X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fanalysis%2FTaxonomyDataManager.java;h=78c75f9b36e0a93d82d95a72bab2c0d450553c3b;hb=1706deea223bc1a30d170596192d726b6847b7eb;hp=ad9ee250d2fff9962c6c2be13388471ce2579a19;hpb=fbb463a0dc277aa6efa5231f6db554de3696b194;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index ad9ee25..78c75f9 100644
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -33,6 +33,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.SortedSet;
 import java.util.TreeSet;
+import java.util.regex.Matcher;
 
 import javax.swing.JOptionPane;
 
@@ -129,10 +130,12 @@ public final class TaxonomyDataManager extends RunnableProcess {
         return _sn_up_cache_map;
     }
 
+    
+    @SuppressWarnings("unchecked")
     private final static UniProtTaxonomy obtainTaxonomy( final HashMap<String, UniProtTaxonomy> cache,
                                                          final Object query,
                                                          final QUERY_TYPE qt ) throws IOException,
-            AncestralTaxonomyInferenceException {
+                                                         AncestralTaxonomyInferenceException {
         if ( cache.containsKey( query ) ) {
             return cache.get( query ).copy();
         }
@@ -153,6 +156,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                     break;
                 case LIN:
                     return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
+                    
                 default:
                     throw new RuntimeException();
             }
@@ -198,7 +202,10 @@ public final class TaxonomyDataManager extends RunnableProcess {
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
-        if ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) {
+        //FIXME fix "SPHAR" issue
+        if ( ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) )
+                || query.equals( "SPHAR" ) /* TODO remove me, is same as Sphingomonas aromaticivorans */
+                ) {
             final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query );
             return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN );
         }
@@ -215,7 +222,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
     synchronized final private static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
                                                                                             final boolean delete,
                                                                                             final boolean allow_to_use_basic_node_names )
-            throws IOException, AncestralTaxonomyInferenceException {
+                                                                                                    throws IOException, AncestralTaxonomyInferenceException {
         clearCachesIfTooLarge();
         final SortedSet<String> not_found = new TreeSet<String>();
         List<PhylogenyNode> not_found_external_nodes = null;
@@ -349,17 +356,17 @@ public final class TaxonomyDataManager extends RunnableProcess {
                 ut = obtainTaxonomy( TaxonomyDataManager.getIdTaxCacheMap(), id, qt );
             }
         }
-        //
-        //        qt = QUERY_TYPE.SN;
-        //        UniProtTaxonomy ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), simple_name, qt );
-        //        if ( ut == null ) {
-        //            qt = QUERY_TYPE.CODE;
-        //            ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), simple_name, qt );
-        //        }
-        //        if ( ut == null ) {
-        //            qt = QUERY_TYPE.CN;
-        //            ut = obtainTaxonomy( TaxonomyDataManager.getCnTaxCacheMap(), simple_name, qt );
-        //        }
+        if ( ut == null ) {
+            String sn = "";
+            final Matcher m = ParserUtils.TAXOMONY_SN_PATTERN_GENUS.matcher( simple_name );
+            if ( m.matches() ) {
+                sn = m.group( 1 );
+            }
+            if ( !ForesterUtil.isEmpty( sn ) ) {
+                qt = QUERY_TYPE.SN;
+                ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), sn, qt );
+            }
+        }
         return ut;
     }
 
@@ -372,7 +379,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         else {
             final List<UniProtTaxonomy> matching_taxonomies = new ArrayList<UniProtTaxonomy>();
             final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
-                    .get( lineage.size() - 1 ) );
+                                                                                         .get( lineage.size() - 1 ) );
             if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
                 for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
                     boolean match = true;
@@ -421,7 +428,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
             }
             else {
                 throw new AncestralTaxonomyInferenceException( "taxonomy \"" + ( lineage.get( lineage.size() - 1 ) )
-                        + "\" not found" );
+                                                               + "\" not found" );
             }
         }
     }
@@ -430,7 +437,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                                                            final PhylogenyNode node,
                                                            final Taxonomy tax,
                                                            final UniProtTaxonomy up_tax )
-            throws PhyloXmlDataFormatException {
+                                                                   throws PhyloXmlDataFormatException {
         if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
                 && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             tax.setScientificName( up_tax.getScientificName() );
@@ -508,7 +515,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                                                JOptionPane.WARNING_MESSAGE );
             }
             catch ( final Exception e ) {
-                // Not important if this fails, do nothing. 
+                // Not important if this fails, do nothing.
             }
             return;
         }
@@ -560,7 +567,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                                                JOptionPane.WARNING_MESSAGE );
             }
             catch ( final Exception e ) {
-                // Not important if this fails, do nothing. 
+                // Not important if this fails, do nothing.
             }
         }
         else {