in progress

[jalview.git] / forester / java / src / org / forester / ws / uniprot / UniProtTaxonomy.java

diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java
index 14fa14a..4f62f77 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java
+++ b/forester/java/src/org/forester/ws/uniprot/UniProtTaxonomy.java
@@ -43,9 +43,10 @@ public final class UniProtTaxonomy {
     private final String                _rank;
     private final String                _id;
     public final static String          CELLULAR_ORGANISMS       = "cellular organisms";
+    public final static String          VIRUSES                  = "Viruses";
     public final static UniProtTaxonomy DROSOPHILA_GENUS         = new UniProtTaxonomy( new String[] {
             CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", "Neoptera",
-            "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae" },
+            "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae", "Drosophila" },
                                                                                         "",
                                                                                         "fruit flies",
                                                                                         "Drosophila",
@@ -54,7 +55,7 @@ public final class UniProtTaxonomy {
                                                                                         "7215" );
     public final static UniProtTaxonomy XENOPUS_GENUS            = new UniProtTaxonomy( new String[] {
             CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Amphibia",
-            "Batrachia", "Anura", "Mesobatrachia", "Pipoidea", "Pipidae", "Xenopodinae" },
+            "Batrachia", "Anura", "Mesobatrachia", "Pipoidea", "Pipidae", "Xenopodinae", "Xenopus" },
                                                                                         "",
                                                                                         "",
                                                                                         "Xenopus",
@@ -63,7 +64,7 @@ public final class UniProtTaxonomy {
                                                                                         "8353" );
     public final static UniProtTaxonomy CAPITELLA_TELATA_SPECIES = new UniProtTaxonomy( new String[] {
             CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Annelida", "Polychaeta", "Scolecida", "Capitellida",
-            "Capitellidae", "Capitella"                                                },
+            "Capitellidae", "Capitella", "Capitella teleta"                            },
                                                                                         "",
                                                                                         "",
                                                                                         "Capitella teleta",
@@ -71,6 +72,8 @@ public final class UniProtTaxonomy {
                                                                                         "species",
                                                                                         "283909" );
 
+    // public final static UniProtTaxonomy NUCLEARIIDAE_AND_FONTICULA = new UniProtTaxonomy( new String[] {
+    //         CELLULAR_ORGANISMS, EUKARYOTA, "Nucleariidae and Fonticula group" }, "", "", "", "", "", "1001604" );
     public UniProtTaxonomy( final String line ) {
         final String[] items = line.split( "\t" );
         if ( items.length < 5 ) {
@@ -88,7 +91,7 @@ public final class UniProtTaxonomy {
             _rank = "";
         }
         String[] lin = null;
-        if ( items.length > 7 ) {
+        if ( items.length > 8 ) {
             lin = items[ 8 ].split( "; " );
         }
         _lineage = new ArrayList<String>();
@@ -133,6 +136,9 @@ public final class UniProtTaxonomy {
         _synonym = synonym;
         _rank = rank;
         _id = id;
+        if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
+            _lineage.add( _scientific_name );
+        }
     }
 
     public UniProtTaxonomy( final String[] lineage,
@@ -143,8 +149,10 @@ public final class UniProtTaxonomy {
                             final String rank,
                             final String id ) {
         _lineage = new ArrayList<String>();
-        for( final String l : lineage ) {
-            _lineage.add( l );
+        if ( lineage != null ) {
+            for( final String l : lineage ) {
+                _lineage.add( l );
+            }
         }
         _code = code;
         _scientific_name = scientific_name;
@@ -152,6 +160,9 @@ public final class UniProtTaxonomy {
         _synonym = synonym;
         _rank = rank;
         _id = id;
+        if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
+            _lineage.add( _scientific_name );
+        }
     }
 
     /**
@@ -185,15 +196,6 @@ public final class UniProtTaxonomy {
         return _lineage;
     }
 
-    public String[] getLineageAsArray() {
-        final String[] str = new String[ _lineage.size() ];
-        int i = 0;
-        for( final String l : _lineage ) {
-            str[ i++ ] = l;
-        }
-        return str;
-    }
-
     public String getRank() {
         return _rank;
     }