sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5d58a9af73ab1a238c7d2ad7b67a4847c1f27dc33764904fc92132632a0db510 | Java | 218 | 12 | package org.molgenis.genotype;
/**
* Query that returns the raw lines of an inpute file
*
* @author erwin
*
*/
public interface RawLineQuery
{
RawLineQueryResult executeQuery(String sequence, int startPos);
}
|
7c2c5cdc97e26e4d1ecf82d1ad9f9855f21d832255af6412ab5b1a5c4d7b8e1e | Java | 229 | 18 | package nl.systemsgenetics.genenetworkbackend;
/**
*
* @author Patrick Deelen
*/
public class PredictGenesetMembers {
/**
* @param args the command line arguments
*/
public static void main(String[] args) {
}
}
|
cb9fdc2fe62dce0ccc0cee1199779680b89a67e774710c8076952b724b10ab28 | Java | 234 | 23 | package umcg.genetica.collections.intervaltree;
/**
*
* @author Patrick Deelen
*/
public interface Range {
/**
* Inclusive
*
* @return
*/
int getStart();
/**
* Inclusive
*
* @return
*/
int getEnd();
}
|
ca8b088ca25235e9972069e7ccd517caebd62c99c3233104f93c909518e960d5 | Java | 237 | 13 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlpermutationtranscriptionfactoranalysis;
/**
*
* @author Matthieu
*/
public class GwasEnrichment {
}
|
d4a6d3df75fe8c45c820d49bac0445bb4f2ebb11177615511dee398fef8e19fe | Java | 240 | 13 | package org.molgenis.genotype.modifiable;
import org.molgenis.genotype.GenotypeDataException;
public class GenotypeModificationException extends GenotypeDataException
{
/**
*
*/
private static final long serialVersionUID = 1L;
}
|
bcae8ac4124ef2df138e8544e030e8016e5cf31dbbfe7dd286a448a1f6c67f17 | Java | 245 | 12 | package org.molgenis.genotype.util;
/**
* Iterable that iterates over a fixed number of elements
*/
public interface FixedSizeIterable<E> extends Iterable<E>
{
/**
* @return the number of items for this iterable
*/
public int size();
}
|
afc4361e2a4041d51f366f00acad80c641f1c3a19f5e898da25be86fbac62496 | Java | 246 | 10 | package nl.umcg.westrah.binarymetaanalyzer.westrah.binarymetaanalyzer.posthoc.ld;
public class SortedBinaryZDataBlock {
public String snp;
public String gene;
public String allele;
public String assessed;
public int n;
public float[] z;
}
|
72d0274de13f7af328c71a2a416ec9b518e86f09a8d7680c2275f25f19adf126 | Java | 247 | 14 | package org.molgenis.genotype.variant.sampleProvider;
public class SampleVariantUniqueIdProvider
{
private static int counter = 0;
public static synchronized int getNextUniqueId()
{
int nextId = counter;
counter++;
return nextId;
}
}
|
f5b819fcf32f27c70935cd3acae8039b57bc18d0ec57d65cd0e38988f6288cd2 | Java | 247 | 12 | package ebi.spot.neo4j2owl;
public class N2OException extends Exception {
public N2OException(String message) {
super(message);
}
public N2OException(String message, Throwable cause) {
super(message, cause);
}
}
|
098187dca2f9528a92e75c0b66c34d68c346d11c158951fe1a55ad55dea7aac8 | Java | 258 | 16 | package org.molgenis.genotype.util;
public class LdCalculatorException extends Exception
{
public LdCalculatorException(String errorString)
{
super(errorString);
}
/**
*
*/
private static final long serialVersionUID = 5013261584683688298L;
}
|
55d0a9a839ee8e2024fd0ce0b61e1b810c1c7f152357d7f81a5dcb4ff287a15e | Java | 263 | 11 | package nl.systemsgenetics.downstreamer.runners.options;
import org.apache.commons.cli.ParseException;
public class OptionsModeUtilities extends OptionsBase {
public OptionsModeUtilities(String[] args) throws ParseException {
super(args);
}
}
|
057ace6fa582f370179d064f4dcbfc1ead917f806d9bd582dc93c48342864556 | Java | 272 | 17 | package edu.cmu.cs.eyetrack.state;
import java.util.ArrayList;
public class History {
private ArrayList<Trial> history;
public History() {
history = new ArrayList<Trial>();
}
protected void addTrial(Trial trial) {
history.add(trial);
}
}
|
f25452605a355baa58595ea56ced53bca9faa2627a1b205133ac894dfad2a805 | Java | 280 | 16 | package umcg.genetica.collections.intervaltree;
import java.util.Comparator;
/**
*
* @author Patrick Deelen
*/
public class RangeStartComparator implements Comparator<Range>{
@Override
public int compare(Range o1, Range o2) {
return o1.getStart() - o2.getStart();
}
}
|
f385c22d0166e41b86f44bd1b7d4edcaf661ad5239808d46abf21c04c618a6f9 | Java | 288 | 15 | package org.molgenis.genotype;
import java.io.Closeable;
import org.molgenis.genotype.variant.GeneticVariant;
/**
* The result of a VariantQuery. Must be closed after use
*
* @author erwin
*
*/
public interface VariantQueryResult extends Closeable, Iterable<GeneticVariant>
{
}
|
93027f5ed314121f4e8cdd921e73b80a14360b96e79ea3651089b8729e367982 | Java | 300 | 7 | package org.molgenis.genotype.variant.sampleProvider;
import org.molgenis.genotype.variant.ReadOnlyGeneticVariantBgen;
public interface SampleVariantProviderBgen extends SampleVariantsProvider {
ReadOnlyGeneticVariantBgen extendReadOnlyGeneticVariantBgen(ReadOnlyGeneticVariantBgen variant);
}
|
bf73dfb618d8e27c5ad388d665bd4668ff67a97111853a658236e12afb131b16 | Java | 304 | 19 | package umcg.genetica.graphics.panels;
import umcg.genetica.graphics.DefaultGraphics;
/**
* Created by hwestra on 7/16/15.
*/
public class SpacerPanel extends Panel {
public SpacerPanel(int nrRows, int nrCols) {
super(nrRows, nrCols);
}
@Override
public void draw(DefaultGraphics g) {
}
}
|
3e87af926f36b21097786eaafd46d7d830ef42d77f5e9ffa12927ce5f0ba6e77 | Java | 305 | 15 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
/**
*
* @author Harm-Jan
*/
public class MetaQTL4QTL {
}
|
232457394ff7591f5798e7c932a011457893e8305347e87b6b26b23d9adc1106 | Java | 306 | 17 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.variantAnnotator;
import umcg.genetica.collections.intervaltree.Range;
/**
*
* @author Patrick Deelen
*/
public interface GenomicRange extends Range {
String getSeqname();
}
|
c2645eb500936715afa1fdce3f8e893f24097ff8ddc905a356d7108a061257d6 | Java | 310 | 23 | package umcg.genetica.io.binInteraction.gene;
/**
*
* @author Patrick Deelen
*/
public interface BinaryInteractionGene {
String getName();
String getChr();
int getStart();
int getEnd();
int[] getVariantPointers();
int getVariantCount();
int getIndexOfVariantPointer(int variantIndex);
}
|
b6a8bfcb5b7e3c1b0d46ff19d88d9c08c7a5cf192271bec22087430ad277a58c | Java | 311 | 17 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import org.molgenis.genotype.Sample;
/**
*
* @author Patrick Deelen
*/
public interface SampleFilter {
public boolean doesSamplePassFilter(Sample sample);
}
|
b00248f750f82057d9b1879f98b2a89e11281475d9221a580018db92c71893ad | Java | 314 | 16 | package mbqtl.gfx;
import umcg.genetica.graphics.DefaultGraphics;
import umcg.genetica.graphics.panels.Panel;
public class QTLDotPlotPanel extends Panel {
public QTLDotPlotPanel(int nrRows, int nrCols) {
super(nrRows, nrCols);
}
@Override
public void draw(DefaultGraphics g) {
}
}
|
8525c2c2e82803b14273f6a4d07508a6933f030c896d3cd0ab16296e49039b6b | Java | 315 | 10 | package nl.systemsgenetics.downstreamer.summarystatistic;
@Deprecated
public interface OverlappableGenomicRange {
int getStart();
int getEnd();
String getSequenceName();
boolean isOverlapping(OverlappableGenomicRange other);
boolean isOverlapping(OverlappableGenomicRange other, int window);
}
|
ca7b255e2ed1b296116909a1c8b080c9b6556a44ec36d5ba4c203b973725c536 | Java | 316 | 22 | package org.molgenis.genotype;
/**
* Represents a genetic sequence for example a chromosome
*
* @author erwin
*
*/
public interface Sequence
{
String getName();
Integer getLength();
/**
* Returns if this sequence represents a chromosome or not
*/
boolean isChromosome();
boolean isAutosome();
}
|
6ebf3129df2e45ba380904cc5c90d10cc6d5b31c87a1d9d61df27fa68a8c4e21 | Java | 317 | 16 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
/**
*
* @author Patrick Deelen
*/
public interface VariantFilterableGenotypeData {
public void setFilter(VariantFilter filter);
public VariantFilter getFilter();
}
|
905589d678ab2af160b68b884c295914daf0e259ea5cab359c61b1cfa4924cb2 | Java | 318 | 15 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.metaqtl4;
/**
*
* @author Harm-Jan
*/
public class MetaQTL4CorrelationTask2 {
}
|
5b4a2b932de405a1a33c097721995ea69653e0181e70acc9da17e5bf7442e021 | Java | 324 | 18 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.containers;
/**
*
* @author harmjan
*/
public class Trio {
public String family;
public Individual parent1;
public Individual parent2;
public Individual child;... |
192931d19226156a02ceddd54aa316fa471064d84d77bad2be751268d7747078 | Java | 329 | 20 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.mixupmapper.containers;
/**
*
* @author harmjan
*/
public class Individual {
public String fatherId;
public String motherId;
public String familyId;
public String sampleN... |
71591f878763b6dcb6e0ce715b4c4b7b21e5391c2cdfc881ebf23e8e49f22bb5 | Java | 338 | 14 | package org.molgenis.genotype.plink.drivers;
import java.io.File;
import java.net.URI;
import java.net.URISyntaxException;
public abstract class AbstractResourceTest
{
protected File getTestResource(String name) throws URISyntaxException
{
URI resource = this.getClass().getResource(name).toURI();
return new Fil... |
3997a125452a0bccf0ba92b0420be51769b482e9e0bc733596ba54671eec8574 | Java | 341 | 21 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gwascatalog;
import java.util.HashSet;
/**
*
* @author harmjan
*/
public class GWASLocus {
int id;
int start;
int end;
byte chr;
HashSet<GWASSNP> snps = new HashSet<GWAS... |
f77b7b0423bb92ba47e846b2c6f608f70bcc4e25335b32f19fabfe5f38ed4e11 | Java | 341 | 14 | package edu.cmu.cs.eyetrack.analysis.score.distance;
import edu.cmu.cs.eyetrack.analysis.struct.Frame;
public class EuclideanDistanceFunction extends DistanceFunction {
public EuclideanDistanceFunction() { }
@Override
public Double distance(Frame a, Frame b) {
return a.getPosition().distance(b.getPo... |
d679f590d21557a9a1eea9429705ee4e4be74215af88670f34bc3e70fef77f9f | Java | 342 | 14 | package org.molgenis.genotype.editable;
import org.molgenis.genotype.variant.GeneticVariantMeta;
import org.molgenis.genotype.variant.sampleProvider.SampleVariantsProvider;
/**
*
* @author Patrick Deelen
*/
public interface EditableSampleVariantsProvider extends SampleVariantsProvider{
GeneticVariantMeta getGene... |
07a10f73e08b418cac6a51eb95f424f409e7feea1037d0d30fb96f4a05c5446d | Java | 343 | 20 | package mbqtl;
public class VariantQCObj {
public int nrMissing = -1;
double maf = 0;
double cr = 0;
double hwep = 0;
boolean passqc = false;
@Override
public String toString() {
return "QCObj{" +
"maf=" + maf +
", cr=" + cr +
", hwep=" + hwep +
", passqc=" + passqc +
", nrMissing=" + nrM... |
6f7a2c96eec7bb1267b48539106e5dbfcd160f00cfcf87c0572b14df655d700e | Java | 344 | 18 | package org.molgenis.genotype.multipart;
import org.molgenis.genotype.GenotypeDataException;
public class IncompatibleMultiPartGenotypeDataException extends GenotypeDataException
{
public IncompatibleMultiPartGenotypeDataException(String message)
{
super(message);
}
/**
*
*/
private static final long se... |
4ecfa0128a42c3ae3b990c0700df20d55459ec190440158911aa326d0f9b999f | Java | 348 | 13 | package edu.cmu.cs.eyetrack.analysis.struct;
import edu.cmu.cs.eyetrack.helper.Coordinate;
public abstract class Frame implements Comparable<Frame> {
public abstract Coordinate<Double> getPosition();
public abstract Long getTimestamp();
public int compareTo(Frame f) {
return getTimestamp().compareTo... |
b6a29b19c5e749ccfe9bceb33e7c29355361fbee6b2f9ccbc13b97a288a138c9 | Java | 352 | 14 | package nl.systemsgenetics.downstreamer.runners.options;
import org.molgenis.genotype.RandomAccessGenotypeDataReaderFormats;
import java.io.File;
public interface GenotypeFileProvider {
String[] getGenotypeBasePath();
RandomAccessGenotypeDataReaderFormats getGenotypeType();
File getGenotypeSamplesFile()... |
a3f8c7b759eaf195cc89ed0d32b095fad50d7186e77659cea681236474baee71 | Java | 357 | 19 | package org.molgenis.genotype.util;
import java.util.Arrays;
import java.util.List;
import static org.testng.Assert.assertEquals;
import org.testng.annotations.Test;
public class UtilsTest {
@Test
public void iteratorToList() {
List<String> list = Arrays.asList("1", "2", null);
assertEquals(Utils.iteratorToL... |
d524aa89f0ad996c75b484ead190a2a9a4cc63f512e3f0105cb6231b593250ee | Java | 357 | 23 | package org.molgenis.genotype.tabix;
import java.io.FileNotFoundException;
/**
*
* @author Patrick Deelen
*/
public class TabixFileNotFoundException extends FileNotFoundException {
private String path;
public TabixFileNotFoundException(String path, String s) {
super(s);
this.path = path;
}
public String... |
bb3aa72c5e149325b29954711f0efcda370064a06d17a7b5efa15d06cf378fcf | Java | 361 | 19 | package umcg.genetica.collections.intervaltree;
import java.util.Comparator;
/**
*
* @author Patrick Deelen
*/
public class RangeEndReverseComparator implements Comparator<Range>{
@Override
/**
* Note: we consider large end values to be smaller for reverse sort
*/
public int compare(Range o1, Range o2) {
... |
0a0858f289e8917ceff5339978fcd91b8915e7debe8cf833063519c2ae62467c | Java | 371 | 18 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.gadocommandline;
/**
*
* @author patri
*/
public enum GadoMode {
PROCESS,
PRIORITIZE,
EXPAND_PREDICTI... |
5aa532396e19ee7d04e9b3bb0c7883aae7a17aae140506a20291f435cd83f5fb | Java | 371 | 27 | package umcg.genetica.io.binInteraction.variant;
import org.molgenis.genotype.Allele;
/**
*
* @author Patrick Deelen
*/
public interface BinaryInteractionVariant {
Allele getAltAllele();
String getChr();
int getGeneCount();
int[] getGenePointers();
String getName();
int getPos();
Allele getRefAllele(... |
a80f1fbe49f62fd26aff1065ff0f73ad7037421cdd585ee9df24a8e92ee9cc2f | Java | 377 | 15 | package org.molgenis.genotype.variant;
public interface GeneticVariantMeta
{
enum Type {INTEGER, FLOAT, STRING, CHAR, ALLELES, INTEGER_LIST, FLOAT_LIST, STRING_LIST, CHAR_LIST; }
Iterable<String> getRecordIds();
/**
*
* @param recordId
* @return record data type or null if a record with the given id does... |
1f0f386589fdf6611673c7a2778bbbbfe78cbcd74a18893a8350138654e2eeda | Java | 381 | 19 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import org.molgenis.genotype.Sample;
/**
*
* @author Patrick Deelen
*/
public class SampleIncludedFilter implements SampleFilter {
@Override
public boolean doesSamplePa... |
cdcb122c70c0b30df34312d0bfbe5449a714a358ec36a6c60bafc7d4f084825c | Java | 387 | 19 | package org.molgenis.genotype;
import java.io.IOException;
import org.molgenis.genotype.variant.NotASnpException;
public interface GenotypeWriter
{
/**
*
* @param path
* @throws IOException
* @throws NotASnpException
* when writer only supports SNPs but is given a non SNP variant
*/
publi... |
e869b37ca11ddda6c993ca500160e2a1c345ac62edea01588456cd4219d987ec | Java | 388 | 16 | package nl.systemsgenetics.downstreamer.summarystatistic.filters;
/**
* The type Field not availible exception.
*/
public class FieldNotAvailibleException extends RuntimeException {
/**
* Instantiates a new Field not availible exception.
*
* @param message the message
*/
public FieldNotA... |
d9f22dc2c3682059672d480cef860e581818993b8195999310170fd2b8dbf79e | Java | 389 | 18 | package eqtlmappingpipeline.util;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
import java.io.IOException;
public class BinaryMatrixConverter {
public void run(String input, String output) {
try {
DoubleMatrixDataset<String, String> ds = DoubleMatrixDataset.loadDoubleBinaryData(input);
ds.save(o... |
3d4e0b047ce29942fbd33077a47475f419305d64a652dcc202e282d59cdc103e | Java | 398 | 22 | package test.java.decon_eQTL;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
public class UtilsTest {
@Before
public void init() {
}
@After
public void tearDown() throws Exception {
//deleteDir(new File(outputDir));
}
@Test
public void readTabDelimitedColumnsest() throws Except... |
34e4b888df794ab229d772f1f5feda03370f0427a109054afe0f09453789908a | Java | 399 | 12 | package org.molgenis.genotype.plink;
import java.io.Closeable;
import java.nio.charset.Charset;
public interface PlinkFileParser extends Closeable
{
public static final Charset FILE_ENCODING = Charset.forName("UTF-8");
public static final char DEFAULT_FIELD_SEPARATOR = ' ';
public static final String DEFAULT_READ_... |
b28d05c497630e0cd8f8181bba241efac0ad99a254a9b25f7f0308fb4e266cbb | Java | 402 | 21 | package umcg.genetica.math.matrix2;
public class DoubleMatrixDatasetRow {
private final double[] data;
private final String rowName;
public DoubleMatrixDatasetRow(double[] data, String rowName) {
this.data = data;
this.rowName = rowName;
}
public double[] getData() {
retu... |
4b17ec188e6561af1eaf7a3035c3916a944f55030046e8ec9f6353ac618eaca4 | Java | 408 | 25 | package umcg.genetica.io.binInteraction;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionCohort {
private final String name;
private final int sampleCount;
public BinaryInteractionCohort(String name, int sampleCount) {
this.name = name;
this.sampleCount = sampleCount;
}
public String ge... |
0ff9d659bf485bff3bef63d1805a139f014529ba35c47dda9ce43000b4a9d6ea | Java | 415 | 21 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
/**
*
* @author ludefranke
*/
public class StringIntegerObject {
public String stringValue;
public int intValue;
public StringIntegerObject(String stringValue, int intV... |
916b5e40d63bfeae25d61ab349d5ab7d62952b5c80e74608b929b4c371d9e47e | Java | 420 | 31 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.util;
/**
*
* @author Patrick Deelen
*/
public class ChrPos {
private final String chr;
private final int pos;
public ChrPos(String chr, int pos) {
this.chr = chr;
this.pos = p... |
3d4c92f8132634a100f9956a00c9b2e7e4e3fa6c9eb8bb2c7c0742c73790ead1 | Java | 422 | 26 | package ebi.spot.neo4j2owl.exporter;
/**
* Datastructure that wraps the returnvalue of neo4j2owl
*/
public class N2OReturnValue {
public String o;
public String log;
public N2OReturnValue() {
}
public void setOntology(String o) {
this.o = o;
}
public void setLog(String log) {
... |
411b071a2a8e23366d0e21b8ca0903959bfbf5200e19d7bcf641ecfb2870ca80 | Java | 422 | 20 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.graphics.curve;
import eqtlmappingpipeline.graphics.Graphics;
/**
*
* @author harm-jan
*/
public class Curve extends Graphics {
public Curve(int width, int height, boolean outputPDF,... |
4a0c85164cedc1225527c8e0d1a683dbdc7d05805aa3fa892b415636a8d778a4 | Java | 424 | 23 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.methylation;
/**
*
* @author Marc Jan
*/
public class DeepCopy {
public static double[][] CopyDoubleArrayArray(double[][] data){
double[][] newData = new double[data.length][data[1].length]... |
f78d0b2faebc92f36c9f577d054f0fff0007971c0460ae1b854051685c6dbc45 | Java | 425 | 21 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.containers;
/**
*
* @author ludefranke
*/
public class StringDoubleObject {
public String stringValue;
public double doubleValue;
public StringDoubleObject(String stringValue, doub... |
1b64e4c464895abfa70573577ee5f606f0f9544e730a43227780d4da8a57f5fb | Java | 427 | 25 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.gtf;
import java.io.IOException;
/**
*
* @author Patrick Deelen
*/
public interface GffReaderInterface extends Iterable<GffElement>{
/**
*
*
* @return next element null when done
... |
3dacf2108ed88f09ec7c834af309945691bf7c1c6e4935ceab772c85d20b0966 | Java | 436 | 21 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variant;
import org.molgenis.genotype.Alleles;
/**
*
* @author Patrick Deelen
*/
public interface GenotypeRecord {
Object getGenotypeRecordData(String recordId);
boolean containsGen... |
9c252e0016add94b1bf74e93972cae0d471e8dace6327b604aa0d2f33ae0c94a | Java | 436 | 23 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.containers;
/**
*
* @author patri
*/
@Deprecated
public class ChrPos {
private final Str... |
79d8923fe17f6f66ec2a83e9c5972fdfa7a1d6ab99665be5da7d0f12b58025cf | Java | 439 | 26 | package umcg.genetica.graphics;
import java.awt.*;
/**
* Created by hwestra on 2/10/15.
*/
public class ColorGenerator {
public static Color generate(double s, double v) {
double golden_ratio_conjugate = 0.618033988749895;
double h = Math.random();
h += golden_ratio_conjugate;
h %= 1;
return Color.get... |
5c7666c91f33676eb728eb5e72ddd127b7c9b465f51d89dc04ca25531f2fccd4 | Java | 442 | 27 | package org.molgenis.genotype;
public class GenotypeDataException extends RuntimeException
{
private static final long serialVersionUID = -4244460220718452547L;
public GenotypeDataException()
{
}
public GenotypeDataException(String message)
{
super(message);
}
public GenotypeDataException(Throwable cause... |
0820d0bc893a2cfc5930c70dbf6e0ce7694992b5652ee807401bd212a4ee21e3 | Java | 443 | 24 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta.graphics;
/**
*
* @author harm-jan
*/
public class PlotPackage {
boolean poison = false;
Double zscore1;
Double zscore2;
int dataset1;
int dataset2;
... |
ce3e5aa6ec4202afb7bde5b87dc3193150996a7e02939b6ba4852a6a6142d1ad | Java | 453 | 24 | package umcg.genetica.io.binInteraction;
/**
*
* @author Patrick Deelen
*/
public class BinaryInteractionFileException extends Exception {
public BinaryInteractionFileException() {
}
public BinaryInteractionFileException(String message) {
super(message);
}
public BinaryInteractionFileException(String mess... |
b869fbe55f2148ccf3c385c5c372c6546f17ae4e286f4c674c31ac605a5438cb | Java | 457 | 21 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
/**
*
* @author ludefranke
*/
public class StringIntegerObject {
public String stringValue;
public int intValue;
public String... |
ac2f5a28263133e29e7c0ed137f5c415d0df261f1e3f3563e9ccc023aa5994f2 | Java | 461 | 21 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.development.originalLude;
/**
*
* @author ludefranke
*/
public class DoubleArrayIntegerObject {
public double[] doubleArray;
public int intValue;
public DoubleArr... |
113c2c313b9ed3cf6db2a9f38ddc66a086c791d15e9a81be6c52d06513c222d0 | Java | 466 | 31 | package umcg.genetica.enums;
/**
* Created by hwestra on 10/24/16.
*/
public enum SNPClass {
NONCODING("Noncoding", 0),
EXONIC("Exonic", 1),
INTRONIC("Intronic", 2),
PROMOTER("Promoter", 3),
INDEL("Indel", 4),
UTR("UTR", 5);
private final String name;
private final int number;
SNPClass(String name, int ... |
4064d90cf39246d1bbaebf227a5573743bfa1cc290d1824b2785f17e46962f51 | Java | 467 | 34 | package org.molgenis.genotype.util;
import org.molgenis.genotype.Allele;
public class MafResult
{
private final Allele minorAllele;
private final double freq;
public MafResult(Allele minorAllele, double freq)
{
super();
this.minorAllele = minorAllele;
this.freq = freq;
}
/**
* @return the minorAllele... |
1fb51654cbb5965edcb79dd6a88424d4ac0b9d7e38a9675a5d01f990a208920f | Java | 471 | 21 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlinteractionanalyser.eqtlinteractionanalyser;
/**
*
* @author ludefranke
*/
public class DoubleArrayIntegerObject {
public double[] doubleArray;
public int intValue;
public... |
9195432025d105f33cbc170f31556c9c96d060777498c3959f59ea4b1599b934 | Java | 481 | 25 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class VariantFilterIsSnp implements VariantFilter {
@Override
public bool... |
be98028d37d86b9953dcd21ec92b789b576f325ea1b8cca5f5a251d7bec4a611 | Java | 481 | 28 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
/**
*
* @author harmjan
*/
public class PValueThreshold {
private double pvalue = Double.MAX_VALUE;
/**
* @return the pvalue
*/
public double getPv... |
6dc737ea9ead13d1a1758eab6a89f37baa88828fdbb5eab36e5f0c36d920b6ed | Java | 483 | 25 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.genenetworkbackend.hpo;
import java.io.File;
/**
*
* @author patri
*/
public class IdentifyOutlierHhoAs... |
1f0079f6028ead0f6b81ac2b1daa04b150294406657b4308c0c6e8ecc4a401a9 | Java | 488 | 21 | package mbqtl.junk;
public class SplitTest {
public static void main(String[] args) {
String data = "-";
for (int i = 0; i < 100; i++) {
if (i == 50) {
data += "\t0.1";
} else {
data += "\t";
}
}
String[] elems = ... |
b37fd2cd09031d28cc68225abb431973118221c70cc8362d0465d1ce5c6ae893 | Java | 488 | 24 | package org.molgenis.genotype.variant;
import org.molgenis.genotype.Alleles;
public class IllegalReferenceAlleleException extends Exception
{
/**
*
*/
private static final long serialVersionUID = 1L;
@SuppressWarnings("unused")
private IllegalReferenceAlleleException()
{
}
public IllegalReferenceAllele... |
115bc15e40d1ffdf0f4c8c8a8ccc7950b0e38bcd856217309e2a1bd19b39adfc | Java | 493 | 19 | package nl.systemsgenetics.downstreamer.io;
import java.io.IOException;
import java.util.Collection;
import java.util.Set;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
public interface BlockDiagonalDoubleMatrixProvider {
DoubleMatrixDataset<String, String> viewBlock(String block, Collection<String> id... |
0eb8446525b650470a80bc54efb9ca8e3d85ce15728a9331ac67b371adddac53 | Java | 499 | 30 | package umcg.genetica.features;
public enum FeatureType {
STARTCODON,
STOPCODON,
CDS,
EXON,
UTR,
OTHER;
public static FeatureType parse(String str) {
String lc = str.toLowerCase();
if (lc.equals("start_codon")) {
return STARTCODON;
} else if (lc.equals("stop_codon")) {
return STOPCODON;
} else... |
74088f7b47ec226e4a921cf18bf25aaa96784e4727f4a17d30d07a5ad477e452 | Java | 506 | 25 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author harmjan
*/
public class VariantFilterAmbigousSnp implements VariantFilter{
@Override
public ... |
0e941e8e25fe6ad2cc1cf42c229069af7ce685c3cef71ebcb22a76a6cb3de498 | Java | 508 | 22 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.sampleFilter;
import java.util.List;
import org.molgenis.genotype.RandomAccessGenotypeData;
import org.molgenis.genotype.Sample;
/**
*
* @author Patrick Deelen
*/
public interface Sampl... |
d1dab82fce36820ace102500c2cde6fa69acc21ffe99d4f9a47ce5dfbf7eaf61 | Java | 511 | 25 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.pathway;
import java.util.ArrayList;
import java.util.List;
/**
*
* @author patri
*/
publi... |
f5489bd7069665efb1a00a619ade71dca03b86ae7c7165cd6a4813a661feb69b | Java | 513 | 25 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author harmjan
*/
public class VariantFilterBiAllelic implements VariantFilter {
@Override
public b... |
f5a81c2626eacd5f47ac12fc75af00c8f3ad29140898af43a2667c0a68934a04 | Java | 514 | 27 | package org.molgenis.genotype.variantFilter;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class VariantFilterMachR2 implements VariantFilter{
private final double minMachR2;
public VariantFilterMachR2(double minMachR2) {
this.minMachR2 = minMachR2;
}
@Over... |
22f77a87e733bc12f72a3fc186a3cad23b1e4c9af89110820848b06a3f3240b4 | Java | 515 | 11 | package edu.cmu.cs.eyetrack.analysis.score.compare;
import edu.cmu.cs.eyetrack.analysis.score.distance.DistanceFunction;
import edu.cmu.cs.eyetrack.analysis.struct.Trajectory;
import edu.cmu.cs.eyetrack.analysis.struct.tobii.TobiiFrame;
import edu.cmu.cs.eyetrack.analysis.struct.trackit.TrackItFrame;
public ab... |
85f168738dbbcbf66909d14559b2b69feb6a5cf6f73d1d8d7515144aeab2c119 | Java | 516 | 27 | package eqtlmappingpipeline;
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
import org.testng.annotations.BeforeMethod;
/**
*
* @author MarcJan
*/
public class NormalizationTest {
public NormalizationTest() {
}
// TODO add test methods here.
... |
4b102bb01a3c9f9379b5fca0eae3434bdb60848aca85f249e4964bd025e55484 | Java | 518 | 29 | package mbqtl.junk;
import mbqtl.Util;
public class ShuffleTest {
public static void main(String[] args) {
double[] v = new double[100];
for (int q = 0; q < v.length; q++) {
v[q] = q;
}
double[][] z = new double[2][100];
for (int p = 0; p < 2; p++) {
double[] vcopy = new double[100];
System.ar... |
81b4284914ce549060ce1dc37ee174f900db89bea82b54897ba5c20fd294f6ae | Java | 524 | 23 | package umcg.genetica.math.stats;
/**
*
* @author juha
*/
public class Normalization {
private Normalization() {
}
public static double[] standardNormalize(double[] vals) {
double[] normalized = new double[vals.length];
double mean = Descriptives.mean(vals);
double std... |
261b781a6f253a4ea833a569378a64cf8e69c3e2a7fb2a882202eea816b764bb | Java | 537 | 22 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.util;
import java.io.IOException;
import umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger;
/**
*
* @author harmjan
*/
public class GenotypeDataMerger {
public void merge(Str... |
9f70e26cc533accc2bd29a2770d0da71b1a00156a16f402bf13eb3c188027223 | Java | 539 | 29 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.ase;
/**
*
* @author Patrick Deelen
*/
public class AseException extends Exception {
/**
* Creates a new instance of
* <code>AseException</code> without detail message.
*/
public ... |
a633feacdf454960664ce7b2fbe3026d1d3863a3dd610f960cf13665b539cf27 | Java | 540 | 24 | package nl.systemsgenetics.downstreamer.summarystatistic.filters;
import nl.systemsgenetics.downstreamer.summarystatistic.SummaryStatisticRecord;
/**
* The interface Summary statistics record filter.
*/
public interface SummaryStatisticsRecordFilter {
/**
* Passes filter boolean.
*
* @param reco... |
c5c3ebbb91691b51a3e3fde2c74fec7417839f6b58c7d8db9bca0a4623fc0b00 | Java | 555 | 29 | package mbqtl.vcf.filter.variantfilters;
import mbqtl.vcf.VCFVariant;
/**
* Created by hwestra on 6/21/17.
*/
public class VCFVariantMissingnessPFilter implements VCFVariantFilter {
private double thresh = 5E-8;
public VCFVariantMissingnessPFilter(double threshold) {
this.thresh = threshold;
}
@Override... |
36d6b758f8b3a2b48f9e84957fd719db5a887607484dd5cfd5225c1f62a4ab36 | Java | 558 | 28 | package mbqtl.vcf.filter.variantfilters;
import mbqtl.vcf.VCFVariant;
/**
* Created by hwestra on 3/21/17.
*/
public class VCFVariantCallRateFilter implements VCFVariantFilter {
private double threshold = 0.3;
public VCFVariantCallRateFilter(double threshold) {
this.threshold = threshold;
}
@Override
publ... |
16e08237053b16e92b3d1fb4f6ca221a08297b0c9ac87163be624a9616efd893 | Java | 561 | 19 | package nl.systemsgenetics.geneticriskscorecalculator;
import gnu.trove.map.hash.TObjectDoubleHashMap;
import org.molgenis.genotype.RandomAccessGenotypeData;
/**
*
* @author Patrick Deelen
*/
public interface GeneticRiskScoreCalculator {
TObjectDoubleHashMap<String> calculateRiskScores(RandomAccessGenotypeData g... |
172518af882f93519ef1d941c0ba1506de8ffbd848ccd556451c2c9f2e3a1c68 | Java | 561 | 25 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public interface VariantFilter {
public boolean doesVariantPassFilter(GeneticVari... |
dd6e9f1b81c71633e4c638bf0092a67fa4f3dae3b3916a5f1a3828828f219e0c | Java | 562 | 30 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.transCorrelationQtl;
/**
*
* @author patri
*/
public class PvalueZscore {
private final double pvalu... |
10782130e709dec2fa18fb114c18acf67fce4b3e3a93e59814b6a394a718726b | Java | 564 | 22 | package edu.cmu.cs.eyetrack.analysis.score.distance;
import edu.cmu.cs.eyetrack.analysis.struct.Frame;
public class FalloffDistanceFunction extends DistanceFunction {
private double exponent;
public FalloffDistanceFunction(double exponent) {
this.exponent = exponent;
}
@Override
public Dou... |
5f2147707a12a8486c9a28648de390488034e93c09548c877a23375d1fc0a211 | Java | 567 | 27 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.downstreamer.gene;
import umcg.genetica.math.matrix2.DoubleMatrixDataset;
/**
*
* @author patri
*/
@Dep... |
95442d05109de5ee715f789a68e1d9a065e051bc4a238e6d645e119cdc415596 | Java | 568 | 25 | package ebi.spot.neo4j2owl.importer;
import org.semanticweb.owlapi.model.OWLEntity;
class N2OOWLRelationship {
private final OWLEntity start;
private final OWLEntity end;
private final String relation;
N2OOWLRelationship(OWLEntity iri_start, OWLEntity iri_end, String relation) {
this.start = i... |
bebb4edebc40ceb470cfd11f48f87a26b09e5041d2a7ad70f39dc1b1b7d526fb | Java | 572 | 27 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.molgenis.genotype.variantFilter;
import java.util.Iterator;
import org.molgenis.genotype.variant.GeneticVariant;
/**
*
* @author Patrick Deelen
*/
public class VariantFilterIterable implements Iterable<G... |
67b1951535a697ca7ea7ce66ab6fecaee8e59174e7f512e7a38db2877ffa1cc2 | Java | 579 | 29 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.io.pileup;
/**
*
* @author Patrick Deelen
*/
public class PileupParseException extends Exception {
/**
* Creates a new instance of
* <code>PileupParseException</code> without detail messag... |
d4111d2d71f4e6436e8e0e4c12ab45c00061233f1eebb8a6f9bff90db62a3d31 | Java | 579 | 29 | /*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package nl.systemsgenetics.eqtlannotation;
/**
*
* @author MarcJan
*/
class ChmmState {
private final long start;
private f... |
37322a19010c3418387a60c6e4baf4f421c2cfee6db95b37d1dff8b84ffffe07 | Java | 580 | 20 | package mbqtl.junk;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.Locale;
public class DFTest {
public static void main(String[] args) {
double d = -3000000.646876876387;
// d = 0.001;
// d = 0.001;
DecimalFormatSymbols symbols = new Decima... |
a2ee151cc4e6f41409fdd85fe1c04934d6c46ed3b58d28d51486b8dc4e0b83dd | Java | 597 | 18 | /*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package umcg.genetica.console;
/**
*
* @author harmjan
*/
public final class ConsoleGUIElems {
public static final String SPACE = " ";
public static final String TAB = "\t";
public static final String... |
59925b9ebea0b999a1c869ac613d06dc84013d9703c5087c36b4db428c4090c4 | Java | 613 | 31 | package org.molgenis.genotype.plink;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
*
* @author Patrick Deelen
*/
public class FormatPlinkChr {
private static final Pattern CHR_PATTERN = Pattern.compile("^chr(.*)$", Pattern.CASE_INSENSITIVE);
public static String formatChr(String chrName)... |
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