X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fanalysis%2FAncestralTaxonomyInference.java;h=94453ff5834713b749ea89852981a135a932e406;hb=2320da44a171273ec44c0adcaf991687a4780b6e;hp=dec0a635a22def5b0097f958aaca0c0fc2fe536e;hpb=c365c2e336ee79677d9e0f5d5c8d280afb56a3ab;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index dec0a63..94453ff 100644
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -20,16 +20,13 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.analysis;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
 
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.phylogeny.Phylogeny;
@@ -38,129 +35,23 @@ import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public final class AncestralTaxonomyInference {
 
-    private static final int                              MAX_CACHE_SIZE           = 100000;
-    private static final int                              MAX_TAXONOMIES_TO_RETURN = 100;
-    private static final HashMap<String, UniProtTaxonomy> _sn_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>();
-
-    synchronized private static void clearCachesIfTooLarge() {
-        if ( getSnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
-            getSnTaxCacheMap().clear();
-        }
-        if ( getCnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
-            getCnTaxCacheMap().clear();
-        }
-        if ( getCodeTaxCacheMap().size() > MAX_CACHE_SIZE ) {
-            getCodeTaxCacheMap().clear();
-        }
-        if ( getIdTaxCacheMap().size() > MAX_CACHE_SIZE ) {
-            getIdTaxCacheMap().clear();
-        }
-    }
-
-    synchronized private static HashMap<String, UniProtTaxonomy> getCnTaxCacheMap() {
-        return _cn_up_cache_map;
-    }
-
-    synchronized private static HashMap<String, UniProtTaxonomy> getCodeTaxCacheMap() {
-        return _code_up_cache_map;
-    }
-
-    synchronized private static HashMap<String, UniProtTaxonomy> getIdTaxCacheMap() {
-        return _id_up_cache_map;
-    }
-
-    synchronized private static HashMap<String, UniProtTaxonomy> getSnTaxCacheMap() {
-        return _sn_up_cache_map;
-    }
-
-    synchronized private static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
-                                                               final String query,
-                                                               final QUERY_TYPE qt ) throws IOException {
-        if ( cache.containsKey( query ) ) {
-            return cache.get( query ).copy();
-        }
-        else {
-            List<UniProtTaxonomy> up_taxonomies = null;
-            switch ( qt ) {
-                case ID:
-                    up_taxonomies = getTaxonomiesFromId( query );
-                    break;
-                case CODE:
-                    up_taxonomies = getTaxonomiesFromTaxonomyCode( query );
-                    break;
-                case SN:
-                    up_taxonomies = getTaxonomiesFromScientificName( query );
-                    break;
-                case CN:
-                    up_taxonomies = getTaxonomiesFromCommonName( query );
-                    break;
-                default:
-                    throw new RuntimeException();
-            }
-            if ( ( up_taxonomies != null ) && ( up_taxonomies.size() == 1 ) ) {
-                final UniProtTaxonomy up_tax = up_taxonomies.get( 0 );
-                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 );
-                }
-                if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
-                    getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
-                }
-                if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
-                    getIdTaxCacheMap().put( up_tax.getId(), up_tax );
-                }
-                return up_tax;
-            }
-            else {
-                return null;
-            }
-        }
-    }
-
-    synchronized private static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query )
-            throws IOException {
-        return UniProtWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
-    }
-
-    synchronized private static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
-        return UniProtWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
-    }
-
-    synchronized private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query )
-            throws IOException {
-        return UniProtWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
-    }
-
-    synchronized private static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query )
-            throws IOException {
-        return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
-    }
-
-    synchronized public static SortedSet<String> inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException {
-        clearCachesIfTooLarge();
-        final SortedSet<String> not_found = new TreeSet<String>();
+    public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
+    AncestralTaxonomyInferenceException {
+        TaxonomyDataManager.clearCachesIfTooLarge();
         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 {
+    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" );
         }
@@ -170,22 +61,34 @@ public final class AncestralTaxonomyInference {
         int shortest_lin_length = Integer.MAX_VALUE;
         for( final PhylogenyNode desc : descs ) {
             if ( desc.getNodeData().isHasTaxonomy()
-                    && ( isHasAppropriateId( desc.getNodeData().getTaxonomy() )
+                    && ( TaxonomyDataManager.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 UniProtTaxonomy up_tax = obtainUniProtTaxonomy( desc.getNodeData().getTaxonomy(), null, null );
-                String[] lineage = null;
-                if ( up_tax != null ) {
-                    //lineage = obtainLineagePlusOwnScientificName( up_tax );
-                    lineage = up_tax.getLineageAsArray();
+                final UniProtTaxonomy up_tax = TaxonomyDataManager.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;
@@ -193,7 +96,6 @@ 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() + "\"";
@@ -201,22 +103,12 @@ public final class AncestralTaxonomyInference {
                 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 );
+                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 ];
@@ -225,26 +117,52 @@ 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( final String[] strings : lineages ) {
-                System.out.print( counter + ": " );
-                ++counter;
-                for( final String string : strings ) {
-                    System.out.print( string + " " );
+        if ( last_common_lineage.isEmpty() ) {
+            boolean saw_viruses = false;
+            boolean saw_cellular_organism = false;
+            boolean saw_x = 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;
+                    }
+                    else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.X ) ) {
+                        saw_x = true;
+                    }
+                    if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
+                        break;
+                    }
+                }
+            }
+            if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
+                last_common_lineage.add( UniProtTaxonomy.X );
+                last_common = UniProtTaxonomy.X;
+            }
+            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;
         }
         final Taxonomy tax = new Taxonomy();
         n.getNodeData().setTaxonomy( tax );
-        tax.setScientificName( last_common_lineage );
-        final UniProtTaxonomy up_tax = obtainUniProtTaxonomyFromSn( last_common_lineage, lineage );
+        tax.setScientificName( last_common );
+        final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomyFromLineage( last_common_lineage );
         if ( up_tax != null ) {
             if ( !ForesterUtil.isEmpty( up_tax.getRank() ) ) {
                 try {
@@ -271,182 +189,20 @@ public final class AncestralTaxonomyInference {
                     }
                 }
             }
-            
-        }
-        for( final PhylogenyNode desc : descs ) {
-            if ( !desc.isExternal() && desc.getNodeData().isHasTaxonomy()
-                    && desc.getNodeData().getTaxonomy().isEqual( tax ) ) {
-                desc.getNodeData().setTaxonomy( null );
-            }
         }
-    }
-
-    synchronized private static boolean isHasAppropriateId( final Taxonomy tax ) {
-        return ( ( tax.getIdentifier() != null ) && ( !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) && ( tax
-                .getIdentifier().getProvider().equalsIgnoreCase( "ncbi" )
-                || tax.getIdentifier().getProvider().equalsIgnoreCase( "uniprot" ) || tax.getIdentifier().getProvider()
-                .equalsIgnoreCase( "uniprotkb" ) ) ) );
-    }
-
-    synchronized public static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
-                                                                                     final boolean delete )
-            throws IOException {
-        clearCachesIfTooLarge();
-        final SortedSet<String> not_found = new TreeSet<String>();
-        List<PhylogenyNode> not_found_external_nodes = null;
-        if ( delete ) {
-            not_found_external_nodes = new ArrayList<PhylogenyNode>();
-        }
-        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();
-            }
-            else if ( node.isExternal() ) {
-                if ( !ForesterUtil.isEmpty( node.getName() ) ) {
-                    not_found.add( node.getName() );
-                }
-                else {
-                    not_found.add( node.toString() );
-                }
-                if ( delete ) {
-                    not_found_external_nodes.add( node );
-                }
-            }
-            UniProtTaxonomy uniprot_tax = null;
-            if ( ( tax != null )
-                    && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() )
-                            || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil.isEmpty( tax
-                            .getCommonName() ) ) ) {
-                uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
-                if ( uniprot_tax != null ) {
-                    updateTaxonomy( qt, node, tax, uniprot_tax );
-                }
-                else {
-                    not_found.add( tax.toString() );
-                    if ( delete && node.isExternal() ) {
-                        not_found_external_nodes.add( node );
-                    }
-                }
-            }
-        }
-        if ( delete ) {
-            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 {
-        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() ) ) {
-            query = tax.getTaxonomyCode();
-            qt = QUERY_TYPE.CODE;
-            return getTaxonomies( getCodeTaxCacheMap(), query, qt );
-        }
-        else {
-            query = tax.getCommonName();
-            qt = QUERY_TYPE.CN;
-            return getTaxonomies( getCnTaxCacheMap(), query, qt );
-        }
-    }
-
-    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();
-        }
-        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 );
-                if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
-                    getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
-                }
-                if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
-                    getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
-                }
-                if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
-                    getIdTaxCacheMap().put( up_tax.getId(), up_tax );
-                }
-                
-            }
-        }
-        return up_tax;
-    }
-
-    synchronized private static void updateTaxonomy( final QUERY_TYPE qt,
-                                                     final PhylogenyNode node,
-                                                     final Taxonomy tax,
-                                                     final UniProtTaxonomy up_tax ) {
-        if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
-                && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
-            tax.setScientificName( up_tax.getScientificName() );
-        }
-        //  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() )
-                && ForesterUtil.isEmpty( tax.getCommonName() ) ) {
-            tax.setCommonName( up_tax.getCommonName() );
-        }
-        if ( !ForesterUtil.isEmpty( up_tax.getSynonym() ) && !tax.getSynonyms().contains( up_tax.getSynonym() ) ) {
-            tax.getSynonyms().add( up_tax.getSynonym() );
-        }
-        if ( !ForesterUtil.isEmpty( up_tax.getRank() ) && ForesterUtil.isEmpty( tax.getRank() ) ) {
-            try {
-                tax.setRank( up_tax.getRank().toLowerCase() );
-            }
-            catch ( final PhyloXmlDataFormatException ex ) {
-                tax.setRank( "" );
-            }
-        }
-        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 ) {
+        if ( ForesterUtil.isEmpty( tax.getLineage() ) ) {
             tax.setLineage( new ArrayList<String>() );
-            for( final String lin : up_tax.getLineage() ) {
+            for( final String lin : last_common_lineage ) {
                 if ( !ForesterUtil.isEmpty( lin ) ) {
                     tax.getLineage().add( lin );
                 }
             }
         }
-        
-    }
-
-    private enum QUERY_TYPE {
-        CODE, SN, CN, ID;
+        for( final PhylogenyNode desc : descs ) {
+            if ( !desc.isExternal() && desc.getNodeData().isHasTaxonomy()
+                    && desc.getNodeData().getTaxonomy().isEqual( tax ) ) {
+                desc.getNodeData().setTaxonomy( null );
+            }
+        }
     }
 }