X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fanalysis%2FAncestralTaxonomyInference.java;h=11d678d323ea2bc092f05866a6a4d5807db861e6;hb=fd93d9051360270863585a005a90e1ee307b314b;hp=09291f6b1a8efb6ccb20c51831b2062744726034;hpb=cd262b9df153624d042b47de8c142f70e27474ec;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index 09291f6..11d678d 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;
@@ -38,128 +35,13 @@ 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 = 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>();
-
-    synchronized private static void clearCachesIfTooLarge() {
-        if ( getSnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
-            getSnTaxCacheMap().clear();
-        }
-        if ( getLineageTaxCacheMap().size() > MAX_CACHE_SIZE ) {
-            getLineageTaxCacheMap().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 HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
-        return _lineage_up_cache_map;
-    }
-
-    synchronized private static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
-                                                               final Object query,
-                                                               final QUERY_TYPE qt ) throws IOException,
+    public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
             AncestralTaxonomyInferenceException {
-        if ( cache.containsKey( query ) ) {
-            return cache.get( query ).copy();
-        }
-        else {
-            List<UniProtTaxonomy> up_taxonomies = null;
-            switch ( qt ) {
-                case ID:
-                    up_taxonomies = getTaxonomiesFromId( ( String ) query );
-                    break;
-                case CODE:
-                    up_taxonomies = getTaxonomiesFromTaxonomyCode( ( String ) query );
-                    break;
-                case SN:
-                    up_taxonomies = getTaxonomiesFromScientificName( ( String ) query );
-                    break;
-                case CN:
-                    up_taxonomies = getTaxonomiesFromCommonName( ( String ) query );
-                    break;
-                case LIN:
-                    return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
-                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 void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
-            AncestralTaxonomyInferenceException {
-        clearCachesIfTooLarge();
+        TaxonomyDataManager.clearCachesIfTooLarge();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             if ( !node.isExternal() ) {
@@ -168,7 +50,7 @@ public final class AncestralTaxonomyInference {
         }
     }
 
-    synchronized private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) 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" );
@@ -179,12 +61,13 @@ 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 );
+                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() ) ) {
@@ -220,17 +103,6 @@ public final class AncestralTaxonomyInference {
                 else {
                     node = "[" + desc.getId() + "]";
                 }
-                //   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 AncestralTaxonomyInferenceException( "node " + node
                         + " has no or inappropriate taxonomic information" );
             }
@@ -252,6 +124,7 @@ public final class AncestralTaxonomyInference {
         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 ) ) {
@@ -260,14 +133,17 @@ public final class AncestralTaxonomyInference {
                     else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.CELLULAR_ORGANISMS ) ) {
                         saw_cellular_organism = true;
                     }
-                    if ( saw_cellular_organism && saw_viruses ) {
+                    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 ) {
-                last_common_lineage.add( UniProtTaxonomy.CELLULAR_ORGANISMS );
-                last_common = UniProtTaxonomy.CELLULAR_ORGANISMS;
+            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";
@@ -286,7 +162,7 @@ public final class AncestralTaxonomyInference {
         final Taxonomy tax = new Taxonomy();
         n.getNodeData().setTaxonomy( tax );
         tax.setScientificName( last_common );
-        final UniProtTaxonomy up_tax = obtainUniProtTaxonomyFromLineage( last_common_lineage );
+        final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomyFromLineage( last_common_lineage );
         if ( up_tax != null ) {
             if ( !ForesterUtil.isEmpty( up_tax.getRank() ) ) {
                 try {
@@ -329,190 +205,4 @@ public final class AncestralTaxonomyInference {
             }
         }
     }
-
-    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, AncestralTaxonomyInferenceException {
-        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;
-    }
-
-    synchronized private 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() ) ) {
-            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();
-            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 obtainUniProtTaxonomyFromLineage( final List<String> lineage )
-            throws AncestralTaxonomyInferenceException, IOException {
-        final String lineage_str = ForesterUtil.stringListToString( lineage, ">" );
-        UniProtTaxonomy up_tax = null;
-        if ( getLineageTaxCacheMap().containsKey( lineage_str ) ) {
-            up_tax = getLineageTaxCacheMap().get( lineage_str ).copy();
-        }
-        else {
-            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 );
-                }
-                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() && ( 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 ) {
-            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, LIN;
-    }
 }