X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fanalysis%2FTaxonomyDataManager.java;h=16526037475e5f3bdaa0f5562d190a1cb9d0c943;hb=fd75019dbb063c8fbead81a2799da9093a5dfae5;hp=1a1bef65828f29b38e50a528834a276c10e5b60e;hpb=cbc5c71b164a57b8ad6c988d015057c7f0972478;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 1a1bef6..1652603 100644
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -47,6 +47,7 @@ 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.util.TaxonomyUtil;
 import org.forester.ws.seqdb.SequenceDbWsTools;
 import org.forester.ws.seqdb.UniProtTaxonomy;
 
@@ -56,7 +57,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         CODE, SN, CN, ID, LIN;
     }
     private static final int                              MAX_CACHE_SIZE           = 100000;
-    private static final int                              MAX_TAXONOMIES_TO_RETURN = 10;
+    private static final int                              MAX_TAXONOMIES_TO_RETURN = 2000;
     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>();
@@ -184,10 +185,21 @@ public final class TaxonomyDataManager extends RunnableProcess {
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query ) throws IOException {
+        if ( query.equalsIgnoreCase( UniProtTaxonomy.BACTERIA ) || query.equalsIgnoreCase( UniProtTaxonomy.ARCHAEA )
+                || query.equalsIgnoreCase( UniProtTaxonomy.VIRUSES )
+                || query.equalsIgnoreCase( UniProtTaxonomy.EUKARYOTA ) || query.equalsIgnoreCase( UniProtTaxonomy.X ) ) {
+            final List<UniProtTaxonomy> l = new ArrayList<UniProtTaxonomy>();
+            l.add( UniProtTaxonomy.createSpecialFromScientificName( query ) );
+            return l;
+        }
         return SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
+        if ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) {
+            final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query );
+            return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN );
+        }
         return SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
     }