[#78] allow labels to be loaded as tsvs

owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java

@@ -2,6 +2,8 @@
 
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableMap;
+import com.google.common.collect.ImmutableSet;
+
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.semanticweb.owlapi.model.OWLOntology;
 
@@ -22,14 +24,15 @@
     private final Map<String, String> curies;
     private final List<String> individualAssociationTsvs;
     private final Map<String, Collection<String>> individualAssociations;
-    //TODO - labels?
+    private final Set<String> labelTsvs;
 
     private OntologySourceData(Builder builder) {
         this.ontologies = distinctImmutableListOf(builder.ontologies);
         this.dataOntologies = distinctImmutableListOf(builder.dataOntologies);
         this.curies = ImmutableMap.copyOf(builder.curies);
         this.individualAssociationTsvs = distinctImmutableListOf(builder.individualAssociationTsvs);
         this.individualAssociations = ImmutableMap.copyOf(builder.individualAssociations);
+        this.labelTsvs = ImmutableSet.copyOf(builder.labelTsvs);
     }
 
     private ImmutableList<String> distinctImmutableListOf(List<String> list) {
@@ -48,6 +51,10 @@ private OntologySourceData(Builder builder) {
         return curies;
     }
 
+    public Set<String> getLabelTsvs() {
+        return labelTsvs;
+    }
+
     public List<String> getIndividualAssociationTsvs() {
         return individualAssociationTsvs;
     }
@@ -65,7 +72,8 @@ public boolean equals(Object o) {
                 Objects.equals(dataOntologies, that.dataOntologies) &&
                 Objects.equals(curies, that.curies) &&
                 Objects.equals(individualAssociationTsvs, that.individualAssociationTsvs) &&
-                Objects.equals(individualAssociations, that.individualAssociations);
+                Objects.equals(individualAssociations, that.individualAssociations) &&
+                Objects.equals(labelTsvs, that.labelTsvs);
     }
 
     @Override
@@ -81,6 +89,7 @@ public String toString() {
                 ", curies=" + curies +
                 ", individualAssociationTsvs=" + individualAssociationTsvs +
                 ", individualAssociations=" + individualAssociations +
+                ", labelTsvs=" + labelTsvs +
                 '}';
     }
 
@@ -95,6 +104,7 @@ public static Builder builder() {
         private Map<String, String> curies = Collections.emptyMap();
         private List<String> individualAssociationTsvs = new ArrayList<>();
         private Map<String, Collection<String>> individualAssociations = new HashMap<>();
+        private Set<String> labelTsvs = Collections.emptySet();
 
         private Builder(){
             //use the static method.
@@ -180,6 +190,11 @@ public Builder individualAssociations(Map<String, ? extends Collection<String>>
             individualAssociations.putAll(mappings);
             return this;
         }
+        
+        public Builder labelTsvs(Set<String> labelTsvs) {
+            this.labelTsvs = labelTsvs;
+            return this;
+        }
 
         public OntologySourceData build() {
             if(ontologies.isEmpty()) {

owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java

@@ -11,6 +11,7 @@
 import java.io.File;
 import java.util.Collection;
 import java.util.Map;
+import java.util.Set;
 
 /**
  * A convenience wrapper to enable easy loading of a {@link BMKnowledgeBase} from OWL ontologies and data files.
@@ -52,6 +53,15 @@ public Loader loadCuries(Map<String, String> curies) {
         }
 
         /**
+         * @param labelTsvs
+         * @return
+         */
+        public Loader loadLabelsFromTsv(Set<String> labelTsvs) {
+            sourceDataBuilder.labelTsvs(labelTsvs);
+            return this;
+        }
+
+        /**
          * Loads an OWL/OBO ontology from a file.
          *
          * @param file