file_name stringlengths 6 86 | file_path stringlengths 45 249 | content stringlengths 47 6.26M | file_size int64 47 6.26M | language stringclasses 1
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value | repo_name stringclasses 767
values | repo_stars int64 8 14.4k | repo_forks int64 0 1.17k | repo_open_issues int64 0 788 | repo_created_at stringclasses 767
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StagingServiceImpl.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/staging/impl/StagingServiceImpl.java | package com.hermesworld.ais.galapagos.staging.impl;
import com.hermesworld.ais.galapagos.applications.ApplicationsService;
import com.hermesworld.ais.galapagos.changes.Change;
import com.hermesworld.ais.galapagos.kafka.KafkaClusters;
import com.hermesworld.ais.galapagos.kafka.config.KafkaEnvironmentConfig;
import com.... | 2,745 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
StagingImpl.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/staging/impl/StagingImpl.java | package com.hermesworld.ais.galapagos.staging.impl;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import com.hermesworld.ais.galapagos.changes.ApplicableChange;
import com.hermesworld.ais.ga... | 15,129 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
TrustStoreController.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/controller/TrustStoreController.java | package com.hermesworld.ais.galapagos.certificates.controller;
import com.hermesworld.ais.galapagos.kafka.KafkaClusters;
import com.hermesworld.ais.galapagos.kafka.auth.KafkaAuthenticationModule;
import lombok.extern.slf4j.Slf4j;
import org.apache.kafka.common.config.SslConfigs;
import org.springframework.http.HttpHea... | 2,892 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CertificateExpiryReminder.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/reminders/CertificateExpiryReminder.java | package com.hermesworld.ais.galapagos.certificates.reminders;
import lombok.Getter;
/**
* Represents a reminder about the expiration of a certificate which should be sent out.
*
* @author AlbrechtFlo
*/
@Getter
public final class CertificateExpiryReminder {
private final String applicationId;
private fi... | 957 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
ReminderType.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/reminders/ReminderType.java | package com.hermesworld.ais.galapagos.certificates.reminders;
import java.time.Instant;
import java.time.temporal.ChronoUnit;
/**
* Types of certificate expiry reminders which are sent. Each type can be queried for the number of days before
* certificate expiry a reminder of this type should be sent.
*/
public enu... | 1,068 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CertificateExpiryReminderService.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/reminders/CertificateExpiryReminderService.java | package com.hermesworld.ais.galapagos.certificates.reminders;
import java.util.List;
/**
* A service which is able to calculate the due reminders for application topic owners about the expiry of one of their
* certificates. The service ensures that one reminder is reported to be sent (each), when
* <ul>
* <li>the... | 1,565 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CertificateExpiryReminderServiceImpl.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/reminders/impl/CertificateExpiryReminderServiceImpl.java | package com.hermesworld.ais.galapagos.certificates.reminders.impl;
import com.hermesworld.ais.galapagos.applications.ApplicationMetadata;
import com.hermesworld.ais.galapagos.applications.ApplicationsService;
import com.hermesworld.ais.galapagos.certificates.reminders.CertificateExpiryReminder;
import com.hermesworld.... | 5,284 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CertificateExpiryReminderRunner.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/reminders/impl/CertificateExpiryReminderRunner.java | package com.hermesworld.ais.galapagos.certificates.reminders.impl;
import com.hermesworld.ais.galapagos.applications.ApplicationMetadata;
import com.hermesworld.ais.galapagos.applications.ApplicationsService;
import com.hermesworld.ais.galapagos.certificates.reminders.CertificateExpiryReminder;
import com.hermesworld.... | 5,596 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
ReminderMetadata.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/reminders/impl/ReminderMetadata.java | package com.hermesworld.ais.galapagos.certificates.reminders.impl;
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import com.hermesworld.ais.galapagos.certificates.reminders.ReminderType;
import com.hermesworld.ais.galapagos.util.HasKey;
import lombok.Getter;
import lombok.Setter;
/**
* Metadata for... | 779 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CaManagerImpl.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/impl/CaManagerImpl.java | package com.hermesworld.ais.galapagos.certificates.impl;
import com.hermesworld.ais.galapagos.certificates.auth.CertificatesAuthenticationConfig;
import com.hermesworld.ais.galapagos.util.CertificateUtil;
import lombok.extern.slf4j.Slf4j;
import org.bouncycastle.asn1.ASN1Encoding;
import org.bouncycastle.asn1.ASN1Obje... | 19,788 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CaData.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/impl/CaData.java | package com.hermesworld.ais.galapagos.certificates.impl;
import java.security.PrivateKey;
import java.security.cert.X509Certificate;
import lombok.Getter;
import lombok.Setter;
@Getter
@Setter
final class CaData {
private X509Certificate caCertificate;
private PrivateKey caPrivateKey;
private long app... | 400 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CertificateSignResult.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/impl/CertificateSignResult.java | package com.hermesworld.ais.galapagos.certificates.impl;
import lombok.Getter;
import java.security.cert.X509Certificate;
import java.util.Optional;
@Getter
public final class CertificateSignResult {
private final X509Certificate certificate;
private final String certificatePemData;
private final Opti... | 669 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CertificatesAuthenticationModule.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/auth/CertificatesAuthenticationModule.java | package com.hermesworld.ais.galapagos.certificates.auth;
import com.hermesworld.ais.galapagos.certificates.impl.CaManagerImpl;
import com.hermesworld.ais.galapagos.certificates.impl.CertificateSignResult;
import com.hermesworld.ais.galapagos.kafka.auth.CreateAuthenticationResult;
import com.hermesworld.ais.galapagos.k... | 10,956 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
CertificatesAuthenticationConfig.java | /FileExtraction/Java_unseen/HermesGermany_galapagos/src/main/java/com/hermesworld/ais/galapagos/certificates/auth/CertificatesAuthenticationConfig.java | package com.hermesworld.ais.galapagos.certificates.auth;
import lombok.Getter;
import lombok.Setter;
import org.springframework.core.io.Resource;
@Getter
@Setter
public class CertificatesAuthenticationConfig {
private Resource caCertificateFile;
private Resource caKeyFile;
private String certificatesWo... | 586 | Java | .java | HermesGermany/galapagos | 81 | 22 | 15 | 2020-10-02T09:40:40Z | 2024-05-08T13:11:33Z |
MLGammaDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLGammaDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.commons.math3.distribution.GammaDistribution;
import org.apache.commons.math3.distribution.NormalDistribution;
import org.apache.commons.math3.s... | 2,432 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MLLogisticDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLLogisticDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.math3.distribution.LogisticDistribution;
import org.apache.commons.math3.distribution.NormalDistribution;
public class MLLogisticDistribution extends MLDistributi... | 1,683 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
EMMain.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/EMMain.java | package de.unijena.bioinf.em;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import ... | 29,660 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MLDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
public abstract class MLDistribution implements InterfaceMLDistribution{
public double shift=+1E-5;
static double borders=+1E-4;
public boolean inverse=false;
public Double inverse_x=null;
public Double max_sam... | 2,275 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
EMResult.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/EMResult.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TreeMap;
import de.unijena.bioinf.em.Sample.Type;
class EMResult implements Comparable<EMResult>{
List<Map<Strin... | 5,949 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
InterfaceMLDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/InterfaceMLDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
public interface InterfaceMLDistribution {
public Map<String, Double> MStep(List<Double> expectation);
public List<Double> EStep(Map<String, Double> parameters) throws Exception;
double getDensity(double x, Map... | 835 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MLWeibullDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLWeibullDistribution.java | package de.unijena.bioinf.em;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.math3.distribution.WeibullDistribution;
import org.apache.commons.math3.special.Gamma;
import umontreal.iro.lecuyer.probdist.WeibullDist;
public class MLWeibullDistribution extends MLDistri... | 3,684 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MLLogNormalDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLLogNormalDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.math3.distribution.LogNormalDistribution;
import org.apache.commons.math3.distribution.NormalDistribution;
public class MLLogNormalDistribution extends MLDistribu... | 1,653 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
EMUtils.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/EMUtils.java | package de.unijena.bioinf.em;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Locale;
import java.util.Ma... | 10,025 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
EM.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/EM.java | package de.unijena.bioinf.em;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.uti... | 4,706 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MLNormalDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLNormalDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.math3.distribution.NormalDistribution;
public class MLNormalDistribution extends MLDistribution implements InterfaceMLDistribution {
public MLNormalDistribution... | 1,560 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MLBetaDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLBetaDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.commons.math3.distribution.BetaDistribution;
import org.apache.commons.math3.distribution.GammaDistribution;
import org.apache.commons.math3.dis... | 1,911 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MLExponentialDistribution.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/MLExponentialDistribution.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.apache.commons.math3.distribution.ExponentialDistribution;
import org.apache.commons.math3.distribution.GammaDistribution;
import org.apache.commons.ma... | 1,619 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Sample.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/em/Sample.java | package de.unijena.bioinf.em;
import java.util.ArrayList;
import java.util.List;
public class Sample {
public enum Type{FalsePositiveMatch, TruePositiveMatch, DecoyMatch}
public List<Double> sample=new ArrayList<Double>();
public List<Type> types=new ArrayList<Type>();
public List<Integer> ranks=new ArrayList... | 2,423 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Main.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/treecomparison/Main.java | package de.unijena.bioinf.treecomparison;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.nio.file.Files;
//generating tree alignments
public class Main {
static String queryLong="Agilent";
static String DBLong="... | 5,153 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ResultList.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/ResultList.java | package de.unijena.bioinf.statistics;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import de.unijena.bioinf.decoy.model.MassBank;... | 4,722 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
HitStatistic.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/HitStatistic.java | package de.unijena.bioinf.statistics;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
impo... | 33,716 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Main.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/Main.java | package de.unijena.bioinf.statistics;
public class Main {
public static void main(String args[]) throws Exception{
String a="-base U:\\MSBlast\\ -ppm 10 -ae 2 -addFolder RPP "
+"-queries "
+"APFilesOriginal-GPTrees "
+"-searchMethodsStatisticsOriginal MassBank "
+"-searchMethods MassBank "
+"-decoyMeth... | 710 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Result.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/Result.java | package de.unijena.bioinf.statistics;
import de.unijena.bioinf.decoy.model.MassBank;
public class Result implements Comparable<Result>{
String resultID;
public int matchedPeaks;
public double score;
boolean isTrueMatch;
MassBank massbank;
public Result(String[] line){
resultID=line[1];
matchedPeaks=Intege... | 956 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
pValues.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/pValues.java | package de.unijena.bioinf.statistics;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import de.unijena.bioinf.em.EMUtils;
import de.unijena.bioinf.em.Sampl... | 4,416 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MainStatistics.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/MainStatistics.java | package de.unijena.bioinf.statistics;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Shape;
import java.awt.Stroke;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import ... | 73,681 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Query.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/Query.java | package de.unijena.bioinf.statistics;
import de.unijena.bioinf.decoy.model.MassBank;
public class Query{
String queryID;
MassBank massbank;
// public Query(String[] line){
// queryID=line[1];
// }
public Query(String queryID){
this.queryID=queryID;
}
public Query(Query q){
this.queryID=q.queryID;
... | 594 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MainOld.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/MainOld.java | package de.unijena.bioinf.statistics;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
... | 7,669 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Plot.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/Plot.java | package de.unijena.bioinf.statistics;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeMap;
import org.jfree.chart.ChartFactory;
import org.jfree.... | 11,452 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Utils.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/Utils.java | package de.unijena.bioinf.statistics;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.Map;
import java.util.TreeMap;
import de.unijena.bioinf.decoy.model.MassBank;
public class Utils {
publ... | 3,326 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
SimilarityMatrix.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/SimilarityMatrix.java | package de.unijena.bioinf.statistics;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import ... | 41,348 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
qValueSummaryMain.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/statistics/qValueSummaryMain.java | package de.unijena.bioinf.statistics;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Locale;
public class qValueSummaryMain {
st... | 2,596 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MSBlastDecoyTrees.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/msblast/MSBlastDecoyTrees.java | package de.unijena.bioinf.msblast;
//Generating Decoy DB
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Local... | 5,911 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Main.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/msblast/Main.java | package de.unijena.bioinf.msblast;
public class Main {
public static void main(String args[]) throws Exception{
// for(String db:new String[]{"agilent","massbankorbi","massbankqtof","massbank"}){
// for(String d:new String[]{"Trees","Files"}){
// for(String method:new String[]{"Original"}){
// MSBl... | 1,754 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ParametersDecoySpectrumConstruction.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/msblast/ParametersDecoySpectrumConstruction.java | package de.unijena.bioinf.msblast;
import java.io.File;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import de.unijena.bioinf.babelms.dot.Graph;
import de.unijena.bioinf.decoy.decoytrees.DefaultDecoyTree;... | 10,251 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodOberacher.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodOberacher.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 3,219 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
PostProcessMethodSimple.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/PostProcessMethodSimple.java | package de.unijena.bioinf.spectralcomparison;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.statistics.Result;
public class PostProce... | 2,006 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
AlignmentMatrix.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/AlignmentMatrix.java | package de.unijena.bioinf.spectralcomparison;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.util.Arrays;
import java.util.List;
import de.unijena.bioinf.statistics.Result;
public class AlignmentMatrix {
String queryFile;
String resultFile;
List<String> left;
List<St... | 1,242 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodTreeAlignment.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodTreeAlignment.java | package de.unijena.bioinf.spectralcomparison;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.... | 5,059 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodCosineDistance.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodCosineDistance.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 3,826 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Main.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/Main.java | package de.unijena.bioinf.spectralcomparison;
public class Main {
public static void main(String args[]) throws Exception{
for (String db1:new String[]{"massbankorbi","massbankqtof","agilent"}){
for (String db2:new String[]{"massbankorbi","massbankqtof","agilent"}){
if(db1.equals(db2))continue;
for (Str... | 1,379 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodMassBank.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodMassBank.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 3,927 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodMassBankEffectivePeaks.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodMassBankEffectivePeaks.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 4,457 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
PostProcessMethodPValue.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/PostProcessMethodPValue.java | package de.unijena.bioinf.spectralcomparison;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Random;
import ja... | 6,110 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodOberacherWithIntensities.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodOberacherWithIntensities.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 3,790 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodOberacherPeakcounting.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodOberacherPeakcounting.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 3,245 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodOberacherWithIntensitiesAndMasses.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodOberacherWithIntensitiesAndMasses.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 4,141 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ParametersSpectralComparison.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ParametersSpectralComparison.java | package de.unijena.bioinf.spectralcomparison;
import java.io.File;
import java.util.Arrays;
import de.unijena.bioinf.msblast.ParametersDecoySpectrumConstruction;
public class ParametersSpectralComparison {
public static enum COMPARISONMETHOD{OBERACHER, OBERACHERWITHINTENSITIES, OBERACHERWITHINTENSITIESANDMASSES, ... | 5,823 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
PostProcessMethodFingerprint.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/PostProcessMethodFingerprint.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.statistics.Result;
public class PostProcessMethodFingerprint implements PostProcessMethod{
static public final String methodNameLong="FP";
Paramet... | 2,943 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethod.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethod.java | package de.unijena.bioinf.spectralcomparison;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.statistics.Result;
public interface ComparisonMethod {
public String getMethodNameLong();
public void setSpectra(List<MassBank> s1, List<MassBank> s2);
// public void setTre... | 536 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ComparisonMethodEquality.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/ComparisonMethodEquality.java | package de.unijena.bioinf.spectralcomparison;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.deocy.Utils;
import de.unijena.bioinf.spectralcomparison.ParametersSpectralComparison.COMPARISONPOSTPROCESS;
import de.unijena.bioinf.statistics.Resu... | 3,352 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
PostProcessMethod.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/PostProcessMethod.java | package de.unijena.bioinf.spectralcomparison;
import de.unijena.bioinf.statistics.Result;
public interface PostProcessMethod {
public Result[][] getResultList(ComparisonMethod cm);
public String getMethodNameLong();
}
| 233 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MSBlastSpectralComparison.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/spectralcomparison/MSBlastSpectralComparison.java | package de.unijena.bioinf.spectralcomparison;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Locale;
import de.unijena.bioinf.decoy.model.MassBank;
import de.unijena.bioinf.msblast.ParametersDecoySpectrumConstruction;
import de.unijena.bioinf.msblast.... | 2,190 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
Utils.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/deocy/Utils.java | package de.unijena.bioinf.deocy;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Rando... | 6,632 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DecoySpectrum.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/decoytrees/DecoySpectrum.java | package de.unijena.bioinf.decoy.decoytrees;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.StringWriter;
import java.io.Writer;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collectio... | 1,430 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DefaultDecoyTree.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/decoytrees/DefaultDecoyTree.java | package de.unijena.bioinf.decoy.decoytrees;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.StringWriter;
import java.io.Writer;
import java.text.DecimalFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arra... | 7,180 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DefaultDecoySpectrum.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/decoytrees/DefaultDecoySpectrum.java | package de.unijena.bioinf.decoy.decoytrees;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.StringWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import de.unijena.bioinf.Chemistry... | 3,398 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
VertexComparator.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/VertexComparator.java | package de.unijena.bioinf.decoy.model;
import java.util.Comparator;
public class VertexComparator implements Comparator<DecoyTreeVertex>{
@Override
public int compare(DecoyTreeVertex o1, DecoyTreeVertex o2) {
return Double.compare(o1.mf.getMass(),o2.mf.getMass());
}
}
| 288 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DecoyTreeVertex.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/DecoyTreeVertex.java | package de.unijena.bioinf.decoy.model;
import java.util.Iterator;
import java.util.Map;
import de.unijena.bioinf.ChemistryBase.chem.MolecularFormula;
import de.unijena.bioinf.babelms.dot.Vertex;
import de.unijena.bioinf.deocy.Utils;
public class DecoyTreeVertex extends Vertex{
public MolecularFormula mf;
public d... | 1,933 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MassBank.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/MassBank.java | package de.unijena.bioinf.decoy.model;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Iterator... | 7,211 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DecoyTreeEdge.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/DecoyTreeEdge.java | package de.unijena.bioinf.decoy.model;
import java.util.Iterator;
import java.util.Map;
import de.unijena.bioinf.ChemistryBase.chem.MolecularFormula;
import de.unijena.bioinf.babelms.dot.Edge;
import de.unijena.bioinf.deocy.Utils;
public class DecoyTreeEdge extends Edge{
public MolecularFormula mf;
public Decoy... | 1,074 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ConditionalPeaksConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/ConditionalPeaksConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Random;
import java.util.Set;
im... | 3,699 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
MixedSpectrumConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/MixedSpectrumConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Random;
import java.util.Set;
import de.unijena.bioinf.babe... | 3,585 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
RandomPeaksConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/RandomPeaksConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Random;
import de.unijena.bioinf.babelms.dot.Graph;
import de.unijena.bioinf.decoy.decoytrees.DecoySpectrum;
import de.unijena.bioinf.decoy.decoytrees.DefaultDeco... | 3,642 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DefaultDecoyFileConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/DefaultDecoyFileConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import java.util.ArrayList;
import java.util.List;
import de.unijena.bioinf.ChemistryBase.chem.MolecularFormula;
import de.unijena.bioinf.babelms.dot.Graph;
import de.unijena.bioinf.decoy.decoytrees.DecoySpectrum;
import de.unijena.bioinf.decoy.decoytrees.D... | 1,339 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DecoySpectrumConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/DecoySpectrumConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import de.unijena.bioinf.babelms.dot.Graph;
import de.unijena.bioinf.decoy.decoytrees.DecoySpectrum;
public interface DecoySpectrumConstructor {
static public final String methodNameLong=null;
public DecoySpectrum getDecoySpectrum();
public void setO... | 395 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
DefaultDecoyTreeConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/DefaultDecoyTreeConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import de.unijena.bioinf.babelms.dot.Graph;
import de.unijena.bioinf.decoy.decoytrees.DecoySpectrum;
import de.unijena.bioinf.decoy.decoytrees.DefaultDecoySpectrum;
import de.unijena.bioinf.decoy.decoytrees.DefaultDecoyTree;
import de.unijena.bioinf.msblast.... | 1,144 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
RerootDecoyTreeConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/RerootDecoyTreeConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Random;
import java.util.Set;
import java.util.TreeMap;
import... | 5,097 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
ConditionalFastConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/ConditionalFastConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.M... | 7,693 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
RandomTreeDecoyTreeConstructor.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/decoy/model/decoytreeconstructors/RandomTreeDecoyTreeConstructor.java | package de.unijena.bioinf.decoy.model.decoytreeconstructors;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Random;
import java.util.Set;
import java.... | 4,442 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
SpectrumComparator.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/pvalue/SpectrumComparator.java | package de.unijena.bioinf.pvalue;
import java.util.Comparator;
class SpectrumComparator implements Comparator<double[]>{
@Override
public int compare(double[] o1, double[] o2) {
return Double.compare(o1[0], o2[0]);
}
} | 239 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
SisterSpectrumGeneratorRandomPeaks.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/pvalue/SisterSpectrumGeneratorRandomPeaks.java | package de.unijena.bioinf.pvalue;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.... | 3,162 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
SisterSpectrumGeneratorConditionalPeaks.java | /FileExtraction/Java_unseen/boecker-lab_passatuto/src/de/unijena/bioinf/pvalue/SisterSpectrumGeneratorConditionalPeaks.java | package de.unijena.bioinf.pvalue;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Random;... | 6,997 | Java | .java | boecker-lab/passatuto | 9 | 1 | 0 | 2017-01-20T09:48:17Z | 2017-01-20T10:23:52Z |
AppTest.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/test/java/org/flashtool/AppTest.java | /*
* This Java source file was generated by the Gradle 'init' task.
*/
package org.flashtool;
import org.testng.annotations.*;
import static org.testng.Assert.*;
import org.flashtool.gui.Main;
public class AppTest {
@Test public void appHasAGreeting() {
Main classUnderTest = new Main();
assert... | 383 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
APKUtility.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/adb/APKUtility.java | package org.flashtool.jna.adb;
import java.io.File;
import lombok.extern.slf4j.Slf4j;
import net.dongliu.apk.parser.ApkFile;
@Slf4j
public class APKUtility {
public static String getPackageName(String apkname) throws Exception {
try (ApkFile apkFile = new ApkFile(new File(apkname))) {
return apkFile.getApk... | 355 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
FastbootUtility.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/adb/FastbootUtility.java | package org.flashtool.jna.adb;
import java.util.Enumeration;
import java.util.Scanner;
import java.util.Vector;
import org.flashtool.system.OS;
import org.flashtool.system.ProcessBuilderWrapper;
import org.flashtool.system.RunOutputs;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class FastbootUtility {
private... | 3,212 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
AdbException.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/adb/AdbException.java | package org.flashtool.jna.adb;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class AdbException extends Exception{
/**
*
*/
private static final long serialVersionUID = 1L;
public AdbException(String msg){
super(msg);
}
public AdbException(String msg, Throwable t){
super(msg,t);
... | 326 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
AdbUtility.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/adb/AdbUtility.java | package org.flashtool.jna.adb;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Properties;
import java.util.Scanner;
import java.util.Vector;
import org.flashtool.system.Devices;
import org.flashtool.system.FTShell;
import org.flashtool... | 19,482 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
JKernel32.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/win32/JKernel32.java | package org.flashtool.jna.win32;
import java.io.IOException;
import org.flashtool.flashsystem.io.USBFlashLinux;
import org.flashtool.jna.linux.JUsb;
import org.flashtool.system.Devices;
import org.flashtool.util.BytesUtil;
import org.flashtool.util.HexDump;
import com.sun.jna.Native;
import com.sun.jna.platform.win3... | 4,010 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
Kernel32RW.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/win32/Kernel32RW.java | package org.flashtool.jna.win32;
import com.sun.jna.platform.win32.Kernel32;
import com.sun.jna.platform.win32.WinNT;
import com.sun.jna.ptr.IntByReference;
public interface Kernel32RW extends Kernel32 {
/**
* CreateFile constants
*/
/**
* Enable read access
*/
int GENERIC_READ ... | 1,121 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
JsetupAPi.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/win32/JsetupAPi.java | package org.flashtool.jna.win32;
import org.flashtool.jna.adb.AdbUtility;
import org.flashtool.jna.linux.JUsb;
import org.flashtool.jna.win32.SetupApi.HDEVINFO;
import org.flashtool.jna.win32.SetupApi.SP_DEVICE_INTERFACE_DETAIL_DATA;
import org.flashtool.jna.win32.SetupApi.SP_DRVINFO_DATA;
import com.sun.jna.platform... | 6,555 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
SetupApi.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/win32/SetupApi.java | package org.flashtool.jna.win32;
import java.util.Arrays;
import java.util.List;
import com.sun.jna.platform.win32.Guid.GUID;
import com.sun.jna.Library;
import com.sun.jna.Pointer;
import com.sun.jna.Structure;
import com.sun.jna.platform.win32.WinBase;
import com.sun.jna.platform.win32.WinDef;
import com.sun.jna.pl... | 4,838 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
User32RW.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/win32/User32RW.java | package org.flashtool.jna.win32;
import java.util.Arrays;
import java.util.List;
import org.flashtool.jna.linux.JUsb;
import com.sun.jna.Native;
import com.sun.jna.Pointer;
import com.sun.jna.Structure;
import com.sun.jna.platform.win32.User32;
import com.sun.jna.platform.win32.WinNT.HANDLE;
import com.sun.jna.win3... | 3,880 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
JUsb.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/linux/JUsb.java | package org.flashtool.jna.linux;
import java.io.ByteArrayInputStream;
import org.flashtool.jna.adb.APKUtility;
import org.flashtool.libusb.LibUsbException;
import org.flashtool.libusb.UsbDevList;
import org.flashtool.libusb.UsbDevice;
import org.flashtool.libusb.UsbSystem;
import org.flashtool.util.BytesUtil;
import... | 2,419 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
libusb_interface.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/libusb/libusb_interface.java | package org.flashtool.jna.libusb;
import java.util.Arrays;
import java.util.List;
import org.flashtool.jna.adb.APKUtility;
import com.sun.jna.Structure;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class libusb_interface extends Structure
{
public libusb_interface_descriptor.ByReference altsetting;
public i... | 1,254 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
LibUsbLibrary.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/libusb/LibUsbLibrary.java | package org.flashtool.jna.libusb;
import org.flashtool.jna.adb.APKUtility;
import com.sun.jna.Library;
import com.sun.jna.Native;
import com.sun.jna.Pointer;
import com.sun.jna.ptr.PointerByReference;
public abstract interface LibUsbLibrary extends Library
{
public static final LibUsbLibrary libUsb = (LibUsbLibrar... | 9,369 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
libusb_config_descriptor.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/libusb/libusb_config_descriptor.java | package org.flashtool.jna.libusb;
import java.util.Arrays;
import java.util.List;
import org.flashtool.jna.adb.APKUtility;
import com.sun.jna.Pointer;
import com.sun.jna.Structure;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class libusb_config_descriptor extends Structure
{
public byte bLength;
public byt... | 1,433 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
libusb_interface_descriptor.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/libusb/libusb_interface_descriptor.java | package org.flashtool.jna.libusb;
import java.util.Arrays;
import java.util.List;
import org.flashtool.jna.adb.APKUtility;
import com.sun.jna.Pointer;
import com.sun.jna.Structure;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class libusb_interface_descriptor extends Structure
{
public byte bLength;
public ... | 3,311 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
libusb_device_descriptor.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/libusb/libusb_device_descriptor.java | package org.flashtool.jna.libusb;
import java.util.Arrays;
import java.util.List;
import org.flashtool.jna.adb.APKUtility;
import com.sun.jna.Structure;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class libusb_device_descriptor extends Structure
{
public byte bLength;
public byte bDescriptorType;
public ... | 1,913 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
libusb_endpoint_descriptor.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/libusb/libusb_endpoint_descriptor.java | package org.flashtool.jna.libusb;
import java.util.Arrays;
import java.util.List;
import org.flashtool.jna.adb.APKUtility;
import com.sun.jna.Pointer;
import com.sun.jna.Structure;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class libusb_endpoint_descriptor extends Structure
{
public byte bLength;
public b... | 2,638 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
libusb_version.java | /FileExtraction/Java_unseen/Androxyde_Flashtool/Flashtool/src/main/java/org/flashtool/jna/libusb/libusb_version.java | package org.flashtool.jna.libusb;
import java.util.Arrays;
import java.util.List;
import org.flashtool.jna.adb.APKUtility;
import com.sun.jna.Pointer;
import com.sun.jna.Structure;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class libusb_version extends Structure
{
public short major;
public short minor;
... | 1,763 | Java | .java | Androxyde/Flashtool | 468 | 244 | 165 | 2014-04-17T19:54:33Z | 2024-03-12T15:17:26Z |
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