From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 15 Nov 2013 09:11:48 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5fa5ccc8d3c9a6f68d3b1078c40113d8b316c6dc;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index 9f18f81..61b9465 100644
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -138,8 +138,8 @@ public final class AncestralTaxonomyInference {
                 }
             }
             if ( saw_cellular_organism && saw_viruses ) {
-                last_common_lineage.add( UniProtTaxonomy.CELLULAR_ORGANISMS );
-                last_common = UniProtTaxonomy.CELLULAR_ORGANISMS;
+                //last_common_lineage.add( UniProtTaxonomy.CELLULAR_ORGANISMS );
+               // last_common = UniProtTaxonomy.CELLULAR_ORGANISMS;
             }
             else {
                 String msg = "no common lineage for:\n";
diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 1a1bef6..79ab713 100644
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -184,6 +184,16 @@ public final class TaxonomyDataManager extends RunnableProcess {
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query ) throws IOException {
+        if ( query.equalsIgnoreCase( UniProtTaxonomy.BACTERIA ) ||
+                query.equalsIgnoreCase( UniProtTaxonomy.ARCHAEA ) ||
+                query.equalsIgnoreCase( UniProtTaxonomy.VIRUSES ) ||
+                query.equalsIgnoreCase( UniProtTaxonomy.EUKARYOTA ) 
+                ) {
+            final List<UniProtTaxonomy> l = new ArrayList<UniProtTaxonomy>();
+            l.add( UniProtTaxonomy.createSpecialFromScientificName( query ) );
+            return l;
+        }
+        
         return SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 92cd3d8..47516e4 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -11511,6 +11511,7 @@ public final class Test {
                 System.out.println( entry4.getMap() );
                 return false;
             }
+           //TODO FIXME gi...
             //
             //TODO fails:
             //            final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
index 2cdd93e..b959899 100644
--- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
@@ -32,9 +32,9 @@ import org.forester.util.ForesterUtil;
 
 public final class UniProtTaxonomy {
 
-    private static final String ARCHAEA            = "Archaea";
-    private static final String BACTERIA           = "Bacteria";
-    private static final String EUKARYOTA          = "Eukaryota";
+    public  static final String ARCHAEA            = "Archaea";
+    public  static final String BACTERIA           = "Bacteria";
+    public  static final String EUKARYOTA          = "Eukaryota";
     private final List<String>  _lineage;
     private final String        _code;
     private final String        _scientific_name;
@@ -107,34 +107,13 @@ public final class UniProtTaxonomy {
         _synonym = synonym;
         _rank = rank;
         _id = id;
-        if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
+        if ( ( _lineage != null &&  _lineage.isEmpty() ) || ( ( !ForesterUtil.isEmpty( _lineage ) ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) ) {
             _lineage.add( _scientific_name );
         }
+      
     }
 
-    public UniProtTaxonomy( final String[] lineage,
-                            final String code,
-                            final String common_name,
-                            final String scientific_name,
-                            final String synonym,
-                            final String rank,
-                            final String id ) {
-        _lineage = new ArrayList<String>();
-        if ( lineage != null ) {
-            for( final String l : lineage ) {
-                _lineage.add( l );
-            }
-        }
-        _code = code;
-        _scientific_name = scientific_name;
-        _common_name = common_name;
-        _synonym = synonym;
-        _rank = rank;
-        _id = id;
-        if ( ( _lineage != null ) && !_lineage.get( _lineage.size() - 1 ).equalsIgnoreCase( _scientific_name ) ) {
-            _lineage.add( _scientific_name );
-        }
-    }
+    
 
     /**
      * Creates deep copy for all fields, except lineage.
@@ -178,4 +157,46 @@ public final class UniProtTaxonomy {
     public String getSynonym() {
         return _synonym;
     }
+    
+    public final static UniProtTaxonomy createSpecialFromScientificName( final String sn ) {
+        
+        List<String> lineage = new ArrayList<String>();
+        String code = "";
+        String common_name = "";
+        String scientific_name = "";
+        String synonym = "";
+        String rank = "";
+        String id = "";
+        
+        if ( sn.equalsIgnoreCase( BACTERIA ) ) {
+            scientific_name = BACTERIA;
+            lineage.add( "cellular organisms" );
+            rank = "superkingdom";
+            id = "2";
+        }
+        else if ( sn.equalsIgnoreCase( ARCHAEA ) ) {
+            scientific_name = ARCHAEA;
+            lineage.add( "cellular organisms" );
+          
+            rank = "superkingdom";
+            id = "2157";
+        }
+        else if ( sn.equalsIgnoreCase( EUKARYOTA ) ) {
+            scientific_name = EUKARYOTA;
+            lineage.add( "cellular organisms" );
+            rank = "superkingdom";
+            id = "2759";
+        }
+        else if ( sn.equalsIgnoreCase( VIRUSES ) ) {
+            scientific_name = VIRUSES;
+            rank = "superkingdom";
+            id = "10239";
+        }
+        else {
+            throw new IllegalArgumentException( "illegal attempt to make UniProt taxonomy for :" + sn );
+        }
+        return new UniProtTaxonomy( lineage, code, common_name, scientific_name, synonym, rank, id );
+        
+        
+    }
 }