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=d0df4c745d4e6ac5420da91fcd535c846d26104c;hpb=17dce416188e13160d9bf0840bb370e3adca041e;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index d0df4c7..1652603 100644
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -50,7 +50,6 @@ import org.forester.util.ForesterUtil;
 import org.forester.util.TaxonomyUtil;
 import org.forester.ws.seqdb.SequenceDbWsTools;
 import org.forester.ws.seqdb.UniProtTaxonomy;
-import org.forester.archaeopteryx.*;
 
 public final class TaxonomyDataManager extends RunnableProcess {
 
@@ -58,7 +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>();
@@ -197,12 +196,10 @@ 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 ) ) {
+        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 );
     }