java | 1,501 | 38 | /*
* 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... |
c0139181c36138eb3a80babf6caffaa6cf4eb93c7ee4b6bd1357d9d6c96aff3e | Java | 1,510 | 40 | /*
* 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... |
f43b41fad2a7b3ee39e0645dc6ef478e7b42a1bfd5410c501dd7796bca1cbde2 | Java | 1,511 | 40 | package arcade.patch.env.lattice;
import arcade.core.env.operation.Operation;
import arcade.core.util.MiniBox;
import arcade.patch.env.operation.PatchOperationDecayer;
import arcade.patch.env.operation.PatchOperationDiffuserTri;
import arcade.patch.env.operation.PatchOperationGenerator;
import arcade.patch.util.PatchE... |
c3ee6d48d046c138ee77c909e8d5a9986e40784152c2c484efa865542194d1de | Java | 1,516 | 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... |
5b592f67e01ab2aa7cf4eb55384f1f18ba5a5d164df03d5a2172509062741e83 | Java | 1,517 | 40 | package arcade.patch.env.lattice;
import arcade.core.env.operation.Operation;
import arcade.core.util.MiniBox;
import arcade.patch.env.operation.PatchOperationDecayer;
import arcade.patch.env.operation.PatchOperationDiffuserRect;
import arcade.patch.env.operation.PatchOperationGenerator;
import arcade.patch.util.Patch... |
9d85a3eecdcab2758a3de214a6a8059dd3eb091aa8b91959abfd2ca1357fcd5a | Java | 1,522 | 58 | package arcade.agent.helper;
import arcade.agent.cell.TissueCell;
/**
* Implementation of {@link arcade.agent.helper.Helper} for time-delayed
* {@link arcade.agent.cell.TissueCell} behaviors.
* <p>
* Each {@code TissueHelper} object is associated with a specific
* {@link arcade.agent.cell.TissueCell} agent.
* ... |
2debeeba9310303633cb3dcd8f96bc43c7026cf5f9d1a0bcf12cdb8d4ae09445 | Java | 1,526 | 39 | /*
* 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... |
970e128a96b5908d79fc793fcba0ba86a3a1c10041f8bd19c5f84b53e099f759 | Java | 1,541 | 47 | package arcade.patch.agent.process;
import ec.util.MersenneTwisterFast;
import arcade.core.agent.process.Process;
import arcade.core.sim.Simulation;
import arcade.core.util.Parameters;
import arcade.patch.agent.cell.PatchCell;
import static arcade.patch.util.PatchEnums.Flag;
/**
* Extension of {@link PatchProcessSig... |
d216efc71a1db8a1f185254818ccac1a1e374b3dce775bd804be04773cd785d4 | Java | 1,541 | 40 | /*
* 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... |
25d812cf7e9d8d11b64bdac8f1cbe75669d9452f87eabe81948dd0f69468bf82 | Java | 1,542 | 51 | package de.uol.neuropsy.recorda.util;
import java.util.List;
public class ListToPrimitiveArray {
public static float[] toFloatArray(List<Float> floats) {
int len = floats.size();
float[] primitiveArray = new float[len];
for (int i = 0; i < len; i++) {
primitiveArray[... |
1cd2e527bef7374030f6ac286517d9e1ae677f3f25408aafbe2d570057fa7d37 | Java | 1,544 | 45 | package org.broadinstitute.dropseqrna;
/*
* The MIT License
*
* Copyright (c) 2009 The 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, includin... |
db796f034b73b965fc5fadaf3b6e3d698ab2b64c07d3ef5b421654ce3b4df971 | Java | 1,546 | 65 | /*
* GoodWordIteratorTest.java
* Copyright 2006 Michigan State University Board of Trustees
*
* Created on June 28, 2002, 12:10 PM
*/
package edu.msu.cme.rdp.classifier.train;
import edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator;
import junit.framework.*;
import java.io.*;
/**
* A test class for ... |
b464dce70d94c115c8d355fe3ed74944eebd4386adbdd71f8a5cf11f049f67a1 | Java | 1,554 | 41 | /*
* 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... |
688e6789425dcd883878c4016e27d825058cc5b350440bd620bd1b85d479e781 | Java | 1,558 | 51 | package arcade.potts.sim.hamiltonian;
import arcade.potts.agent.cell.PottsCell;
/**
* A {@code Hamiltonian} object represents a term in a CPM Hamiltonian equation.
*
* <p>Each {@link arcade.potts.sim.Potts} instance is contains a list of {@code Hamiltonian} terms
* associated with the simulation. For each flip, c... |
1ecb0a7ab0dcbee048fbe87932ccd4fd47d8ac7a47b2be062f161b45b557519a | Java | 1,563 | 44 | /*
* 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... |
1148348eba242bf716561d09f9066c374a0572ad75fe022f35eb6bc93ad2bda1 | Java | 1,565 | 42 | /*-
* #%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... |
424b2c9fe594d5e53c4942ef494fbef69b3a329bfe7fc0328ccdc74f43cc1e4a | Java | 1,585 | 39 | /*
* 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... |
75bd350ea2bea406502ec2986e932b86ac9093569d28238c26bd1f2a2599b844 | Java | 1,598 | 58 | package org.broadinstitute.dropseqrna.utils;
import htsjdk.samtools.metrics.MetricBase;
import htsjdk.samtools.util.Histogram;
/**
* A structure to track how many reads have been accepted or rejected
* @author nemesh
*
*/
public class FilteredReadsMetric extends MetricBase {
public long READS_REJECTED;
public l... |
8873a2ac90905e4e26cf94d526237517b112ba2e6f006ef9586126839f928245 | Java | 1,603 | 42 | package arcade.potts.sim;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import arcade.core.agent.cell.*;
import arcade.core.env.location.*;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCellFactory;
import arcade.potts.env.location.PottsLocationFactory3D;
import static org.junit.j... |
f89fac252a3a5ea734b98af4b42fb8a7b4f91428389e12ad4696e045ac33bb29 | Java | 1,603 | 42 | package arcade.potts.sim;
import java.util.HashMap;
import org.junit.jupiter.api.Test;
import arcade.core.agent.cell.*;
import arcade.core.env.location.*;
import arcade.core.util.MiniBox;
import arcade.potts.agent.cell.PottsCellFactory;
import arcade.potts.env.location.PottsLocationFactory2D;
import static org.junit.j... |
5663ed1f566a2b1725a1e694597f60c81ae094d5108b07d96b65c8b1768a8aad | Java | 1,623 | 40 | package arcade.patch.env.location;
import java.util.ArrayList;
/**
* Concrete implementation of {@link PatchLocationFactory} for hexagonal geometry.
*
* <p>Cell agents exist on a hexagonal grid and molecules in the environment diffuse on a triangular
* lattice, such that each hexagon corresponds to 6 triangles. T... |
d30c6ddba2d599c16833d6fa8d2be9069bbc7b311cc8c9d9f8190546306c108a | Java | 1,624 | 39 | /*
* 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... |
39e8e47b7951aa5f13e8929ad3bdd47c17ce4cfbe0bf0554e3776c0a3d653651 | Java | 1,627 | 49 | package arcade.core.util.distributions;
import ec.util.MersenneTwisterFast;
import arcade.core.util.MiniBox;
import arcade.core.util.exceptions.OutOfBoundsException;
/** Container class for fractional normal distribution. */
public class NormalFractionalDistribution extends NormalDistribution {
/**
* Creates... |
adee36bf2d2ea8f866fe838beffb81a3a73a7f89f5191055123710cc60560e13 | Java | 1,631 | 61 | package arcade.potts.env.grid;
import java.util.HashMap;
import sim.util.Bag;
import arcade.core.agent.cell.Cell;
import arcade.core.env.grid.Grid;
import arcade.core.env.location.Location;
/**
* Implementation of {@link Grid} for potts models.
*
* <p>{@code PottsGrid} uses the cell id as the index to map to agent... |
50b16c90c75664e4cc8d31fa02bc7f9b4e351f545f043238f3085f3b7e52abc5 | Java | 1,635 | 91 | /*
* SeqInfo.java
*
* Created on November 10, 2003, 5:25 PM
*/
package edu.msu.cme.rdp.classifier.comparison;
import java.util.Iterator;
import java.util.NoSuchElementException;
/**
*
* @author wangqion
*/
public class SeqInfo {
private String name;
private String title;
private Score firstScore; // th... |
e21b9da538b83881706f4bdc7635a1676c583bb4aa0ac44aa24fb9b890f06c69 | Java | 1,637 | 49 | package arcade.potts.env.location;
import java.util.ArrayList;
/** Concrete implementation of {@link PottsLocationFactory} for 2D. */
public final class PottsLocationFactory2D extends PottsLocationFactory {
/** Creates a factory for making 2D {@link PottsLocation} instances. */
public PottsLocationFactory2D()... |
2d739be79f3e954a2734b08cb6e6d8f27662fb827444caab0dd22d541e4b492d | Java | 1,639 | 66 | package arcade.patch.env.location;
/**
* Representation of (u, v, w, z) coordinate.
*
* <p>Each coordinate is defined by (u, v, w, z) values. Two coordinate objects are considered equal
* if they have matching (u, v, w, z) values.
*/
public final class CoordinateUVWZ extends Coordinate {
/** Coordinate u valu... |
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