Autogenerated markdown documentation

bio4j · Mar 5, 2016 · 3fd386d · 3fd386d
1 parent a36f2e4
commit 3fd386d
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Showing 3 changed files with 15 additions and 48 deletions.
diff --git a/docs/src/main/java/com/bio4j/model/ncbiTaxonomy/NCBITaxonomyGraph.java.md b/docs/src/main/java/com/bio4j/model/ncbiTaxonomy/NCBITaxonomyGraph.java.md
@@ -98,8 +98,6 @@ public abstract class NCBITaxonomyGraph<
 
   public final id id = new id();
   public final name name = new name();
-  public final comment comment = new comment();
-  public final scientificName scientificName = new scientificName();
   public final taxonomicRank taxonomicRank = new taxonomicRank();
 
   public NCBITaxonType(RVT raw) {
@@ -140,30 +138,6 @@ public abstract class NCBITaxonomyGraph<
     }
   }
 
-  public final class comment
-    extends
-    NCBITaxonomyVertexProperty<NCBITaxon<I, RV, RVT, RE, RET>, NCBITaxonType, comment, String> {
-    public comment() {
-    super(NCBITaxonType.this);
-    }
-
-    public Class<String> valueClass() {
-    return String.class;
-    }
-  }
-
-  public final class scientificName
-    extends
-    NCBITaxonomyVertexProperty<NCBITaxon<I, RV, RVT, RE, RET>, NCBITaxonType, scientificName, String> {
-    public scientificName() {
-    super(NCBITaxonType.this);
-    }
-
-    public Class<String> valueClass() {
-    return String.class;
-    }
-  }
-
   public final class taxonomicRank
     extends
     NCBITaxonomyVertexProperty<NCBITaxon<I, RV, RVT, RE, RET>, NCBITaxonType, taxonomicRank, String> {

diff --git a/.../src/main/java/com/bio4j/model/ncbiTaxonomy/programs/ImportNCBITaxonomy.java.md b/.../src/main/java/com/bio4j/model/ncbiTaxonomy/programs/ImportNCBITaxonomy.java.md
@@ -106,23 +106,23 @@ public abstract class ImportNCBITaxonomy<I extends UntypedGraph<RV,RVT,RE,RET>,R
 
       String[] columns = line.split("\\|");
 
-      if (columns[columns.length - 1].trim().equals("scientific name")) {
+      if (columns[3].trim().equals("scientific name")) {
 
-      String taxId = columns[0].trim();
-      String scientificNameSt = columns[1].trim();
+        String taxId = columns[0].trim();
+        String taxName = columns[1].trim();
 
-      Optional<NCBITaxon<I,RV,RVT,RE,RET>> optionalTaxon = ncbiTaxonomyGraph.nCBITaxonIdIndex().getVertex(taxId);
-      if(optionalTaxon.isPresent()){
-        NCBITaxon<I,RV,RVT,RE,RET> taxon = optionalTaxon.get();
-        taxon.set(ncbiTaxonomyGraph.NCBITaxon().scientificName, scientificNameSt);
-      }else{
-        Logger.getLogger(ImportNCBITaxonomy.class.getName()).log(Level.INFO, "Taxon with id: " + taxId + " was not found and its name could not be added... :(");
-      }
+        Optional<NCBITaxon<I,RV,RVT,RE,RET>> optionalTaxon = ncbiTaxonomyGraph.nCBITaxonIdIndex().getVertex(taxId);
+        if(optionalTaxon.isPresent()){
+          NCBITaxon<I,RV,RVT,RE,RET> taxon = optionalTaxon.get();
+          taxon.set(ncbiTaxonomyGraph.NCBITaxon().name, taxName);
+        }else{
+          Logger.getLogger(ImportNCBITaxonomy.class.getName()).log(Level.INFO, "Taxon with id: " + taxId + " was not found and its name could not be added... :(");
+        }
 
-      linesCounter++;
-      if((linesCounter % limitForTransaction) == 0){
-        ncbiTaxonomyGraph.raw().commit();
-      }
+        linesCounter++;
+        if((linesCounter % limitForTransaction) == 0){
+          ncbiTaxonomyGraph.raw().commit();
+        }
 
       }
 
@@ -208,6 +208,7 @@ public abstract class ImportNCBITaxonomy<I extends UntypedGraph<RV,RVT,RE,RET>,R
   }
 
 }
+
 ```
 
 

diff --git a/docs/src/main/java/com/bio4j/model/ncbiTaxonomy/vertices/NCBITaxon.java.md b/docs/src/main/java/com/bio4j/model/ncbiTaxonomy/vertices/NCBITaxon.java.md
@@ -39,14 +39,6 @@ public final class NCBITaxon<I extends UntypedGraph<RV, RVT, RE, RET>, RV, RVT,
   return get(type().name);
   }
 
-  public String comment() {
-  return get(type().comment);
-  }
-
-  public String scientificName() {
-  return get(type().scientificName);
-  }
-
   public String taxonomicRank() {
   return get(type().taxonomicRank);
   }