sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6fef9d8001bb4fc8644e7de5208216728b6e790aa9f0b66b9950351fbea7e369 | Java | 610 | 26 | package phylonet.coalescent;
import java.util.HashSet;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
public class WQClusterCollection extends AbstractClusterCollection{
public WQClusterCollection(int len) {
initialize(len);
}
@Override
public AbstractClusterCollection newInstance(int size) {
return... |
9d8dda17d53a3d5b7eea5d112af980e18dd6bccd36e95ece262c7f061faffff9 | Java | 611 | 25 | /**
*
*/
package phylonet.coalescent;
import java.util.ArrayList;
import phylonet.tree.model.sti.STITreeCluster;
/**
* @author chaos
*
*/
public abstract class AbstractPartition {
public static AbstractPartition createPartition(ArrayList<STITreeCluster> clusters){
return createPartition(clusters.toArray(new... |
2315f5694c9114f676b760d846f45d80abff739383a53e77aa8f27ecfa11228e | Java | 836 | 38 | package hu.elte.imagej.plugins.contractilityanalyzer;
import java.util.List;
public class Statistic {
public static double sum(List<? extends Number> values) {
double d = 0;
for (Number number : values) {
d += number.doubleValue();
}
return d;
}
public static double mean(List<? extends Number> values)... |
26f56d0e513b128ebc1b6ee6ea29a1fc900f1b71f310abb76cfb745c3a84d54d | Java | 874 | 38 | package phylonet.coalescent;
public class QuartetCollection {
// public class Quartet {
// int a,b,c,d;
// }
float [][] quartetWeights;
float [][] quartSumWeights;
int twoNmin3;
public QuartetCollection(int n) {
twoNmin3 = 2 * n - 3;
quartetWeights = new float[n*(n-1)/2][n*(n-1)/2];
quartSumWeights =... |
4be88ba97691d6aba0b06121932fa9b7d5569f1c1bf5a37a67104087c7bbe934 | Java | 1,139 | 63 | package hu.elte.imagej.plugins.contractilityanalyzer;
import java.util.ArrayList;
import java.util.List;
public class DataPoint {
List<Double> data;
public List<Double> getData() {
return data;
}
Double mean;
Double sem;
Double sd;
public DataPoint(double value) {
data = new ArrayList<Double>();
data.a... |
bb2a86ec21bd52f9b8801c592363d78a7548ebe24abe05c158fed329c990d3e8 | Java | 1,253 | 59 | package tools;
public class Correlation implements Comparable<Correlation> {
private int count;
private double r;
public Correlation(double[] v1, double[] v2) {
double sum_xy = 0, sum_x = 0, sum_y = 0, sum_sqx = 0, sum_sqy = 0;
count = 0;
r =0;
if (v1 == null || v2 == null) {
return;
}... |
838e54ea790f85f0273375c059fd64957d5290893b7e58172b7b2eee0cecd317 | Java | 1,278 | 50 | package phylonet.coalescent;
import java.util.List;
import phylonet.coalescent.IClusterCollection.VertexPair;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
public class WQComputeMinCostTask extends AbstractComputeMinCostTask<Tripartition>{
WQDataCollection wqDataCollection;... |
732563f38b321d6b67564e2fca008f1f2a1dfe959d259608b58d2cee60cc7499 | Java | 1,413 | 70 | package hu.elte.imagej.plugins.contractilityanalyzer;
import java.awt.Point;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Stack;
/**
* Find the 8-connected area on an image.
*
*/
public class FloodFill {
boolean[] pix;
int w;
int h;
List<AbstractBlob> blobs;
... |
4ccad0e38a7b1ac709fed7fd8b6fd0449adfcd5586eed07cccca23e7f937e296 | Java | 1,417 | 63 | package phylonet.coalescent;
import phylonet.tree.model.sti.STITreeCluster;
public class Polytomy extends AbstractPartition {
STITreeCluster[] clusters;
private int _hash = 0;
public Polytomy(STITreeCluster[] cs){
clusters = new STITreeCluster[cs.length];
int[] ns = new int[cs.length];
for (int i = 0; i ... |
d1411a2fb9a210d6f021610bf23da4a20dd1a6c617f16aa23fcec5761c5fe511 | Java | 1,678 | 77 | package phylonet.coalescent;
import java.util.Set;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
/***
* Contains a set of clusters (used to implement X in ASTRAL/DynaDup).
* @author smirarab
*
*/
public interface IClusterCollection {
/**
* Every cluster in the clustercollection is a subset
* of th... |
13b076d7e317771d80232ffccd41616736c9bb5ca8ac7607738b865222258f3c | Java | 1,721 | 62 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import phylonet.tree.model.sti.STITreeCluster;
public class TaxonIdentifier {
private HashMap<String, Integer> nameToId = new HashMap<String, Integer>();
private List<String> idToName = new ArrayList<Str... |
bab31c568393835a2025e778c6987ab3e45785772d5fb9c1032b2214d6a84c9f | Java | 1,869 | 78 | package tools;
import java.io.*;
import java.util.*;
import java.lang.reflect.Field;
public class FileR {
String filename;
RandomAccessFile raf;
BufferedReader reader;
long currentOffset = 0;
long previousOffset = -1;
long index = 0;
public FileR (String f) {
try {
fi... |
485319e460d48eaa725083b45bda363f467b7f55a0266a4890743f14330d373f | Java | 1,955 | 76 | package phylonet.coalescent;
import java.util.HashMap;
import java.util.List;
import phylonet.tree.model.Tree;
public abstract class AbstractWeightCalculator<T> implements Cloneable {
private static final boolean TESTRUN = false;
private int callcounter = 0;
protected HashMap<T, Long> weights;
boolean save;
l... |
c00dec5779b94c5575284cb6fc5a91bf8a0bb07ebcfc60f65ce324709d5b5866 | Java | 1,961 | 83 | package hu.elte.imagej.plugins.contractilityanalyzer;
import java.awt.Rectangle;
import java.util.List;
import ij.IJ;
import ij.ImagePlus;
import ij.measure.ResultsTable;
import ij.plugin.filter.GaussianBlur;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;
public class SpheroidPerimeterPlugin... |
7bd3b33e58ef6c3df6a42162bb844f679016b3373c7f43a5f5cd5f7bcf193a15 | Java | 2,159 | 104 | package hu.elte.imagej.plugins.contractilityanalyzer;
import java.util.Arrays;
import java.util.List;
import ij.process.ByteProcessor;
public class BooleanImage implements Cloneable {
int width;
int height;
boolean[] pixels;
public BooleanImage(int width, int height, boolean[] pixels) {
super();
this.width ... |
3d0b5ab37383e9a0656437b7d956a773d1fbfaf3255bdff8f41fd8999790b240 | Java | 2,232 | 79 | package hu.elte.imagej.plugins.contractilityanalyzer;
import ij.process.AutoThresholder;
import ij.process.ByteProcessor;
import ij.process.FloatProcessor;
import ij.process.ImageProcessor;
import ij.process.ShortProcessor;
public class ImageBinarizator {
public static BooleanImage makeBinary(ImageProcessor ip,
... |
8d0a12cab4da94b275433192d8f3ccf7a531d5eed831bb75dfb93f15af042d58 | Java | 2,278 | 98 | package tools;
public class LinearRegression {
private int n;
private double intercept, slope;
private double r2;
private double svar, svar0, svar1;
public LinearRegression(double[] x, double[] y) {
n = 0;
slope = intercept = r2 = svar = svar0 = svar1 = Double.NaN;
if (x == null || y == null) {
... |
83369d70653a9848756f61b7f8282775888d2f6332744157c0baeee19f59ebee | Java | 2,324 | 81 | package phylonet.coalescent;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITreeCluster;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
import phylonet.util.BitSet;
/**
* This class is used in ... |
e6b15364f56301e7763909662b9d21c22c52db6bb246a87de03cc94c9cd8c8ca | Java | 2,418 | 93 | package hu.elte.imagej.plugins.contractilityanalyzer;
import ij.io.OpenDialog;
import ij.io.SaveDialog;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.ObjectInputStream;
import j... |
32dd8d89999f73ec30b2fdf0a21353fea4c17c38edfdbde319be9c3301bb12a1 | Java | 2,442 | 94 | package phylonet.coalescent;
import phylonet.tree.model.sti.STITreeCluster;
public class Tripartition extends AbstractPartition {
STITreeCluster cluster1;
STITreeCluster cluster2;
STITreeCluster cluster3;
private int _hash = 0;
public Tripartition(STITreeCluster c1, STITreeCluster c2) {
STITreeCluster c3 ... |
41d8280451842c6d962de9686b914051908f0c0d20d60404c4c09d9a7c8d3a76 | Java | 2,573 | 100 | package hu.elte.imagej.plugins.contractilityanalyzer;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.GenericDialog;
import ij.measure.ResultsTable;
import ij.plugin.filter.PlugInFilter;
import ij.process.ImageProcessor;
public class H... |
ab7219a5ffe2f31a11b2043a6c5387a641acd2e8b9c001f138fc842039cccd83 | Java | 2,896 | 93 | package phylonet.coalescent;
import phylonet.tree.model.sti.STITreeCluster;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
import phylonet.util.BitSet;
public class STBipartition {
STITreeCluster cluster1;
STITreeCluster cluster2;
STITreeCluster c;
private int _hash = 0;
public STBipartition(STITree... |
98e00ed6e51e421bf4b7620300d9bc89557c29d750d3ea56157f4d3995b7a081 | Java | 2,987 | 96 | package phylonet.coalescent;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import phylonet.tree.model.Tree;
import phylonet.tree.util.Trees;
/**
* Maps gene names to species names (as strings)
*
* @author smirarab
*
*/
public class TaxonNameMap {
private Map<String, String> taxon... |
cbdbb5d21fc56f19939178c25a25207c9ec8ed770cbd81924f7d6690d3b95318 | Java | 3,085 | 109 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.List;
import phylonet.tree.model.MutableTree;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITree;
import phylonet.util.BitSet;
/**
* This class keeps track of a single-individual sample
* of a multi-individual dataset. F... |
9c1b66814da47e10ead55b23a1182d507a63a9099772a31630935d89f2bb4be8 | Java | 3,189 | 160 | /*
* Copyright (c) 2012 Rice University.
*
* This file is part of PhyloNet.
*
* PhyloNet 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 3 of the License, or
* (at your option) any later... |
72a350a2f8999f29a214d021d461f99d0e3425bfd19a0d1192d993d23a0cb786 | Java | 3,701 | 119 | package phylonet.coalescent;
import java.util.List;
import phylonet.coalescent.IClusterCollection.VertexPair;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITreeCluster;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
public class DLComputeMinCostTask extends AbstractComputeMinCostTask<STBi... |
52652e68ed40d8ce0c5bc1223c8c1557c20fb07a6428924db75827dc2569c543 | Java | 3,775 | 139 | package phylonet.coalescent;
import java.util.ConcurrentModificationException;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import phylonet.tree.model.sti.STITreeCluster;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
public class DLClusterCollection extends AbstractClusterCo... |
90382c69567154babd10461ad8db8118168fb45ab7b8b8f8eb9e6f6a86e795d8 | Java | 4,181 | 215 | package hu.elte.imagej.plugins.contractilityanalyzer;
import java.awt.Point;
import java.awt.Rectangle;
import java.io.Serializable;
import java.util.HashSet;
/**
* This is an basic blob class which contains several general function and
* manages base of serialization.
*/
public class AbstractBlob implements Seria... |
a1d8de6e36929d1a896590cd618cd93d1ea403609f05af1fc4f93f8d1997a3dc | Java | 4,322 | 169 | package phylonet.coalescent;
import cern.jet.stat.Gamma;
import cern.jet.stat.Probability;
/***
* Computes branch length and posterior support
* @author smirarab
*
*/
public class Posterior extends cern.jet.math.Constants{
private double f1;
private double f2;
private double f3;
private double n;
private dou... |
67d96a488650f8a4c4b9af9c6c9bd5a53f8d81fdfaa5bc1ae8d079e5296ea1f9 | Java | 4,762 | 233 | package phylonet.coalescent;
public class Options {
private boolean rooted;
private boolean extrarooted;
private boolean exactSolution;
private boolean duploss;
private int alg;
private int addExtra;
private boolean outputCompletedGenes;
private boolean outputSearchSpace;
private boolean runSearch;
private i... |
df10686bba3d97eaca7afde635dcb0dfd04a0ae7be0636b6746c368ea7f0ac2e | Java | 4,983 | 208 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.ConcurrentModificationException;
import java.util.HashSet;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Set;
import phylonet.tree.model.sti.STITreeCluster;
import phylonet.tree.model.sti.STITreeCluster.Ve... |
5d2fb70c2a6cede619dc0d0ef53414d823d69133c84e1250b63092c699296cdc | Java | 5,152 | 146 | package phylonet.coalescent;
import java.util.List;
import java.util.Stack;
import phylonet.lca.SchieberVishkinLCA;
import phylonet.tree.model.TNode;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITree;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
public class DLInference extends Abstra... |
9f8687481f5db26c0101cf17ff00bede1bb243c4d008233d29d70baa2f41b603 | Java | 5,265 | 206 | /* specialFunctions.java
20-July-1997
Bryan Lewis
Department of Mathematics and Computer Science
Kent State University
This software is in the public domain and can
be copied, modified and used without restriction.
(*) Press, Flannery, Teukolsky, Vetterling, Numerical Recipes,
Cambridge University Press, 19... |
f79bb9860d934b7a99016333448f12e6ad06a35fb2a3d3ceb3c466c475eb6f08 | Java | 6,014 | 185 | package phylonet.coalescent;
import java.util.AbstractMap.SimpleEntry;
import java.util.HashSet;
import java.util.List;
import java.util.Map.Entry;
import java.util.Set;
import java.util.Stack;
import phylonet.lca.SchieberVishkinLCA;
import phylonet.tree.model.TNode;
import phylonet.tree.model.Tree;
import phylonet.t... |
fa78b50d8d3799e88c2bbf4bf6d6d4e03468f711a81a965d5eaaeb4e5937d962 | Java | 7,977 | 332 | package phylonet.tree.model.sti;
import phylonet.coalescent.GlobalMaps;
import phylonet.coalescent.TaxonIdentifier;
import phylonet.coalescent.IClusterCollection.VertexPair;
import phylonet.util.BitSet;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* A subset of a set of taxa
*... |
5fd04b15f03c640b743f9d11e0cb597b14ad91a9f4b0afce605a4e0a6b25a3db | Java | 8,119 | 299 | package tools;
import java.io.*;
import java.util.*;
import java.util.stream.*;
class Embedding extends Hegemon {
int blocksize_ = 8000;
int[][] be;
int axis = 0;
int count1 = 0;
int count2 = 0;
int x0_ = 1;
int x1_ = 400;
int x2_ = 400;
int x3_ = 1;
public Embedding(String p) {
super(p);
... |
28ed7b6682ad8957d91255cb6be0e9647092da6eb109c079b1d77c03eb3f069b | Java | 10,766 | 360 | package phylonet.coalescent;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Deque;
import java.util.Iterator;
import java.util.List;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITreeCluster;
// TODO: why extend the abstract? It doesn't seem to follow the same pattern ... |
bee25784fcba1fab70ea30bea3dcd5c52505db51f60d202fe5e24ac796f21b0a | Java | 11,085 | 365 | package tools;
import java.io.*;
import java.util.*;
class RankCorrelation {
String file;
int start, end;
public RankCorrelation(String f) {
file = f;
start = 2;
String[] headers = getHeaders();
end = headers.length - 1;
}
public String[] getHeaders() {
try {
String exprFile = fi... |
19c98dc0747a7e282e679dc91d52e098874c81ed837d7175e131c98e67278b0e | Java | 12,042 | 395 | /* The MIT License
Copyright (c) 2010 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, mo... |
b146b812617b499ac4875e38b54e06f24536a8638dbc7ce17a3514e9ae2cd4d0 | Java | 12,253 | 412 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import phylonet.coalescent.WQWeightCalculator.CondensedTraversalWeightCalculator;
import phylonet.tree.model.TNode;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITr... |
6e4b4c7a58c96ba45ac0ba3fc3880faec2437ae393b4d956ba9c8395debe3912 | Java | 12,718 | 356 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Stack;
import phylonet.tree.model.MutableTree;
import phylonet.tree.model.TMutableNode;
import phylonet.tree.model.TN... |
42d368780f5d2149896e76b2032ead2e9d3b65d3a5dbe795728cdcd397641603 | Java | 12,746 | 420 | package phylonet.coalescent;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
import java.util.Stack;
import phylonet.tree.model.MutableTree;
import phylonet.tree.model... |
98e03288e3e3f1f63aad0a1c2854d91bbd42b97377db6139691a08864f3c8987 | Java | 13,280 | 436 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Stack;
import phylonet.tree.model.TMutableNode;
import phylonet.tree.model.TNode;
import phylonet.tree.model.Tree;
imp... |
34073f151dc4b3266441ed3862fb85d9fb0013d850d93dbd8b0fb6910e290168 | Java | 13,546 | 440 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import phylonet.coalescent.IClusterCollection.VertexPair;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITreeC... |
053dff2cc161472b3fb5c88d2d7e4fc7607e6f208b7694af98f46f31cb1b76b5 | Java | 14,932 | 562 | package phylonet.util;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.ObjectStreamField;
import java.io.Serializable;
import java.util.Arrays;
public class BitSet implements Cloneable, Serializable {
int hash = 0;
private static final int ADDR... |
768a5376a16f1304c8658d90ca183949a9d7ab318fbcecae0659c7355db84884 | Java | 16,500 | 595 | package tools;
import java.io.*;
import java.util.*;
class BooleanNet {
String pre;
PrintStream out = System.out;
String[] headers;
int start;
int end;
public BooleanNet(String p) {
pre = p;
start = 2;
headers = getHeaders();
end = headers.length - 1;
}
public boolean isExpr() {
... |
9dbc16e3662aa881e108da027ea9be04558c0b0a292c7791a8dbf2323b78839a | Java | 17,321 | 586 | package phylonet.coalescent;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map.Entry;
import java.util.TreeSet;
import phylonet.tree.model.TNode;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.S... |
49e1444ac8ebb353f465e0fef9e9562205f032c370aaf8967e3e0c7a74cd0031 | Java | 17,808 | 491 | package phylonet.coalescent;
import java.util.AbstractMap;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import phylonet.tree.model.TNode;
import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STINode;
impo... |
70184e2f475d5201bd8edb80c4f13f8f13e5e2d3464bee87085caebd3650330b | Java | 19,893 | 728 | package phylonet.coalescent;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.... |
c20d0f263ba3489e683bab9ed680c98fc8bd8f4d9f0a1fe624e1388eb9b98240 | Java | 23,443 | 691 | package phylonet.coalescent;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collecti... |
7153c6c0a5f213754ad2951007c6f14cba1d8559cdfc9c7bae58e71d4b0e940b | Java | 28,261 | 822 | package phylonet.coalescent;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Deque;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List... |
5ff788af19b82e7f5da0528860cc0bf5d8d0ac92f8715f19e5c987066332913d | Java | 38,101 | 868 | package phylonet.coalescent;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.StringReader;
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port: 8080,
timeout: 120 * 1000
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