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dl4el
dl4el-master/jrk/java/StrIntMap.java
package jrk.java; import java.util.*; import java.io.Serializable; import gnu.trove.map.hash.*; public class StrIntMap implements Serializable { public TObjectIntHashMap<String> str2int; public ArrayList<String> int2str; StrIntMap() { str2int = new TObjectIntHashMap<>(); int2str = new ArrayL...
1,072
19.634615
84
java
eigenthemes
eigenthemes-master/jrk/java/FreebaseE2W.java
package jrk.java; import java.io.*; import java.util.*; import gnu.trove.map.hash.*; import gnu.trove.map.*; import gnu.trove.set.hash.*; import gnu.trove.set.*; import gnu.trove.iterator.*; public class FreebaseE2W { static int nHop = 0; static StrIntMap dict = null; static StrIntMap entId = null; sta...
13,444
34.474934
105
java
eigenthemes
eigenthemes-master/jrk/java/FreebaseTriples.java
package jrk.java; import java.io.*; import java.util.*; import gnu.trove.map.hash.*; import gnu.trove.map.*; import gnu.trove.set.hash.*; import gnu.trove.set.*; import gnu.trove.iterator.*; public class FreebaseTriples { static Set<String> entSet = null; static final String prefix = "http://rdf.freebase.com/n...
3,136
31.010204
90
java
eigenthemes
eigenthemes-master/jrk/java/Pair.java
package jrk.java; import java.io.Serializable; public class Pair<A, B> implements Serializable { public final A fst; public final B snd; public Pair(A fst, B snd) { this.fst = fst; this.snd = snd; } public A getKey() { return fst; } public B getValue() { ...
1,110
21.22
71
java
eigenthemes
eigenthemes-master/jrk/java/StrIntMap.java
package jrk.java; import java.util.*; import java.io.Serializable; import gnu.trove.map.hash.*; public class StrIntMap implements Serializable { public TObjectIntHashMap<String> str2int; public ArrayList<String> int2str; StrIntMap() { str2int = new TObjectIntHashMap<>(); int2str = new ArrayL...
1,072
19.634615
84
java
null
CoMeT-main/benchmarks/jikes/probes/Dacapo2006Callback.java
import dacapo.Callback; public class Dacapo2006Callback extends Callback { public Dacapo2006Callback() { super(); ProbeMux.init(); } public void startWarmup(String benchmark) { ProbeMux.begin(benchmark, true); super.startWarmup(benchmark); } public void stopWarmup() { super.stopWarmup()...
557
18.241379
50
java
null
CoMeT-main/benchmarks/jikes/probes/DacapoBachCallback.java
import org.dacapo.harness.Callback; import org.dacapo.harness.CommandLineArgs; public class DacapoBachCallback extends Callback { public DacapoBachCallback(CommandLineArgs cla) { super(cla); ProbeMux.init(); } public void start(String benchmark) { ProbeMux.begin(benchmark, isWarmup()); super.st...
524
20
50
java
null
CoMeT-main/benchmarks/jikes/probes/MMTkProbe.java
import java.lang.reflect.*; public class MMTkProbe implements Probe { private Method beginMethod; private Method endMethod; public void init() { try { Class harnessClass = Class.forName("org.mmtk.plan.Plan"); beginMethod = harnessClass.getMethod("harnessBegin"); endMethod = harnessClass.ge...
1,138
24.886364
100
java
null
CoMeT-main/benchmarks/jikes/probes/PJBB2005Callback.java
import harness.Callback; public class PJBB2005Callback extends Callback { public PJBB2005Callback() { super(); ProbeMux.init(); } public void begin(int iteration, boolean warmup) { ProbeMux.begin("pjbb2005", warmup); super.begin(iteration, warmup); } public void end(int iteration, boolean ...
433
19.666667
52
java
null
CoMeT-main/benchmarks/jikes/probes/Probe.java
public interface Probe { public void init(); public void begin(String benchmark, int iteration, boolean warmup); public void end(String benchmark, int iteration, boolean warmup); public void report(String benchmark, int iteration, boolean warmup); public void cleanup(); }
285
30.777778
70
java
null
CoMeT-main/benchmarks/jikes/probes/ProbeMux.java
import java.io.*; import java.lang.reflect.*; public class ProbeMux { private static Probe[] probes; private static int iteration; private static String benchmark; public static void init() { String probesProperty = System.getProperty("probes"); if (probesProperty == null) { System.err.println("...
1,800
28.52459
100
java
null
CoMeT-main/benchmarks/jikes/probes/ReplayProbe.java
import java.lang.reflect.*; public class ReplayProbe implements Probe { private Method compileAll; private static final String PRECOMPILE_CLASS = "org.jikesrvm.adaptive.recompilation.BulkCompile"; private static final String PRECOMPILE_METHOD = "compileAllMethods"; public void init() { try { Class p...
1,084
32.90625
99
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/Main.java
package stationary; import static picocli.CommandLine.Command; import static picocli.CommandLine.Option; import static picocli.CommandLine.Parameters; import static picocli.CommandLine.ParentCommand; import de.tum.in.naturals.set.NatBitSets; import de.tum.in.naturals.set.RoaringNatBitSetFactory; import de.tum.in.prob...
11,117
38.565836
136
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/StationaryDistributionEstimator.java
package stationary; import de.tum.in.naturals.map.Nat2ObjectDenseArrayMap; import de.tum.in.probmodels.explorer.DefaultExplorer; import de.tum.in.probmodels.explorer.SelfLoopHandling; import de.tum.in.probmodels.generator.Generator; import de.tum.in.probmodels.graph.Component; import de.tum.in.probmodels.graph.SccDeco...
22,354
42.156371
140
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/StationaryDistributionSolver.java
package stationary; import de.tum.in.naturals.bitset.BitSets; import de.tum.in.probmodels.explorer.DefaultExplorer; import de.tum.in.probmodels.explorer.SelfLoopHandling; import de.tum.in.probmodels.generator.Generator; import de.tum.in.probmodels.graph.BsccComponentAnalyser; import de.tum.in.probmodels.graph.Componen...
3,681
41.321839
139
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/component/AbsorbingComponent.java
package stationary.component; import de.tum.in.probmodels.values.Bounds; import it.unimi.dsi.fastutil.ints.IntSet; public final class AbsorbingComponent extends BottomComponent { private final int state; public AbsorbingComponent(int index, int state) { super(index); this.state = state; } @Override ...
848
15.98
63
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/component/BottomComponent.java
package stationary.component; import de.tum.in.probmodels.values.Bounds; import it.unimi.dsi.fastutil.HashCommon; import it.unimi.dsi.fastutil.ints.IntSet; public abstract class BottomComponent { public final int index; private int visits = 0; public BottomComponent(int index) { this.index = index; } ...
1,025
17.654545
48
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/component/NontrivialApproximatingComponent.java
package stationary.component; import de.tum.in.probmodels.graph.Component; import de.tum.in.probmodels.model.distribution.Distribution; import de.tum.in.probmodels.util.Util; import de.tum.in.probmodels.values.Bounds; import it.unimi.dsi.fastutil.ints.Int2IntOpenHashMap; import it.unimi.dsi.fastutil.ints.IntHeapPriori...
5,965
30.072917
111
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/component/NontrivialApproximationSolvingComponent.java
package stationary.component; import de.tum.in.probmodels.graph.Component; import de.tum.in.probmodels.model.distribution.Distribution; import de.tum.in.probmodels.util.Util; import de.tum.in.probmodels.values.Bounds; import it.unimi.dsi.fastutil.ints.Int2IntOpenHashMap; import it.unimi.dsi.fastutil.ints.Int2ObjectMap...
4,112
30.396947
127
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/component/NontrivialComponent.java
package stationary.component; import de.tum.in.probmodels.graph.Component; import it.unimi.dsi.fastutil.ints.IntSet; import it.unimi.dsi.fastutil.ints.IntSets; import java.time.Duration; public abstract class NontrivialComponent extends BottomComponent { private long updateTime = 0L; final Component component; ...
1,178
22.58
129
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/component/NontrivialSolvingComponent.java
package stationary.component; import de.tum.in.naturals.Indices; import de.tum.in.probmodels.graph.Component; import de.tum.in.probmodels.model.distribution.Distribution; import de.tum.in.probmodels.util.Util; import de.tum.in.probmodels.values.Bounds; import it.unimi.dsi.fastutil.ints.Int2DoubleMap; import it.unimi.d...
2,682
32.123457
103
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/util/Check.java
package stationary.util; import de.tum.in.probmodels.model.distribution.Distribution; import de.tum.in.probmodels.util.Util; import it.unimi.dsi.fastutil.ints.Int2DoubleMap; import it.unimi.dsi.fastutil.ints.Int2DoubleOpenHashMap; import it.unimi.dsi.fastutil.ints.IntSet; import java.util.function.IntFunction; import ...
1,305
41.129032
142
java
stationary-distribution-sampling
stationary-distribution-sampling-master/src/main/java/stationary/util/FrequencyRecord.java
package stationary.util; public record FrequencyRecord(double frequency, double error) {}
91
22
64
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/AlignmentParsingException.java
package org.bbop.apollo.sequence.search; public class AlignmentParsingException extends Exception { private static final long serialVersionUID = 1L; public AlignmentParsingException(String error) { super(error); } }
244
19.416667
58
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/SequenceSearchTool.java
package org.bbop.apollo.sequence.search; import java.util.Collection; import org.bbop.apollo.sequence.search.blast.BlastAlignment; import org.codehaus.groovy.grails.web.json.JSONObject; public abstract class SequenceSearchTool { public abstract void parseConfiguration(JSONObject config) throws SequenceSearchToo...
653
30.142857
142
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/SequenceSearchToolException.java
package org.bbop.apollo.sequence.search; public class SequenceSearchToolException extends Exception { private static final long serialVersionUID = 1L; public SequenceSearchToolException(String message) { super(message); } public SequenceSearchToolException(String message, Throwable cause...
368
22.0625
73
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/blast/BlastAlignment.java
package org.bbop.apollo.sequence.search.blast; public class BlastAlignment { private String queryId; private String subjectId; private double percentId; private int alignmentLength; private int numMismatches; private int numGaps; private int queryStrand; private int subjectStrand; ...
2,855
24.052632
143
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/blast/BlastCommandLine.java
package org.bbop.apollo.sequence.search.blast; import org.bbop.apollo.sequence.search.AlignmentParsingException; import org.bbop.apollo.sequence.search.SequenceSearchTool; import org.bbop.apollo.sequence.search.SequenceSearchToolException; import org.bbop.apollo.sequence.search.blast.BlastAlignment; import org.bbop.ap...
5,977
37.076433
134
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/blast/TabDelimittedAlignment.java
package org.bbop.apollo.sequence.search.blast; import org.bbop.apollo.sequence.search.AlignmentParsingException; public class TabDelimittedAlignment extends BlastAlignment { private final static int EXPECTED_NUM_FIELDS = 12; private final static String DELIMITER = "\t"; public TabDelimittedAlignment(Str...
1,917
38.958333
143
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/blat/BlatCommandLine.java
package org.bbop.apollo.sequence.search.blat; import org.bbop.apollo.sequence.search.AlignmentParsingException; import org.bbop.apollo.sequence.search.SequenceSearchTool; import org.bbop.apollo.sequence.search.SequenceSearchToolException; import org.bbop.apollo.sequence.search.blast.BlastAlignment; import org.bbop.apo...
5,779
36.532468
134
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/blat/BlatCommandLineNucleotideToNucleotide.java
package org.bbop.apollo.sequence.search.blat; public class BlatCommandLineNucleotideToNucleotide extends BlatCommandLine { }
127
20.333333
76
java
Apollo
Apollo-master/src/groovy/org/bbop/apollo/sequence/search/blat/BlatCommandLineProteinToNucleotide.java
package org.bbop.apollo.sequence.search.blat; public class BlatCommandLineProteinToNucleotide extends BlatCommandLine { public BlatCommandLineProteinToNucleotide() { blatOptions = new String[]{ "-t=dnax", "-q=prot" }; } }
245
23.6
73
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/AlleleInfoPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.EditTextCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.cell.client.TextCell; import com.google.gwt.core.client.GWT; import com.google.gwt.dom.client.DivElement; import com.google.gwt.event.dom.client.ClickEvent; import c...
18,986
44.099762
146
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/AnnotationContainerWidget.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.json.client.JSONObject; import com.google.gwt.user.client.ui.HTML; /** * Created by ndunn on 1/8/15. */ public class AnnotationContainerWidget extends HTML{ private JSONObject internalData ; public AnnotationC...
1,277
28.045455
106
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/Annotator.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.EntryPoint; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.Scheduler; import com.google.gwt.dom.client.Style; import com.google.gwt.event.shared.EventBus; import com.google.gwt.event.shared.SimpleEventBus; import com.google...
7,032
38.511236
131
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/AnnotatorPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.ClickableTextCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.cell.client.NumberCell; import com.google.gwt.cell.client.TextCell; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.Scheduler; import c...
58,638
43.322751
266
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/AttributePanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.EditTextCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ChangeEvent; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.KeyUpE...
17,659
37.72807
152
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/CommentPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.EditTextCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ChangeEvent; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.KeyUpE...
13,628
37.94
141
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/DateFormatService.java
package org.bbop.apollo.gwt.client; import com.google.gwt.i18n.client.DateTimeFormat; import java.util.Date; public class DateFormatService { private static DateTimeFormat outputFormatDate = DateTimeFormat.getFormat("MMM dd, yyyy"); private static DateTimeFormat outputFormatDateTime = DateTimeFormat.getForma...
748
30.208333
106
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/DbXrefPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.EditTextCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.KeyUpEvent; import com.google.gwt.http.client.Request; imp...
17,677
37.347072
227
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/ErrorDialog.java
package org.bbop.apollo.gwt.client; import com.google.gwt.dom.client.NativeEvent; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.ClickHandler; import com.google.gwt.event.dom.client.KeyCodes; import com.google.gwt.user.client.Event.NativePreviewEvent; import com.google.gwt.us...
1,724
28.741379
122
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/ExonDetailPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.NumberCell; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.BlurEvent; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.KeyCodes; import com.google.gwt.event.dom.client.KeyDownEv...
14,882
36.394472
167
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/ExportPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.ClickHandler; import com.google.gwt.user.client.Window; import com.google.gwt.user.client.ui.HTML; import org.bbop.apollo.gwt.client.dto.OrganismInfo; i...
12,880
33.07672
138
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ChangeEvent; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.logical.shared.SelectionEvent; import com.google.gwt.event.logical.shared.SelectionHandler; import com.google.gwt...
17,495
38.58371
234
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/GeneProductPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.*; import com.google.gwt.event.logical.shared.SelectionEvent; import com.google.gwt.event.logical.shared.SelectionHandler; import com.google.gwt.http.client.Request; import com.google.gwt.http.client.Reque...
20,498
33.510101
235
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/GoPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.*; import com.google.gwt.event.logical.shared.SelectionEvent; import com.google.gwt.event.logical.shared.SelectionHandler; import com.google.gwt.http.client.Request; import com.google.gwt.http.client.Reque...
26,459
35
235
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/GroupPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.CheckboxCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.cell.client.NumberCell; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.Scheduler; import com.google.gwt.event.dom.client.ClickEvent; import...
23,336
38.892308
168
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/LinkDialog.java
package org.bbop.apollo.gwt.client; import com.google.gwt.user.client.ui.HTML; import org.gwtbootstrap3.client.ui.Modal; import org.gwtbootstrap3.client.ui.ModalBody; import org.gwtbootstrap3.client.ui.constants.ModalBackdrop; /** * Created by ndunn on 4/30/15. */ public class LinkDialog extends Modal { publi...
815
24.5
78
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/LoadingDialog.java
package org.bbop.apollo.gwt.client; import com.google.gwt.user.client.ui.HTML; import com.google.gwt.user.client.ui.PopupPanel; import com.google.gwt.user.client.ui.VerticalPanel; import org.gwtbootstrap3.client.ui.Modal; import org.gwtbootstrap3.client.ui.ModalBody; import org.gwtbootstrap3.client.ui.constants.ModalB...
1,144
24.444444
78
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/LoginDialog.java
package org.bbop.apollo.gwt.client; import com.google.gwt.uibinder.client.UiBinder; import com.google.gwt.uibinder.client.UiField; import com.google.gwt.uibinder.client.UiHandler; import com.google.gwt.core.client.Scheduler; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.Click...
3,006
27.913462
93
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/MainPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.JavaScriptObject; import com.google.gwt.core.client.Scheduler; import com.google.gwt.dom.client.Element; import com.google.gwt.event.dom.client.ChangeEvent; import com.google.gwt.event.dom.client.ClickEvent; im...
52,554
37.361314
229
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/MutableBoolean.java
package org.bbop.apollo.gwt.client; /** * Created by nathandunn on 3/21/16. */ public class MutableBoolean { private Boolean booleanValue ; public MutableBoolean(boolean booleanValue){ this.booleanValue = booleanValue ; } public Boolean getBooleanValue() { return booleanValue; ...
429
18.545455
55
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/OrganismPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.NumberCell; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.*; import com.google.gwt.http.client.Request; import com.google.gwt.http.client.RequestCallback; import com.google.gwt.http.client.Response; import com.google....
32,097
40.151282
404
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/PreferencePanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.http.client.*; import com.google.gwt.uibinder.client.UiBinder; import com.google.gwt.uibinder.client.UiField; import com.google.gwt.uibinder.client.UiHandler; import com.g...
2,561
36.130435
123
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/ProvenancePanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.*; import com.google.gwt.event.logical.shared.SelectionEvent; import com.google.gwt.event.logical.shared.SelectionHandler; import com.google.gwt.http.client.Request; import com.google.gwt.http.client.Reque...
20,436
32.836093
235
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/RegisterDialog.java
package org.bbop.apollo.gwt.client; import com.google.gwt.dom.client.NativeEvent; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.ClickHandler; import com.google.gwt.event.dom.client.KeyCodes; import com.google.gwt.http.client.Request; import com.google.gwt.http.client.Request...
5,552
37.832168
166
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/RepeatRegionDetailPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.i18n.client.HasDirection; import com.google.gwt.uibinder.client.UiBinder; import org.bbop.apollo.gwt.client.dto.AnnotationInfo; import com.google.gwt.event.dom.client.Chan...
12,430
39.229773
234
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/SearchPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.cell.client.NumberCell; import com.google.gwt.cell.client.SelectionCell; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.http.client.Request; import ...
20,812
48.554762
3,890
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/SequencePanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.NumberCell; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.Scheduler; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.DoubleClickEvent; import com.google.gwt.event.dom.client.Double...
26,039
41.899506
268
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/SuggestedGeneProductOracle.java
package org.bbop.apollo.gwt.client; 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.JSONParser; import com.google.gwt.user.client.ui.Su...
2,928
33.458824
130
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/SuggestedNameOracle.java
package org.bbop.apollo.gwt.client; 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.JSONObject; ...
3,840
34.897196
138
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/TrackPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.Scheduler; import com.google.gwt.dom.client.Document; import com.google.gwt.dom.client.Element; import com.google.gwt.event.dom.client.*; import com.google.gwt.event.logical.shared.ValueChangeEvent; import com....
37,509
36.965587
202
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ChangeEvent; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.http.client.Request; import com.google.gwt.http.client.RequestCallback; import com.google.gwt.http.client.Response; imp...
16,483
39.204878
234
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/UploadDialog.java
package org.bbop.apollo.gwt.client; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.ClickHandler; 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.JSONArr...
15,600
65.387234
871
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/UrlDialogBox.java
package org.bbop.apollo.gwt.client; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.ClickHandler; import com.google.gwt.user.client.ui.*; /** * Created by ndunn on 4/8/15. */ public class UrlDialogBox extends DialogBox{ private VerticalPanel panel = new VerticalPanel()...
1,194
27.452381
96
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/UserPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.CheckboxCell; import com.google.gwt.cell.client.ClickableTextCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.Scheduler; import com.google.gwt.event.dom.client.ChangeEvent...
32,476
40.006313
181
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/VariantAllelesPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.cell.client.TextCell; import com.google.gwt.core.client.GWT; import com.google.gwt.http.client.*; import com.google.gwt.json.client.*; import com.google.gwt.uibinder.client.UiBinder; import com.google.gwt.uibinder...
19,264
44.223005
154
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/VariantDetailPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.core.client.GWT; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.i18n.client.HasDirection; import com.google.gwt.uibinder.client.UiBinder; import org.bbop.apollo.gwt.client.dto.AnnotationInfo; import com.google.gwt.event.dom.client.Chan...
12,958
39.623824
234
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/VariantInfoPanel.java
package org.bbop.apollo.gwt.client; import com.google.gwt.cell.client.EditTextCell; import com.google.gwt.cell.client.FieldUpdater; import com.google.gwt.core.client.GWT; import com.google.gwt.dom.client.DivElement; import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.FocusEvent; i...
17,177
43.851175
149
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/WebApolloSimplePager.java
package org.bbop.apollo.gwt.client; import com.google.gwt.user.cellview.client.SimplePager; import com.google.gwt.view.client.Range; public class WebApolloSimplePager extends SimplePager { public WebApolloSimplePager() { this.setRangeLimited(true); } public WebApolloSimplePager(TextLocation lo...
1,242
31.710526
157
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/comparators/AlphanumericSorter.java
package org.bbop.apollo.gwt.client.comparators; import java.util.Comparator; /** * Created by ndunn on 1/27/15. * Inspired / borrowed from: http://sanjaal.com/java/206/java-data-structure/alphanumeric-string-sorting-in-java-implementation/ */ public class AlphanumericSorter implements Comparator<String> { @O...
2,821
28.092784
129
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/comparators/OrganismComparator.java
package org.bbop.apollo.gwt.client.comparators; import org.bbop.apollo.gwt.client.dto.OrganismInfo; import java.util.Comparator; public class OrganismComparator implements Comparator<OrganismInfo> { @Override public int compare(OrganismInfo o1, OrganismInfo o2) { if(o1.getGenus()==null && o2.getGenus()!=null...
1,101
39.814815
113
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AllelePropertyInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.shared.FeatureStringEnum; public class AllelePropertyInfo { private String variant; private String bases; private String tag; private String v...
2,151
28.081081
117
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AlternateAlleleInfo.java
package org.bbop.apollo.gwt.client.dto; 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.shared.FeatureStringEnum; import com.google.gwt.core.client.GWT; import java.util.*; /** * Created by deepak.unn...
5,872
43.157895
241
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONArray; import com.google.gwt.json.client.JSONObject; import org.bbop.apollo.gwt.shared.go.GoAnnotation; import java.util.*; /** * Created by ndunn on 1/27/15. */ public class AnnotationInfo { private String uniqueName; private St...
9,944
28.686567
301
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AnnotationInfoConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONArray; import com.google.gwt.json.client.JSONObject; import org.bbop.apollo.gwt.client.VariantDetailPanel; import org.bbop.apollo.gwt.shared.FeatureStringEnum; import java.util.ArrayList; import java.util.List; /** * Created by nathandunn...
6,554
56
185
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AppInfoConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; import com.google.gwt.user.client.Window; import org.bbop.apollo.gwt.shared.FeatureStringEnum; import java.util.List; /** * Created by ndunn on 3/31/15. */ public class AppInfoConverter { public static AppStateInfo convertFr...
1,518
38.973684
138
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AppStateInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONArray; import com.google.gwt.json.client.JSONNumber; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.shared.FeatureStringEnum; import java.util.List; /** * Created by ...
3,316
29.154545
117
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AttributeInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.shared.FeatureStringEnum; /** * Created by deepak.unni3 on 9/16/16. */ public class AttributeInfo { private String tag; private String value; p...
1,542
29.86
115
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/AttributeInfoConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.core.client.GWT; 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.shared.FeatureStringEnum; import java.util.ArrayList; import java.util.List...
1,427
38.666667
105
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/CommentInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.shared.FeatureStringEnum; /** * Created by deepak.unni3 on 9/16/16. */ public class CommentInfo { private String comment; public CommentInfo() { ...
1,173
26.302326
117
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/CommentInfoConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.core.client.GWT; 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.shared.FeatureStringEnum; import java.util.ArrayList; import java.util.List...
1,487
35.292683
110
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/DbXRefInfoConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.core.client.GWT; 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.shared.FeatureStringEnum; import java.util.ArrayList; import java.util.List...
1,747
39.651163
105
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/DbXrefInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.shared.FeatureStringEnum; /** * Created by deepak.unni3 on 9/16/16. */ public class DbXrefInfo { private String tag; private String value; publ...
1,530
29.62
115
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/ExportInfo.java
package org.bbop.apollo.gwt.client.dto; import java.util.List; /** * Created by ndunn on 3/31/15. */ public class ExportInfo { private String type ; private List<SequenceInfo> sequenceInfoList ; private String generatedUrl ; public String getType() { return type; } public void set...
778
19.5
74
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/GeneProductConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.*; import org.bbop.apollo.gwt.shared.geneProduct.Reference; import org.bbop.apollo.gwt.shared.geneProduct.WithOrFrom; import org.bbop.apollo.gwt.shared.geneProduct.GeneProduct; import java.util.ArrayList; import java.util.List; /** * Created ...
3,825
38.854167
131
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/GoAnnotationConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.core.client.GWT; import com.google.gwt.json.client.*; import org.bbop.apollo.gwt.shared.go.Aspect; import org.bbop.apollo.gwt.shared.go.GoAnnotation; import org.bbop.apollo.gwt.shared.go.Reference; import org.bbop.apollo.gwt.shared.go.WithOrFrom; import ja...
4,482
40.897196
121
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/GroupInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONArray; import com.google.gwt.json.client.JSONNumber; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import java.util.HashMap; import java.util.List; import java.util.Map; /** * Created by ndunn...
4,167
29.202899
106
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/GroupOrganismPermissionInfo.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 GroupOrganismPermissionInfo extends Orga...
1,110
26.775
72
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/HasJSON.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; /** * Created by ndunn on 4/17/15. * TODO: switch the name . . horrible */ public interface HasJSON { JSONObject toJSON() ; }
225
15.142857
45
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/OrganismInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.core.client.GWT; import com.google.gwt.core.client.JsonUtils; import com.google.gwt.json.client.JSONBoolean; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import com.google.gwt.user.client.Window; import java.u...
5,608
22.273859
99
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/OrganismInfoConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.core.client.GWT; import com.google.gwt.json.client.*; import com.google.gwt.user.client.Window; import java.util.ArrayList; import java.util.List; /** * Created by ndunn on 3/31/15. */ public class OrganismInfoConverter { public static OrganismIn...
5,554
43.087302
131
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/OrganismPermissionInfo.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; import org.bbop.apollo.gwt.shared.PermissionEnum; /** * Created by ndunn on 3/24/15. */ abs...
1,655
20.506494
57
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/ProvenanceConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.core.client.GWT; import com.google.gwt.json.client.*; import org.bbop.apollo.gwt.shared.provenance.Provenance; import org.bbop.apollo.gwt.shared.provenance.Reference; import org.bbop.apollo.gwt.shared.provenance.WithOrFrom; import java.util.ArrayList; impo...
3,899
38.393939
130
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/SequenceInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONNumber; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.client.comparators.AlphanumericSorter; /** * Created by ndunn on 12/18/14. */ public class SequenceInfo impleme...
3,152
21.361702
77
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/SequenceInfoConverter.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONArray; import com.google.gwt.json.client.JSONObject; import java.util.ArrayList; import java.util.List; /** * Created by ndunn on 4/20/15. */ public class SequenceInfoConverter { public static SequenceInfo convertFromJson(JSONObject ...
1,980
41.148936
134
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/StatusInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.shared.FeatureStringEnum; /** * Created by deepak.unni3 on 9/16/16. */ public class StatusInfo { private String status; public StatusInfo() { }...
1,158
25.953488
117
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/TrackInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.json.client.JSONObject; /** * Created by ndunn on 12/18/14. */ public class TrackInfo implements Comparable<TrackInfo> { public static final String TRACK_UNCATEGORIZED = "Uncategorized"; private String name; private String label; priva...
3,681
23.546667
131
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/UserInfo.java
package org.bbop.apollo.gwt.client.dto; import com.google.gwt.http.client.URL; import com.google.gwt.json.client.JSONArray; import com.google.gwt.json.client.JSONNumber; import com.google.gwt.json.client.JSONObject; import com.google.gwt.json.client.JSONString; import org.bbop.apollo.gwt.shared.PermissionEnum; import...
6,240
28.861244
105
java
Apollo
Apollo-master/src/gwt/org/bbop/apollo/gwt/client/dto/UserInfoConverter.java
package org.bbop.apollo.gwt.client.dto; 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.user.client.Window; import org.bbop.apollo.gwt.shared.FeatureStringEnum; import org.gwtbootstrap3.extras.bootbox.client....
5,681
46.35
161
java