Merge branch 'release-1.4'

gotrack/pom.xml

@@ -4,7 +4,7 @@
     <groupId>ubc.pavlab</groupId>
     <artifactId>gotrack</artifactId>
     <packaging>war</packaging>
-    <version>1.3</version>
+    <version>1.4</version>
     <name>gotrack</name>
     <url>http://maven.apache.org</url>
 

gotrack/src/main/java/ubc/pavlab/gotrack/beans/GraphFactory.java

@@ -31,7 +31,11 @@ public class GraphFactory implements Serializable {
      * Entry point for fetching data necessary to create an ancestry DAG for a term
      */
     public void fetchGraph( GeneOntologyTerm term ) {
-        Graph graph = Graph.fromGO( term );
+        fetchGraph( term, true );
+    }
+
+    public void fetchGraph( GeneOntologyTerm term, boolean showChildren ) {
+        Graph graph = Graph.fromGO( term, showChildren );
         RequestContext.getCurrentInstance().addCallbackParam( "graph_data", graph.getJsonString() );
     }
 

gotrack/src/main/java/ubc/pavlab/gotrack/beans/TermView.java

@@ -21,7 +21,6 @@
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
-import com.google.common.collect.Sets;
 import com.google.gson.Gson;
 import lombok.Getter;
 import lombok.Setter;
@@ -32,6 +31,7 @@
 import ubc.pavlab.gotrack.model.*;
 import ubc.pavlab.gotrack.model.chart.ChartValues;
 import ubc.pavlab.gotrack.model.chart.Series;
+import ubc.pavlab.gotrack.model.chart.SeriesExtra;
 import ubc.pavlab.gotrack.model.go.GeneOntologyTerm;
 import ubc.pavlab.gotrack.model.go.Relation;
 import ubc.pavlab.gotrack.model.go.RelationshipType;
@@ -56,7 +56,6 @@
  * Backing bean for the term tracking functionality.
  *
  * @author mjacobson
- * @version $Id$
  */
 @Log4j
 @Named
@@ -134,7 +133,8 @@ public String init() throws TermNotFoundException {
     }
 
     public boolean displayInferred() {
-        return cache.getInferredAnnotationCount( cache.getCurrentEditions( session.getSpecies() ), currentTerm ) <= MAX_INFERRED_GENES_DISPLAY_COUNT;
+        Integer cnt = cache.getInferredAnnotationCount( cache.getCurrentEditions( session.getSpecies() ), currentTerm );
+        return cnt == null || cnt  <= MAX_INFERRED_GENES_DISPLAY_COUNT;
     }
 
     public Map<Gene, Boolean> fetchCurrentGenesMap() {
@@ -162,29 +162,6 @@ public List<Relation<GeneOntologyTerm>> getChildTerms( GeneOntologyTerm term ) {
                 .collect( Collectors.toList() );
     }
 
-    /**
-     * entry point to fetch data to create the most current ancestry DAG
-     */
-    public void fetchDAGData() {
-
-//        Collection<String> goids = Sets.newHashSet("GO:0005783","GO:0005886","GO:0005887","GO:0008021","GO:0009986","GO:0014069","GO:0017146","GO:0030054","GO:0030425","GO:0043005","GO:0043083","GO:0043195","GO:0043197","GO:0045202","GO:0045211","GO:0060076");
-
-
-        Set<GeneOntologyTerm> terms = Sets.newHashSet();
-        terms.add( currentTerm );
-
-//        for ( String goid : goids ) {
-//            GeneOntologyTerm t = cache.getCurrentTerm( goid );
-//            if (t != null) {
-//                terms.add( t );
-//            }
-//        }
-
-        Graph eles = Graph.fromGO( terms );
-
-        RequestContext.getCurrentInstance().addCallbackParam( "graph_data", eles.getJsonString() );
-    }
-
     private Map<String, Object> createHCCallbackParamMap( ChartValues chart ) {
         Map<String, Object> hcGsonMap = Maps.newHashMap();
         hcGsonMap.put( "success", true );
@@ -286,7 +263,8 @@ public void fetchGeneChart() {
 
             if ( eds != null ) {
 
-                Series s = new Series( allSpecies ? sp.getScientificName() : "All" );
+                SeriesExtra s = new SeriesExtra( allSpecies ? sp.getScientificName() : "All" );
+                s.putExtra( "visible", false );
                 Series s2 = new Series( allSpecies ? sp.getScientificName() + " Direct" : "Direct Only" );
                 series.put( sp, s );
                 directSeries.put( sp, s2 );

gotrack/src/main/java/ubc/pavlab/gotrack/beans/Trends.java

@@ -28,6 +28,7 @@
 import ubc.pavlab.gotrack.model.Species;
 import ubc.pavlab.gotrack.model.chart.ChartValues;
 import ubc.pavlab.gotrack.model.chart.Series;
+import ubc.pavlab.gotrack.model.chart.SeriesExtra;
 import ubc.pavlab.gotrack.model.go.GeneOntology;
 
 import javax.annotation.PostConstruct;
@@ -81,21 +82,18 @@ public void postConstruct() {
             multifunctionalityChart.setSubtitle( sp.getScientificName() );
             geneJaccardChart.setSubtitle( sp.getScientificName() );
 
-            geneCountChart.setMin( 0 );
-            termsForGeneChart.setMin( 0 );
             geneJaccardChart.setMin( 0 );
-            inferredGenesForTermChart.setMin( 0 );
-            multifunctionalityChart.setMin( 0 );
-
             geneJaccardChart.setMax( 1 );
 
             Series geneCountSeries = new Series( "Distinct Genes" );
             Series directTermsForGeneSeries = new Series( "Direct" );
-            Series inferredTermsForGeneSeries = new Series( "Inferred" );
+            SeriesExtra inferredTermsForGeneSeries = new SeriesExtra( "Inferred" );
+            inferredTermsForGeneSeries.putExtra( "visible", false );
             Series inferredGenesForTermSeries = new Series( "Group Size" );
             Series multifunctionalitySeries = new Series( "Multifunctionality" );
             Series geneDirectJaccardSeries = new Series( "Direct" );
-            Series geneInferredJaccardSeries = new Series( "Inferred" );
+            SeriesExtra geneInferredJaccardSeries = new SeriesExtra( "Inferred" );
+            geneInferredJaccardSeries.putExtra( "visible", false );
 
             for ( Edition ed : cache.getAllEditions( sp ) ) {
 

gotrack/src/main/java/ubc/pavlab/gotrack/beans/service/AnnotationService.java

@@ -528,6 +528,12 @@ public Stream<Gene> fetchDirectGenes( GeneOntologyTerm term, Edition edition ) {
         } ).filter( Objects::nonNull );
     }
 
+    public Stream<Tuples.Tuple2<Gene, GeneOntologyTerm>> streamEditionSimple(Species species, Edition edition) {
+        return annotationDAO.simpleAnnotationSingleEditionCompleteSpecies( species, edition).stream()
+                .map( tup -> new Tuples.Tuple2<>( cache.getCurrentGene( tup.getT1() ), cache.getTerm( edition, tup.getT2()) ) )
+                .filter( t -> t.getT1() != null && t.getT2() != null && t.getT1().getSpecies().equals( species ) );
+    }
+
     public Map<Gene, Set<GeneOntologyTerm>> fetchEditionSimple(Species species, Edition edition) {
 
         List<Tuples.Tuple2<String, String>> resultset = annotationDAO.simpleAnnotationSingleEditionCompleteSpecies( species, edition);

gotrack/src/main/java/ubc/pavlab/gotrack/model/Annotation.java

@@ -19,65 +19,23 @@
 
 package ubc.pavlab.gotrack.model;
 
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.RequiredArgsConstructor;
 import ubc.pavlab.gotrack.model.go.GeneOntologyTerm;
 
 /**
  * Represents an annotation, only makes sense when used to connect a {@link GeneOntologyTerm} and {@link Gene}
  * 
  * @author mjacobson
- * @version $Id$
  */
+@Getter
+@RequiredArgsConstructor
+@EqualsAndHashCode
 public final class Annotation {
 
     private final String qualifier;
     private final Evidence evidence;
     private final String reference;
 
-    public Annotation( String qualifier, Evidence evidence, String reference ) {
-        super();
-        this.qualifier = qualifier;
-        this.evidence = evidence;
-        this.reference = reference;
-    }
-
-    public String getQualifier() {
-        return qualifier;
-    }
-
-    public Evidence getEvidence() {
-        return evidence;
-    }
-
-    public String getReference() {
-        return reference;
-    }
-
-    @Override
-    public int hashCode() {
-        final int prime = 31;
-        int result = 1;
-        result = prime * result + ( ( evidence == null ) ? 0 : evidence.hashCode() );
-        result = prime * result + ( ( qualifier == null ) ? 0 : qualifier.hashCode() );
-        result = prime * result + ( ( reference == null ) ? 0 : reference.hashCode() );
-        return result;
-    }
-
-    @Override
-    public boolean equals( Object obj ) {
-        if ( this == obj ) return true;
-        if ( obj == null ) return false;
-        if ( getClass() != obj.getClass() ) return false;
-        Annotation other = ( Annotation ) obj;
-        if ( evidence == null ) {
-            if ( other.evidence != null ) return false;
-        } else if ( !evidence.equals( other.evidence ) ) return false;
-        if ( qualifier == null ) {
-            if ( other.qualifier != null ) return false;
-        } else if ( !qualifier.equals( other.qualifier ) ) return false;
-        if ( reference == null ) {
-            if ( other.reference != null ) return false;
-        } else if ( !reference.equals( other.reference ) ) return false;
-        return true;
-    }
-
 }

gotrack/src/main/java/ubc/pavlab/gotrack/model/FullAnnotation.java

@@ -0,0 +1,35 @@
+/*
+ * The gotrack project
+ * 
+ * Copyright (c) 2015 University of British Columbia
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ubc.pavlab.gotrack.model;
+
+import lombok.EqualsAndHashCode;
+import lombok.Getter;
+import lombok.RequiredArgsConstructor;
+import ubc.pavlab.gotrack.model.go.GeneOntologyTerm;
+
+@Getter
+//@EqualsAndHashCode( exclude = ("direct") ) // Exclude direct as we only want a single term-annotation pair in a set at once
+@EqualsAndHashCode
+@RequiredArgsConstructor
+public class FullAnnotation {
+    private final GeneOntologyTerm annotatedTerm;
+    private final Annotation annotation;
+    private final boolean direct;
+}

gotrack/src/main/java/ubc/pavlab/gotrack/model/go/GeneOntologyTerm.java

@@ -24,10 +24,15 @@
 import lombok.EqualsAndHashCode;
 import lombok.Getter;
 import lombok.ToString;
+import ubc.pavlab.gotrack.model.Annotation;
 import ubc.pavlab.gotrack.model.Aspect;
+import ubc.pavlab.gotrack.model.FullAnnotation;
 import ubc.pavlab.gotrack.model.dto.GOTermDTO;
 
-import java.util.*;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -179,19 +184,24 @@ static Stream<GeneOntologyTerm> propagate( Stream<GeneOntologyTerm> terms, boole
         return terms.flatMap( t -> t.propagate( includePartOf ) );
     }
 
-    public static <A> Map<GeneOntologyTerm, Set<A>> propagateAnnotations( Stream<Map.Entry<GeneOntologyTerm, Set<A>>> termEntries ) {
-        return propagateAnnotations( termEntries, true );
+
+    public static Map<GeneOntologyTerm, Set<FullAnnotation>> propagateAnnotations( Stream<Map.Entry<GeneOntologyTerm, Set<Annotation>>> annotations ) {
+        return propagateAnnotations( annotations, true );
     }
 
     /**
      * Propagates terms and their annotations to parents terms
      *
      * @return Map of all propagated terms to their propagated annotations
      */
-    static <A> Map<GeneOntologyTerm, Set<A>> propagateAnnotations( Stream<Map.Entry<GeneOntologyTerm, Set<A>>> termEntries, boolean includePartOf ) {
-        Map<GeneOntologyTerm, Set<A>> propagatedAnnotations = new HashMap<>();
-        termEntries.forEach( entry -> entry.getKey().propagate(includePartOf)
-                .forEach( p -> propagatedAnnotations.computeIfAbsent( p, k -> new HashSet<>() ).addAll( entry.getValue() ) ) );
+    static Map<GeneOntologyTerm, Set<FullAnnotation>> propagateAnnotations( Stream<Map.Entry<GeneOntologyTerm, Set<Annotation>>> annotations, boolean includePartOf ) {
+        Map<GeneOntologyTerm, Set<FullAnnotation>> propagatedAnnotations = new HashMap<>();
+
+        annotations.forEach( entry -> entry.getKey().propagate(includePartOf)
+                .forEach( p -> propagatedAnnotations.computeIfAbsent( p, k -> new HashSet<>() )
+                        .addAll( entry.getValue().stream()
+                                .map( a -> new FullAnnotation( entry.getKey(), a, p.equals( entry.getKey() ) ) )
+                                .collect( Collectors.toList()) ) ) );
 
         return propagatedAnnotations;
     }