X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fanalysis%2FAncestralTaxonomyInference.java;h=dec0a635a22def5b0097f958aaca0c0fc2fe536e;hb=c365c2e336ee79677d9e0f5d5c8d280afb56a3ab;hp=7ddfe99cda099da044e63f09039fc09e3d8518e4;hpb=93b3ffddb203151c92200b3498d5559cc4de7d18;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index 7ddfe99..dec0a63 100644
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -151,27 +151,6 @@ public final class AncestralTaxonomyInference {
         final SortedSet<String> not_found = new TreeSet<String>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
-            // final QUERY_TYPE qt = null;
-            // Taxonomy tax = null;
-            // if ( node.getNodeData().isHasTaxonomy() ) {
-            // tax = node.getNodeData().getTaxonomy();
-            // }
-            // UniProtTaxonomy up_tax = null;
-            // if ( ( tax != null )
-            // && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty(
-            // tax.getScientificName() )
-            // || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ||
-            // !ForesterUtil.isEmpty( tax
-            // .getCommonName() ) ) ) {
-            // final String query = null;
-            // up_tax = obtainUniProtTaxonomy( tax, query, qt );
-            // if ( up_tax == null ) {
-            // not_found.add( query );
-            // }
-            // else {
-            // updateTaxonomy( qt, node, tax, up_tax );
-            // }
-            // }
             if ( !node.isExternal() ) {
                 inferTaxonomyFromDescendents( node, not_found );
             }
@@ -195,14 +174,16 @@ public final class AncestralTaxonomyInference {
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
                             .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
-                final QUERY_TYPE qt = null;
-                final String query = null;
-                final UniProtTaxonomy up_tax = obtainUniProtTaxonomy( desc.getNodeData().getTaxonomy(), query, qt );
+             
+                final UniProtTaxonomy up_tax = obtainUniProtTaxonomy( desc.getNodeData().getTaxonomy(), null, null );
                 String[] lineage = null;
                 if ( up_tax != null ) {
-                    lineage = obtainLineagePlusOwnScientificName( up_tax );
+                    //lineage = obtainLineagePlusOwnScientificName( up_tax );
+                    lineage = up_tax.getLineageAsArray();
                 }
                 if ( ( lineage == null ) || ( lineage.length < 1 ) ) {
+                    //TODO remove me
+                    System.out.println( "node " + desc.getNodeData().getTaxonomy().toString() + " has no lineage!" );
                     not_found.add( desc.getNodeData().getTaxonomy().asText().toString() );
                     return;
                 }
@@ -213,9 +194,25 @@ public final class AncestralTaxonomyInference {
             }
             else {
                 String msg = "Node(s) with no or inappropriate taxonomic information found";
+                String node = "";
                 if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
-                    msg = "Node " + desc.getName() + " has no or inappropriate taxonomic information";
+                    node = "\"" + desc.getName() + "\"";
                 }
+                else {
+                    node = "[" + desc.getId() + "]";
+                }
+                msg = "Node " + node + " has no or inappropriate taxonomic information";
+             //   final List<PhylogenyNode> e = desc.getAllExternalDescendants();
+                //TODO remove me!
+//                System.out.println();
+//                int x = 0;
+//                for( final PhylogenyNode object : e ) {
+//                    System.out.println( x + ":" );
+//                    System.out.println( object.getName() + "  " );
+//                    x++;
+//                }
+//                System.out.println();
+                //
                 throw new IllegalArgumentException( msg );
             }
         }
@@ -232,15 +229,22 @@ public final class AncestralTaxonomyInference {
             }
         }
         if ( last_common_lineage == null ) {
+            System.out.println( "No common lineage for:" );
+            int counter = 0;
+            for( final String[] strings : lineages ) {
+                System.out.print( counter + ": " );
+                ++counter;
+                for( final String string : strings ) {
+                    System.out.print( string + " " );
+                }
+                System.out.println();
+            }
             return;
         }
-        // if ( !n.getNodeData().isHasTaxonomy() ) {
-        // n.getNodeData().setTaxonomy( new Taxonomy() );
-        // }
         final Taxonomy tax = new Taxonomy();
         n.getNodeData().setTaxonomy( tax );
         tax.setScientificName( last_common_lineage );
-        final UniProtTaxonomy up_tax = obtainUniProtTaxonomyFromSn( last_common_lineage );
+        final UniProtTaxonomy up_tax = obtainUniProtTaxonomyFromSn( last_common_lineage, lineage );
         if ( up_tax != null ) {
             if ( !ForesterUtil.isEmpty( up_tax.getRank() ) ) {
                 try {
@@ -259,6 +263,15 @@ public final class AncestralTaxonomyInference {
             if ( !ForesterUtil.isEmpty( up_tax.getSynonym() ) && !tax.getSynonyms().contains( up_tax.getSynonym() ) ) {
                 tax.getSynonyms().add( up_tax.getSynonym() );
             }
+            if ( up_tax.getLineage() != null ) {
+                tax.setLineage( new ArrayList<String>() );
+                for( final String lin : up_tax.getLineage() ) {
+                    if ( !ForesterUtil.isEmpty( lin ) ) {
+                        tax.getLineage().add( lin );
+                    }
+                }
+            }
+            
         }
         for( final PhylogenyNode desc : descs ) {
             if ( !desc.isExternal() && desc.getNodeData().isHasTaxonomy()
@@ -302,14 +315,14 @@ public final class AncestralTaxonomyInference {
                     not_found_external_nodes.add( node );
                 }
             }
-            UniProtTaxonomy up_tax = null;
+            UniProtTaxonomy uniprot_tax = null;
             if ( ( tax != null )
                     && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() )
                             || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil.isEmpty( tax
                             .getCommonName() ) ) ) {
-                up_tax = obtainUniProtTaxonomy( tax, null, qt );
-                if ( up_tax != null ) {
-                    updateTaxonomy( qt, node, tax, up_tax );
+                uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
+                if ( uniprot_tax != null ) {
+                    updateTaxonomy( qt, node, tax, uniprot_tax );
                 }
                 else {
                     not_found.add( tax.toString() );
@@ -320,34 +333,38 @@ public final class AncestralTaxonomyInference {
             }
         }
         if ( delete ) {
-            for( PhylogenyNode node : not_found_external_nodes ) {
-                phy.deleteSubtree( node, false );
+            for( final PhylogenyNode node : not_found_external_nodes ) {
+                phy.deleteSubtree( node, true );
             }
+            phy.externalNodesHaveChanged();
+            phy.hashIDs();
             phy.recalculateNumberOfExternalDescendants( true );
         }
         return not_found;
     }
 
-    synchronized private static String[] obtainLineagePlusOwnScientificName( final UniProtTaxonomy up_tax ) {
-        final String[] lineage = up_tax.getLineage();
-        final String[] lin_plus_self = new String[ lineage.length + 1 ];
-        for( int i = 0; i < lineage.length; ++i ) {
-            lin_plus_self[ i ] = lineage[ i ];
-        }
-        lin_plus_self[ lineage.length ] = up_tax.getScientificName();
-        return lin_plus_self;
-    }
-
+    // TODO this might not be needed anymore
+    //  synchronized private static String[] obtainLineagePlusOwnScientificName( final UniProtTaxonomy up_tax ) {
+    //      final String[] lineage = up_tax.getLineageAsArray();
+    //      final String[] lin_plus_self = new String[ lineage.length + 1 ];
+    //      for( int i = 0; i < lineage.length; ++i ) {
+    //          lin_plus_self[ i ] = lineage[ i ];
+    //      }
+    //      lin_plus_self[ lineage.length ] = up_tax.getScientificName();
+    //      return lin_plus_self;
+    //  }
     synchronized private static UniProtTaxonomy obtainUniProtTaxonomy( final Taxonomy tax, String query, QUERY_TYPE qt )
             throws IOException {
         if ( isHasAppropriateId( tax ) ) {
             query = tax.getIdentifier().getValue();
             qt = QUERY_TYPE.ID;
+            System.out.println( "query by id: " + query);
             return getTaxonomies( getIdTaxCacheMap(), query, qt );
         }
         else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             query = tax.getScientificName();
             qt = QUERY_TYPE.SN;
+            System.out.println( "query by sn: " + query);
             return getTaxonomies( getSnTaxCacheMap(), query, qt );
         }
         else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
@@ -362,7 +379,7 @@ public final class AncestralTaxonomyInference {
         }
     }
 
-    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromSn( final String sn ) throws IOException {
+    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromSn( final String sn, List<String> lineage ) throws IOException {
         UniProtTaxonomy up_tax = null;
         if ( getSnTaxCacheMap().containsKey( sn ) ) {
             up_tax = getSnTaxCacheMap().get( sn ).copy();
@@ -381,6 +398,7 @@ public final class AncestralTaxonomyInference {
                 if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
                     getIdTaxCacheMap().put( up_tax.getId(), up_tax );
                 }
+                
             }
         }
         return up_tax;
@@ -394,9 +412,9 @@ public final class AncestralTaxonomyInference {
                 && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             tax.setScientificName( up_tax.getScientificName() );
         }
-        if ( node.isExternal()
-                && ( ( qt != QUERY_TYPE.CODE ) && !ForesterUtil.isEmpty( up_tax.getCode() ) && ForesterUtil
-                        .isEmpty( tax.getTaxonomyCode() ) ) ) {
+        //  if ( node.isExternal()
+        if ( ( qt != QUERY_TYPE.CODE ) && !ForesterUtil.isEmpty( up_tax.getCode() )
+                && ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
             tax.setTaxonomyCode( up_tax.getCode() );
         }
         if ( ( qt != QUERY_TYPE.CN ) && !ForesterUtil.isEmpty( up_tax.getCommonName() )
@@ -417,6 +435,15 @@ public final class AncestralTaxonomyInference {
         if ( ( qt != QUERY_TYPE.ID ) && !ForesterUtil.isEmpty( up_tax.getId() ) && ( tax.getIdentifier() == null ) ) {
             tax.setIdentifier( new Identifier( up_tax.getId(), "uniprot" ) );
         }
+        if ( up_tax.getLineage() != null ) {
+            tax.setLineage( new ArrayList<String>() );
+            for( final String lin : up_tax.getLineage() ) {
+                if ( !ForesterUtil.isEmpty( lin ) ) {
+                    tax.getLineage().add( lin );
+                }
+            }
+        }
+        
     }
 
     private enum QUERY_TYPE {