repo stringlengths 1 191 ⌀ | file stringlengths 23 351 | code stringlengths 0 5.32M | file_length int64 0 5.32M | avg_line_length float64 0 2.9k | max_line_length int64 0 288k | extension_type stringclasses 1
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Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/UserOrganismPermissionInfo.java | package org.bbop.apollo.gwt.client.dto;
import com.google.gwt.json.client.JSONBoolean;
import com.google.gwt.json.client.JSONNumber;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.client.JSONString;
/**
* Created by ndunn on 3/24/15.
*/
public class UserOrganismPermissionInfo extends Organ... | 1,098 | 27.179487 | 71 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/VariantPropertyInfo.java | package org.bbop.apollo.gwt.client.dto;
import org.bbop.apollo.gwt.shared.FeatureStringEnum;
import com.google.gwt.json.client.JSONString;
import com.google.gwt.json.client.JSONObject;
/**
* Created by deepak.unni3 on 9/16/16.
*/
public class VariantPropertyInfo {
private String tag;
private String value;
... | 1,446 | 31.155556 | 115 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/AnnotationInfoChangeEvent.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.GwtEvent;
import org.bbop.apollo.gwt.client.dto.AnnotationInfo;
/**
* Created by ndunn on 2/2/15.
*/
public class AnnotationInfoChangeEvent extends GwtEvent<AnnotationInfoChangeEventHandler>{
public static Type<AnnotationInfoChangeEve... | 1,323 | 23.518519 | 109 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/AnnotationInfoChangeEventHandler.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.EventHandler;
/**
* Created by ndunn on 1/19/15.
*/
public interface AnnotationInfoChangeEventHandler extends EventHandler{
void onAnnotationChanged(AnnotationInfoChangeEvent annotationInfoChangeEvent);
}
| 293 | 20 | 82 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/ExportEvent.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.GwtEvent;
import org.bbop.apollo.gwt.client.dto.OrganismInfo;
import org.bbop.apollo.gwt.client.dto.SequenceInfo;
import java.util.List;
/**
* Created by ndunn on 1/19/15.
*/
public class ExportEvent extends GwtEvent<ExportEventHandler> {... | 1,211 | 23.24 | 115 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/ExportEventHandler.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.EventHandler;
/**
* Created by ndunn on 1/19/15.
*/
public interface ExportEventHandler extends EventHandler{
void onExport(ExportEvent exportEvent);
}
| 240 | 16.214286 | 57 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/GroupChangeEvent.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.GwtEvent;
import org.bbop.apollo.gwt.client.dto.GroupInfo;
import java.util.List;
/**
* Created by ndunn on 1/19/15.
*/
public class GroupChangeEvent extends GwtEvent<GroupChangeEventHandler>{
public static Type<GroupChangeEventHandl... | 1,672 | 22.9 | 91 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/GroupChangeEventHandler.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.EventHandler;
/**
* Created by ndunn on 1/19/15.
*/
public interface GroupChangeEventHandler extends EventHandler{
void onGroupChanged(GroupChangeEvent authenticationEvent);
}
| 263 | 19.307692 | 62 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/OrganismChangeEvent.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.GwtEvent;
import org.bbop.apollo.gwt.client.dto.OrganismInfo;
import java.util.List;
/**
* Created by ndunn on 1/19/15.
*/
public class OrganismChangeEvent extends GwtEvent<OrganismChangeEventHandler>{
public static Type<OrganismChan... | 1,882 | 24.106667 | 109 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/OrganismChangeEventHandler.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.EventHandler;
/**
* Created by ndunn on 1/19/15.
*/
public interface OrganismChangeEventHandler extends EventHandler{
void onOrganismChanged(OrganismChangeEvent authenticationEvent);
}
| 273 | 18.571429 | 68 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/UserChangeEvent.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.core.client.GWT;
import com.google.gwt.event.shared.GwtEvent;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;
import org.bbop.apollo.gwt.client.dto.OrganismInfo;
import org.bbop.apollo.gwt.client.dto.UserInfo;
im... | 2,360 | 25.233333 | 89 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/event/UserChangeEventHandler.java | package org.bbop.apollo.gwt.client.event;
import com.google.gwt.event.shared.EventHandler;
/**
* Created by ndunn on 1/19/15.
*/
public interface UserChangeEventHandler extends EventHandler{
void onUserChanged(UserChangeEvent authenticationEvent);
}
| 260 | 19.076923 | 61 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/go/GoEvidenceCode.java | package org.bbop.apollo.gwt.client.go;
/**
* Matching order and descriptions here: http://geneontology.org/docs/guide-go-evidence-codes/
*/
public enum GoEvidenceCode {
EXP("experimental evidence used in manual assertion","ECO:0000269"),
IDA("direct assay evidence used in manual assertion","ECO:0000314"),
... | 2,747 | 35.157895 | 95 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/go/GoService.java | package org.bbop.apollo.gwt.client.go;
public class GoService {
}
| 69 | 9 | 38 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/oracles/BiolinkLookup.java | package org.bbop.apollo.gwt.client.oracles;
public enum BiolinkLookup {
GO,
ECO,
RO
}
| 100 | 10.222222 | 43 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/oracles/BiolinkOntologyOracle.java | package org.bbop.apollo.gwt.client.oracles;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.RequestException;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.clie... | 7,068 | 39.164773 | 157 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/oracles/BiolinkSuggestBox.java | package org.bbop.apollo.gwt.client.oracles;
import org.gwtbootstrap3.client.ui.SuggestBox;
public class BiolinkSuggestBox extends SuggestBox {
public BiolinkSuggestBox(BiolinkOntologyOracle oracle) {
super(oracle);
}
@Override
public void showSuggestionList() {
if(getText().length()... | 384 | 19.263158 | 60 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/oracles/ReferenceSequenceOracle.java | package org.bbop.apollo.gwt.client.oracles;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.RequestException;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSON... | 3,011 | 39.16 | 138 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/resources/TableResources.java | package org.bbop.apollo.gwt.client.resources;
import com.google.gwt.resources.client.ClientBundle;
import org.gwtbootstrap3.client.ui.gwt.DataGrid;
/**
* Created by ndunn on 12/19/14.
*/
public class TableResources implements ClientBundle{
// TableCss cell table
public interface TableCss extends DataGrid.R... | 565 | 28.789474 | 66 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/resources/TreeResources.java | package org.bbop.apollo.gwt.client.resources;
import com.google.gwt.resources.client.ClientBundle;
import com.google.gwt.user.cellview.client.CellTree;
public interface TreeResources extends CellTree.Resources {
@ClientBundle.Source("org/bbop/apollo/gwt/client/resources/Tree.css")
public CellTree.Style cellTr... | 333 | 32.4 | 73 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/AnnotationRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.json.client.*;
import org.bbop.apollo.gwt.client.Annotator;
import org.bbop.apo... | 9,919 | 56.674419 | 456 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/AttributeRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.client.JSONString;
import org.bbop.apollo.gwt.client.dto.*;
import org... | 6,420 | 68.043011 | 408 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/AvailableStatusRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.client.JSONString;
import org.bbop.apollo.gwt.client.MainPanel;
import org.bbop.apollo.gwt.client.dto.Annotat... | 5,211 | 56.274725 | 273 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/CommentRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.client.JSONString;
import org.bbop.apollo.gwt.client.MainPanel;
import... | 6,591 | 61.780952 | 273 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/DbXrefRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;... | 6,796 | 61.357798 | 273 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/GeneProductRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;... | 6,238 | 50.139344 | 141 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/GoRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.http.client.*;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.client.JSONParser;
import com.google.gwt.json.client.JSONString;
import com.google.gwt.user.client.ui.Anchor;
import org.bb... | 6,665 | 48.746269 | 144 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/GroupRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.json.client.*;
import com.google.gwt.user.client.Window;
import org.bbop.apollo... | 11,005 | 47.484581 | 164 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/OrganismRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.http.client.*;
import com.google.gwt.json.client.*;
import com.google.gwt.user.client.Window;
import org.bbop.apollo.gwt.client.Annotator;
import org.bbop.apollo.gwt.client.ErrorDialog;
import org.bbop.apollo.gwt.client.LoadingDialog;
import org.bbop.apoll... | 8,042 | 46.035088 | 149 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/ProvenanceRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.json.client.JSONArray;
import com.google.gwt.json.client.JSONObject;... | 6,085 | 46.92126 | 138 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/ProxyRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.http.client.URL;
import com.google.gwt.json.client.*;
import com.google.gwt.use... | 1,222 | 33.942857 | 110 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/RestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.RequestException;
import com.google.gwt.http.client.URL;
import com.google.gwt.json.client.JSONObject;
import org.bbop.apollo.gwt.client.Annota... | 2,850 | 36.513158 | 138 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/SearchRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.client.JSONString;
/**
*
*/
public class SearchRestService {
public static void getTools(RequestCallback requ... | 1,144 | 32.676471 | 129 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/SequenceRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.json.client.*;
import org.bbop.apollo.gwt.client.Annotator;
import org.bbop.apo... | 8,622 | 49.426901 | 219 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/rest/UserRestService.java | package org.bbop.apollo.gwt.client.rest;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.Response;
import com.google.gwt.http.client.URL;
import com.google.gwt.json.client.*;
import com.google.gwt.use... | 13,378 | 43.448505 | 200 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/client/track/TrackConfigurationTemplate.java | package org.bbop.apollo.gwt.client.track;
import com.google.gwt.core.client.GWT;
import com.google.gwt.json.client.JSONObject;
import com.google.gwt.json.client.JSONString;
import com.google.gwt.user.client.Window;
import org.bbop.apollo.gwt.shared.track.TrackTypeEnum;
public class TrackConfigurationTemplate {
p... | 10,164 | 39.823293 | 126 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/ClientTokenGenerator.java | package org.bbop.apollo.gwt.shared;
import java.util.Random;
/**
* Created by ndunn on 4/15/16.
*/
public class ClientTokenGenerator {
private final static Random random = new Random(); // or SecureRandom
public static final int DEFAULT_LENGTH = 20 ;
public static final int MIN_TOKEN_LENGTH = 10;
... | 849 | 26.419355 | 73 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java | package org.bbop.apollo.gwt.shared;
/**
* Created by ndunn on 4/2/15.
*/
public enum FeatureStringEnum {
ID,
FEATURES,
SUPPRESS_HISTORY,
SUPPRESS_EVENTS,
FEATURE_PROPERTY,
ANNOTATION_COUNT,
PARENT,
PARENT_ID,
PARENT_NAME,
USERNAME,
... | 5,684 | 24.958904 | 83 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/GlobalPermissionEnum.java | package org.bbop.apollo.gwt.shared;
import java.util.ArrayList;
import java.util.List;
/**
* The "value" is mapping for Apollo 1
* Relateive ranks are for allowing bulk accesses. For that WRITE access will have additional permissions (including export).
* We will likely be adding additional permissions, as well.... | 1,625 | 24.40625 | 127 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/PermissionEnum.java | package org.bbop.apollo.gwt.shared;
import java.util.ArrayList;
import java.util.List;
/**
* The "value" is mapping for Apollo 1
* Relateive ranks are for allowing bulk accesses. For that WRITE access will have additional permissions (including export).
* We will likely be adding additional permissions, as well.... | 1,882 | 24.794521 | 127 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/geneProduct/GeneProduct.java | package org.bbop.apollo.gwt.shared.geneProduct;
import java.util.ArrayList;
import java.util.List;
public class GeneProduct {
private Long id;
private String feature; // I think this is the gene it refers to? I think the uniquename
private String productName ;
private Reference reference;
private List<Str... | 2,367 | 20.527273 | 90 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/geneProduct/Reference.java | package org.bbop.apollo.gwt.shared.geneProduct;
public class Reference {
private String prefix;
private String lookupId;
public final static String NOT_PROVIDED = "NOT_PROVIDED";
public final static String UNKNOWN = "UNKNOWN";
public Reference(String display) {
assert display.contains("... | 1,039 | 20.666667 | 61 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/geneProduct/WithOrFrom.java | package org.bbop.apollo.gwt.shared.geneProduct;
public class WithOrFrom {
private String prefix;
private String lookupId;
public WithOrFrom(String prefix, String lookup) {
this.prefix = prefix;
this.lookupId = lookup;
}
public WithOrFrom(String lookup) {
this.prefix = loo... | 769 | 19.263158 | 53 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/go/Aspect.java | package org.bbop.apollo.gwt.shared.go;
public enum Aspect {
BP("biological process"),
MF("molecular function"),
CC("cellular component"),
;
private String lookup;
private Aspect(String lookupValue){
this.lookup = lookupValue ;
}
public String getLookup() {
return loo... | 333 | 15.7 | 39 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/go/GoAnnotation.java | package org.bbop.apollo.gwt.shared.go;
import java.util.ArrayList;
import java.util.List;
public class GoAnnotation {
private Long id;
private Aspect aspect;
private String gene; // I think tis is the gene it refers to? I think the uniquename
private String goTerm;
private String goTermLabel;
private S... | 2,972 | 19.93662 | 86 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/go/GoGene.java | package org.bbop.apollo.gwt.shared.go;
/**
* Placeholder for a feature
*/
public class GoGene {
// points to annotation features
private Long id;
private String name ;
private String uniqueName ;
public Long getId() {
return id;
}
public void setId(Long id) {
this.id = ... | 628 | 16 | 50 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/go/GoTerm.java | package org.bbop.apollo.gwt.shared.go;
/**
* Placeholder for a feature with a single annotaiton
*/
public class GoTerm {
// Long id;
private String name;
private String prefix;
private String lookupId;
public GoTerm(String lookup) {
if(lookup.contains(":")){
this.prefix =... | 1,458 | 18.453333 | 53 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/go/Qualifier.java | package org.bbop.apollo.gwt.shared.go;
public enum Qualifier {
NOT,
CONTRIBUTES_TO
}
| 95 | 11 | 38 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/go/Reference.java | package org.bbop.apollo.gwt.shared.go;
public class Reference {
private String prefix;
private String lookupId;
public final static String NOT_PROVIDED = "NOT_PROVIDED";
public final static String UNKNOWN = "UNKNOWN";
public Reference(String display) {
assert display.contains(":");
... | 1,020 | 20.270833 | 61 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/go/WithOrFrom.java | package org.bbop.apollo.gwt.shared.go;
public class WithOrFrom {
private String prefix;
private String lookupId;
public WithOrFrom(String prefix, String lookup) {
this.prefix = prefix;
this.lookupId = lookup;
}
public WithOrFrom(String lookup) {
this.prefix = lookup.split... | 760 | 19.026316 | 53 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/provenance/Provenance.java | package org.bbop.apollo.gwt.shared.provenance;
import java.util.ArrayList;
import java.util.List;
public class Provenance {
private Long id;
private String feature; // I think this is the gene it refers to? I think the uniquename
private String field;
private Reference reference;
private List<String> note... | 2,140 | 20.19802 | 90 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/provenance/ProvenanceField.java | package org.bbop.apollo.gwt.shared.provenance;
public enum ProvenanceField {
TYPE,
SYMBOL,
NAME,
SYNONYM,
DESCRIPTION,
DB_XREF,
ATTRIBUTE,
COMMENT,
}
| 183 | 13.153846 | 46 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/provenance/Reference.java | package org.bbop.apollo.gwt.shared.provenance;
public class Reference {
private String prefix;
private String lookupId;
public final static String NOT_PROVIDED = "NOT_PROVIDED";
public final static String UNKNOWN = "UNKNOWN";
public Reference(String display) {
assert display.contains(":... | 1,038 | 20.645833 | 61 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/provenance/WithOrFrom.java | package org.bbop.apollo.gwt.shared.provenance;
public class WithOrFrom {
private String prefix;
private String lookupId;
public WithOrFrom(String prefix, String lookup) {
this.prefix = prefix;
this.lookupId = lookup;
}
public WithOrFrom(String lookup) {
this.prefix = look... | 768 | 19.236842 | 53 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/sequence/SearchHit.java | package org.bbop.apollo.gwt.shared.sequence;
public class SearchHit {
String id;
Long start;
Long end;
Integer strand;
Double score;
Double significance;
Double identity;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public Long getStart() {
... | 1,143 | 14.888889 | 52 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/sequence/SearchResults.java | package org.bbop.apollo.gwt.shared.sequence;
import java.util.List;
public class SearchResults {
List<SearchHit> searchHitList;
public List<SearchHit> getSearchHitList() {
return searchHitList;
}
public void setSearchHitList(List<SearchHit> searchHitList) {
this.searchHitList = searchHitList;
}
}... | 321 | 17.941176 | 63 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/track/NclistColumnEnum.java | package org.bbop.apollo.gwt.shared.track;
/**
* Created by nathandunn on 12/3/15.
*/
public enum NclistColumnEnum {
START,
END,
STRAND,
SCORE,
TYPE,
SUBFEATURES,
SUBLIST,
SEQ_ID,
ID,
SOURCE,
NAME,
ALIAS,
CHUNK,
PHASE;
private String value;
NclistColu... | 566 | 14.324324 | 94 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/track/SequenceTypeEnum.java | package org.bbop.apollo.gwt.shared.track;
public enum SequenceTypeEnum {
FA("fa"),
FASTA("fasta"),
FNA("fna"),
FA_GZ("fa.gz","gz"),
FASTA_GZ("fasta.gz","gz"),
FNA_GZ("fna.gz","gz"),
FA_ZIP("fa.zip","zip"),
FASTA_ZIP("fasta.zip","zip"),
FNA_ZIP("fna.zip","zip"),
FA_TGZ("fa.tgz"... | 1,884 | 24.821918 | 75 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/track/TrackIndex.java | package org.bbop.apollo.gwt.shared.track;
/**
* Created by nathandunn on 12/2/15.
*/
public class TrackIndex {
// index locations . . .
private Integer start;
private Integer end;
private Integer source;
private Integer strand;
private Integer phase;
private Integer type;
private Inte... | 4,117 | 20.010204 | 130 | java |
Apollo | Apollo-master/src/gwt/org/bbop/apollo/gwt/shared/track/TrackTypeEnum.java | package org.bbop.apollo.gwt.shared.track;
public enum TrackTypeEnum {
BAM("bam","bam.bai"),
BAM_CANVAS("bam","bam.bai"),
BIGWIG_HEAT_MAP("bw"),
BIGWIG_XY("bw"),
VCF("vcf.gz","vcf.gz.tbi"),
VCF_CANVAS("vcf.gz","vcf.gz.tbi"),
// GFF3_JSON(new String[]{"gff","gff3","gff.gz","gff3.gz"}),
// ... | 2,344 | 25.055556 | 97 | java |
Apollo | Apollo-master/src/java/org/bbop/apollo/ImprovedH2Dialect.java | package org.bbop.apollo;
import org.hibernate.dialect.H2Dialect;
public class ImprovedH2Dialect extends H2Dialect {
@Override
public String getDropSequenceString(String sequenceName) {
// Adding the "if exists" clause to avoid warnings
return "drop sequence if exists " + sequenceName;
}
... | 592 | 28.65 | 78 | java |
Apollo | Apollo-master/src/java/org/bbop/apollo/ImprovedPostgresDialect.java | package org.bbop.apollo;
import org.hibernate.dialect.PostgresPlusDialect;
public class ImprovedPostgresDialect extends PostgresPlusDialect {
@Override
public String getDropSequenceString(String sequenceName) {
// Adding the "if exists" clause to avoid warnings
return "drop sequence if exists ... | 618 | 29.95 | 78 | java |
Apollo | Apollo-master/src/java/org/bbop/apollo/Pair.java | package org.bbop.apollo;
public class Pair<T, U> {
private T first;
private U second;
public Pair(T first, U second) {
this.first = first;
this.second = second;
}
public Pair(Pair<T, U> pair) {
this.first = pair.first;
this.second = pair.second;
}
... | 552 | 17.433333 | 71 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/classifiers/DummyClassifier.java | /*
* Copyright 2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in complia... | 3,564 | 29.470085 | 115 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/converters/MapMeshResults.java | /*
* Copyright 2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in complia... | 3,054 | 29.247525 | 140 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/converters/OBOToHier.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 7,254 | 30.681223 | 125 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/core/Graph.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 4,884 | 31.350993 | 96 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/CalculatedMeasures.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 2,843 | 23.730435 | 75 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/ExactAnswer.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 2,644 | 26.268041 | 81 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/PubMedDocument.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 1,538 | 23.428571 | 103 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/Question.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 3,773 | 21.070175 | 75 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/Snippet.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 5,046 | 29.221557 | 126 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/Task1bData.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 22,193 | 37.397924 | 168 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/TaskADataParser.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 4,387 | 29.685315 | 90 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/Triple.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 2,247 | 26.753086 | 90 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/data/PreProcess/ExtractVocabulary.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 15,632 | 31.981013 | 156 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/evaluation/ConfusionMatrix.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 1,723 | 20.822785 | 75 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/evaluation/Evaluator.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 16,349 | 31.248521 | 130 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/evaluation/EvaluatorTask1b.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 32,682 | 32.76343 | 159 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/evaluation/QuestionAnswerEvaluator.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 27,544 | 34.772727 | 212 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/stats/WilcoxonSignedRanksTest.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 3,946 | 20.451087 | 98 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/tools/DrawStatisticsForPubMedData.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 6,069 | 32.351648 | 102 | java |
biobert-pytorch | biobert-pytorch-master/question-answering/scripts/bioasq_eval/flat/BioASQEvaluation/src/tools/MathUtils.java | /*
* Copyright 2013,2014 BioASQ project: FP7/2007-2013, ICT-2011.4.4(d),
* Intelligent Information Management,
* Targeted Competition Framework grant agreement n° 318652.
* www: http://www.bioasq.org
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in co... | 11,015 | 26.402985 | 115 | java |
null | aspiration-study-main/code/org/sas/benchmark/req/spo/AutoRun.java | package org.sas.benchmark.req.spo;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.math.BigDecimal;
import org.femosaa.core.SASAlgorithmAdaptor;
import org.femosaa.seed.FixedSeeder;
i... | 10,054 | 27.244382 | 183 | java |
null | aspiration-study-main/code/org/sas/benchmark/req/spo/BenchmarkDelegate.java | package org.sas.benchmark.req.spo;
import java.util.HashMap;
import org.ssase.model.Delegate;
public class BenchmarkDelegate implements Delegate{
private int obj_index = 0;
public BenchmarkDelegate(int obj_index) {
super();
this.obj_index = obj_index;
}
public double predict(double[] xValue) {
... | 1,717 | 17.673913 | 95 | java |
null | aspiration-study-main/code/org/sas/benchmark/req/spo/LatexRunner.java | package org.sas.benchmark.req.spo;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import org.sas.benchmark.pw.Data.Pack;
public ... | 4,854 | 25.530055 | 143 | java |
null | aspiration-study-main/code/org/sas/benchmark/req/spo/Parser.java | package org.sas.benchmark.req.spo;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.math.BigDecimal;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashMap;
import ja... | 38,120 | 25.751579 | 217 | java |
null | aspiration-study-main/code/org/sas/benchmark/req/spo/PythonRunner.java | package org.sas.benchmark.req.spo;
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.HashMap;
import java.util.Map;
public class PythonRunner {
static... | 9,298 | 69.984733 | 453 | java |
null | aspiration-study-main/code/org/sas/benchmark/req/spo/Simulator.java | package org.sas.benchmark.req.spo;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map.Entry;
import java.util.Set;
import org.femosaa.core.EAConfigure;
import org.femosaa.core.SASA... | 9,067 | 26.149701 | 79 | java |
null | aspiration-study-main/code/org/sas/benchmark/req/spo/VariableOrder.java | package org.sas.benchmark.req.spo;
import java.util.ArrayList;
import java.util.List;
public class VariableOrder {
private static List<String> SS_N = new ArrayList<String>();/*diffcult*/
private static List<String> SS_O = new ArrayList<String>();/*diffcult*/
private static List<String> SS_M = new ArrayList<Strin... | 9,730 | 20.720982 | 193 | java |
null | Causal-Learner-main/Code/common/Feast/FEAST/java/src/main/java/craigacp/feast/Dataset.java | /*
** Dataset.java
**
** Initial Version - 07/01/2017
** Author - Adam Pocock
**
** Part of the FEAture Selection Toolbox (FEAST), please reference
** "Conditional Likelihood Maximisation: A Unifying Framework for Information
** Theoretic Feature Selection"
** G. Brown, A. Pocock, M.-J. Zhao, M. Lujan
** Journal of Ma... | 2,331 | 38.525424 | 83 | java |
null | Causal-Learner-main/Code/common/Feast/FEAST/java/src/main/java/craigacp/feast/FEAST.java | /*
** FEAST.java
**
** Initial Version - 07/01/2017
** Author - Adam Pocock
**
** Part of the FEAture Selection Toolbox (FEAST), please reference
** "Conditional Likelihood Maximisation: A Unifying Framework for Information
** Theoretic Feature Selection"
** G. Brown, A. Pocock, M.-J. Zhao, M. Lujan
** Journal of Mach... | 6,081 | 38.23871 | 134 | java |
null | Causal-Learner-main/Code/common/Feast/FEAST/java/src/main/java/craigacp/feast/FEASTUtil.java | /*
** FEASTUtil.java
**
** Initial Version - 07/01/2017
** Author - Adam Pocock
**
** Part of the FEAture Selection Toolbox (FEAST), please reference
** "Conditional Likelihood Maximisation: A Unifying Framework for Information
** Theoretic Feature Selection"
** G. Brown, A. Pocock, M.-J. Zhao, M. Lujan
** Journal of ... | 4,297 | 30.144928 | 83 | java |
null | Causal-Learner-main/Code/common/Feast/FEAST/java/src/main/java/craigacp/feast/ScoredFeatures.java | /*
** ScoredFeatures.java
**
** Initial Version - 07/01/2017
** Author - Adam Pocock
**
** Part of the FEAture Selection Toolbox (FEAST), please reference
** "Conditional Likelihood Maximisation: A Unifying Framework for Information
** Theoretic Feature Selection"
** G. Brown, A. Pocock, M.-J. Zhao, M. Lujan
** Journa... | 2,497 | 40.633333 | 83 | java |
null | Causal-Learner-main/Code/common/Feast/FEAST/java/src/main/java/craigacp/feast/Test.java | /*
** Test.java
**
** Initial Version - 07/01/2017
** Author - Adam Pocock
**
** Part of the FEAture Selection Toolbox (FEAST), please reference
** "Conditional Likelihood Maximisation: A Unifying Framework for Information
** Theoretic Feature Selection"
** G. Brown, A. Pocock, M.-J. Zhao, M. Lujan
** Journal of Machi... | 13,379 | 41.884615 | 113 | java |
null | Causal-Learner-main/Code/common/Feast/FEAST/java/src/main/java/craigacp/feast/WeightedFEAST.java | /*
** WeightedFEAST.java
**
** Initial Version - 07/01/2017
** Author - Adam Pocock
**
** Part of the Feature Selection Toolbox, please reference
** "Information Theoretic Feature Selection for Cost-Sensitive Problems"
** A. Pocock, N. Edakunni, M.-J. Zhao, M. Lujan, G. Brown
** ArXiv, 2017
**
** Please check www.gith... | 5,342 | 40.742188 | 140 | java |
SeqTrans | SeqTrans-master/Migration/src/collect/AccumulateGroundTruth.java | package collect;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util... | 10,276 | 36.370909 | 122 | java |
SeqTrans | SeqTrans-master/Migration/src/collect/CollectAndroidDiff.java | package collect;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.net.URL;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.ut... | 11,497 | 35.971061 | 122 | java |
SeqTrans | SeqTrans-master/Migration/src/collect/CollectApiDiffs.java | package collect;
import structure.API;
import utils.ReadAPI;
import java.io.*;
import java.util.ArrayList;
import java.util.LinkedHashSet;
public class CollectApiDiffs {
private static LinkedHashSet<API> apis = new LinkedHashSet<API>();
public static void main(String args[]) throws Exception{
String path = "a... | 1,787 | 24.913043 | 69 | java |
SeqTrans | SeqTrans-master/Migration/src/collect/CollectCommitDiff.java | package collect;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.net.URL;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.uti... | 11,142 | 36.267559 | 122 | java |
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