X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fanalysis%2FAncestralTaxonomyInference.java;h=73af2c142c86be1e23ec5858599e7b0db661a8fe;hb=8cb65713b89737f529cedce7bcd39f2b9f9fc8a1;hp=fb34a14eaa199b61dd3c4f56a7c957a301242d43;hpb=9bb791edf52887de31d1a49ff9606f85724a09a8;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index fb34a14..73af2c1 100644
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -44,8 +44,9 @@ import org.forester.ws.uniprot.UniProtWsTools;
 public final class AncestralTaxonomyInference {
 
     private static final int                              MAX_CACHE_SIZE           = 100000;
-    private static final int                              MAX_TAXONOMIES_TO_RETURN = 100;
+    private static final int                              MAX_TAXONOMIES_TO_RETURN = 10;
     private static final HashMap<String, UniProtTaxonomy> _sn_up_cache_map         = new HashMap<String, UniProtTaxonomy>();
+    private static final HashMap<String, UniProtTaxonomy> _lineage_up_cache_map    = new HashMap<String, UniProtTaxonomy>();
     private static final HashMap<String, UniProtTaxonomy> _code_up_cache_map       = new HashMap<String, UniProtTaxonomy>();
     private static final HashMap<String, UniProtTaxonomy> _cn_up_cache_map         = new HashMap<String, UniProtTaxonomy>();
     private static final HashMap<String, UniProtTaxonomy> _id_up_cache_map         = new HashMap<String, UniProtTaxonomy>();
@@ -54,6 +55,9 @@ public final class AncestralTaxonomyInference {
         if ( getSnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
             getSnTaxCacheMap().clear();
         }
+        if ( getLineageTaxCacheMap().size() > MAX_CACHE_SIZE ) {
+            getLineageTaxCacheMap().clear();
+        }
         if ( getCnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
             getCnTaxCacheMap().clear();
         }
@@ -81,9 +85,14 @@ public final class AncestralTaxonomyInference {
         return _sn_up_cache_map;
     }
 
+    synchronized private static HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
+        return _lineage_up_cache_map;
+    }
+
     synchronized private static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
-                                                               final String query,
-                                                               final QUERY_TYPE qt ) throws IOException {
+                                                               final Object query,
+                                                               final QUERY_TYPE qt ) throws IOException,
+            AncestralTaxonomyInferenceException {
         if ( cache.containsKey( query ) ) {
             return cache.get( query ).copy();
         }
@@ -91,17 +100,19 @@ public final class AncestralTaxonomyInference {
             List<UniProtTaxonomy> up_taxonomies = null;
             switch ( qt ) {
                 case ID:
-                    up_taxonomies = getTaxonomiesFromId( query );
+                    up_taxonomies = getTaxonomiesFromId( ( String ) query );
                     break;
                 case CODE:
-                    up_taxonomies = getTaxonomiesFromTaxonomyCode( query );
+                    up_taxonomies = getTaxonomiesFromTaxonomyCode( ( String ) query );
                     break;
                 case SN:
-                    up_taxonomies = getTaxonomiesFromScientificName( query );
+                    up_taxonomies = getTaxonomiesFromScientificName( ( String ) query );
                     break;
                 case CN:
-                    up_taxonomies = getTaxonomiesFromCommonName( query );
+                    up_taxonomies = getTaxonomiesFromCommonName( ( String ) query );
                     break;
+                case LIN:
+                    return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
                 default:
                     throw new RuntimeException();
             }
@@ -146,21 +157,19 @@ public final class AncestralTaxonomyInference {
         return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
-    synchronized public static SortedSet<String> inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException {
+    synchronized public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
+            AncestralTaxonomyInferenceException {
         clearCachesIfTooLarge();
-        final SortedSet<String> not_found = new TreeSet<String>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             if ( !node.isExternal() ) {
-                inferTaxonomyFromDescendents( node, not_found );
+                inferTaxonomyFromDescendents( node );
             }
         }
-        return not_found;
     }
 
-    synchronized private static void inferTaxonomyFromDescendents( final PhylogenyNode n,
-                                                                   final SortedSet<String> not_found )
-            throws IOException {
+    synchronized private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException,
+            AncestralTaxonomyInferenceException {
         if ( n.isExternal() ) {
             throw new IllegalArgumentException( "attempt to infer taxonomy from descendants of external node" );
         }
@@ -172,21 +181,31 @@ public final class AncestralTaxonomyInference {
             if ( desc.getNodeData().isHasTaxonomy()
                     && ( isHasAppropriateId( desc.getNodeData().getTaxonomy() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
+                            || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() )
                             || !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 );
-                String[] lineage = null;
-                if ( up_tax != null ) {
-                    //lineage = obtainLineagePlusOwnScientificName( up_tax );
-                    lineage = up_tax.getLineageAsArray();
+                final UniProtTaxonomy up_tax = obtainUniProtTaxonomy( desc.getNodeData().getTaxonomy(), null, null );
+                if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
+                    String desc_str = "";
+                    if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
+                        desc_str = "\"" + desc.getName() + "\"";
+                    }
+                    else {
+                        desc_str = "[" + desc.getId() + "]";
+                    }
+                    System.out.println( desc.getNodeData().getTaxonomy().toString() );
+                    System.out.println( ForesterUtil.stringListToString( desc.getNodeData().getTaxonomy().getLineage(),
+                                                                         "  >  " ) );
+                    throw new AncestralTaxonomyInferenceException( "a taxonomy for node " + desc_str
+                            + " could not be established from the database" );
                 }
+                String[] lineage = ForesterUtil.stringListToArray( desc.getNodeData().getTaxonomy().getLineage() );
                 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;
+                    lineage = ForesterUtil.stringListToArray( up_tax.getLineage() );
+                }
+                if ( ( lineage == null ) || ( lineage.length < 1 ) ) {
+                    throw new AncestralTaxonomyInferenceException( "a taxonomic lineage for node \""
+                            + desc.getNodeData().getTaxonomy().toString() + "\" could not be established" );
                 }
                 if ( lineage.length < shortest_lin_length ) {
                     shortest_lin_length = lineage.length;
@@ -194,7 +213,6 @@ public final class AncestralTaxonomyInference {
                 lineages.add( lineage );
             }
             else {
-                String msg = "Node(s) with no or inappropriate taxonomic information found";
                 String node = "";
                 if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
                     node = "\"" + desc.getName() + "\"";
@@ -202,22 +220,23 @@ public final class AncestralTaxonomyInference {
                 else {
                     node = "[" + desc.getId() + "]";
                 }
-                msg = "Node " + node + " has no or inappropriate taxonomic information";
-                List<PhylogenyNode> e = desc.getAllExternalDescendants();
+                //   final List<PhylogenyNode> e = desc.getAllExternalDescendants();
                 //TODO remove me!
-                System.out.println();
-                int x = 0;
-                for( PhylogenyNode object : e ) {
-                    System.out.println( x + ":" );
-                    System.out.println( object.getName() + "  " );
-                    x++;
-                }
-                System.out.println();
+                //                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 );
+                throw new AncestralTaxonomyInferenceException( "node " + node
+                        + " has no or inappropriate taxonomic information" );
             }
         }
-        String last_common_lineage = null;
+        final List<String> last_common_lineage = new ArrayList<String>();
+        String last_common = null;
         if ( shortest_lin_length > 0 ) {
             I: for( int i = 0; i < shortest_lin_length; ++i ) {
                 final String lineage_0 = lineages.get( 0 )[ i ];
@@ -226,29 +245,48 @@ public final class AncestralTaxonomyInference {
                         break I;
                     }
                 }
-                last_common_lineage = lineage_0;
+                last_common_lineage.add( lineage_0 );
+                last_common = lineage_0;
             }
         }
-        if ( last_common_lineage == null ) {
-            System.out.println( "No common lineage for:" );
-            int counter = 0;
-            for( String[] strings : lineages ) {
-                System.out.print( counter + ": " );
-                ++counter;
-                for( String string : strings ) {
-                    System.out.print( string + " " );
+        if ( last_common_lineage.isEmpty() ) {
+            boolean saw_viruses = false;
+            boolean saw_cellular_organism = false;
+            for( final String[] lineage : lineages ) {
+                if ( lineage.length > 0 ) {
+                    if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.VIRUSES ) ) {
+                        saw_viruses = true;
+                    }
+                    else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.CELLULAR_ORGANISMS ) ) {
+                        saw_cellular_organism = true;
+                    }
+                    if ( saw_cellular_organism && saw_viruses ) {
+                        break;
+                    }
+                }
+            }
+            if ( saw_cellular_organism && saw_viruses ) {
+                last_common_lineage.add( UniProtTaxonomy.CELLULAR_ORGANISMS );
+                last_common = UniProtTaxonomy.CELLULAR_ORGANISMS;
+            }
+            else {
+                String msg = "no common lineage for:\n";
+                int counter = 0;
+                for( final String[] strings : lineages ) {
+                    msg += counter + ": ";
+                    ++counter;
+                    for( final String string : strings ) {
+                        msg += string + " ";
+                    }
+                    msg += "\n";
                 }
-                System.out.println();
+                throw new AncestralTaxonomyInferenceException( msg );
             }
-            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 );
+        tax.setScientificName( last_common );
+        final UniProtTaxonomy up_tax = obtainUniProtTaxonomyFromLineage( last_common_lineage );
         if ( up_tax != null ) {
             if ( !ForesterUtil.isEmpty( up_tax.getRank() ) ) {
                 try {
@@ -267,6 +305,22 @@ 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 );
+                    }
+                }
+            }
+        }
+        if ( ForesterUtil.isEmpty( tax.getLineage() ) ) {
+            tax.setLineage( new ArrayList<String>() );
+            for( final String lin : last_common_lineage ) {
+                if ( !ForesterUtil.isEmpty( lin ) ) {
+                    tax.getLineage().add( lin );
+                }
+            }
         }
         for( final PhylogenyNode desc : descs ) {
             if ( !desc.isExternal() && desc.getNodeData().isHasTaxonomy()
@@ -285,7 +339,7 @@ public final class AncestralTaxonomyInference {
 
     synchronized public static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
                                                                                      final boolean delete )
-            throws IOException {
+            throws IOException, AncestralTaxonomyInferenceException {
         clearCachesIfTooLarge();
         final SortedSet<String> not_found = new TreeSet<String>();
         List<PhylogenyNode> not_found_external_nodes = null;
@@ -310,14 +364,14 @@ 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() );
@@ -328,35 +382,34 @@ 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;
     }
 
-    // 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 {
+    synchronized public static UniProtTaxonomy obtainUniProtTaxonomy( final Taxonomy tax, Object query, QUERY_TYPE qt )
+            throws IOException, AncestralTaxonomyInferenceException {
         if ( isHasAppropriateId( tax ) ) {
             query = tax.getIdentifier().getValue();
             qt = QUERY_TYPE.ID;
             return getTaxonomies( getIdTaxCacheMap(), query, qt );
         }
         else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
-            query = tax.getScientificName();
-            qt = QUERY_TYPE.SN;
-            return getTaxonomies( getSnTaxCacheMap(), query, qt );
+            if ( !ForesterUtil.isEmpty( tax.getLineage() ) ) {
+                query = tax.getLineage();
+                qt = QUERY_TYPE.LIN;
+                return getTaxonomies( getLineageTaxCacheMap(), query, qt );
+            }
+            else {
+                query = tax.getScientificName();
+                qt = QUERY_TYPE.SN;
+                return getTaxonomies( getSnTaxCacheMap(), query, qt );
+            }
         }
         else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
             query = tax.getTaxonomyCode();
@@ -370,16 +423,41 @@ public final class AncestralTaxonomyInference {
         }
     }
 
-    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromSn( final String sn ) throws IOException {
+    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromLineage( final List<String> lineage )
+            throws AncestralTaxonomyInferenceException, IOException {
+        final String lineage_str = ForesterUtil.stringListToString( lineage, ">" );
         UniProtTaxonomy up_tax = null;
-        if ( getSnTaxCacheMap().containsKey( sn ) ) {
-            up_tax = getSnTaxCacheMap().get( sn ).copy();
+        if ( getLineageTaxCacheMap().containsKey( lineage_str ) ) {
+            up_tax = getLineageTaxCacheMap().get( lineage_str ).copy();
         }
         else {
-            final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( sn );
-            if ( ( up_taxonomies != null ) && ( up_taxonomies.size() == 1 ) ) {
-                up_tax = up_taxonomies.get( 0 );
-                getSnTaxCacheMap().put( sn, up_tax );
+            final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
+                    .get( lineage.size() - 1 ) );
+            if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
+                for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
+                    boolean match = true;
+                    I: for( int i = 0; i < lineage.size(); ++i ) {
+                        if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) {
+                            match = false;
+                            break I;
+                        }
+                    }
+                    if ( match ) {
+                        if ( up_tax != null ) {
+                            throw new AncestralTaxonomyInferenceException( "lineage \""
+                                    + ForesterUtil.stringListToString( lineage, " > " ) + "\" is not unique" );
+                        }
+                        up_tax = up_taxonomy;
+                    }
+                }
+                if ( up_tax == null ) {
+                    throw new AncestralTaxonomyInferenceException( "lineage \""
+                            + ForesterUtil.stringListToString( lineage, " > " ) + "\" not found" );
+                }
+                getLineageTaxCacheMap().put( lineage_str, up_tax );
+                if ( !ForesterUtil.isEmpty( up_tax.getScientificName() ) ) {
+                    getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
+                }
                 if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
                     getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
                 }
@@ -402,9 +480,8 @@ 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() && ( 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() )
@@ -422,12 +499,21 @@ public final class AncestralTaxonomyInference {
                 tax.setRank( "" );
             }
         }
-        if ( ( qt != QUERY_TYPE.ID ) && !ForesterUtil.isEmpty( up_tax.getId() ) && ( tax.getIdentifier() == null ) ) {
+        if ( ( qt != QUERY_TYPE.ID ) && !ForesterUtil.isEmpty( up_tax.getId() )
+                && ( ( tax.getIdentifier() == null ) || ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) ) {
             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 {
-        CODE, SN, CN, ID;
+        CODE, SN, CN, ID, LIN;
     }
 }