in progress

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 31de4f9..d0df4c7 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -47,8 +47,10 @@ 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;
+import org.forester.archaeopteryx.*;
 
 public final class TaxonomyDataManager extends RunnableProcess {
 
@@ -195,6 +197,12 @@ 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 ) ) {
+            final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query );
+            return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN );
+ 
+        }
+        
         return SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index c548685..9f7dd65 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -129,6 +129,7 @@ import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
 import org.forester.util.SequenceAccessionTools;
+import org.forester.util.TaxonomyUtil;
 
 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
 

diff --git a/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java b/forester/java/src/org/forester/util/TaxonomyUtil.java
similarity index 94%
rename from forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java
rename to forester/java/src/org/forester/util/TaxonomyUtil.java
index 9a29863..38c8da2 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TaxonomyUtil.java
+++ b/forester/java/src/org/forester/util/TaxonomyUtil.java
@@ -1,14 +1,23 @@
 
-package org.forester.archaeopteryx;
+package org.forester.util;
 
 import java.util.HashMap;
 import java.util.Map;
 
-final class TaxonomyUtil {
+public final class TaxonomyUtil {
 
-    static String getTaxGroupByTaxCode( final String code ) {
+    public static String getTaxGroupByTaxCode( final String code ) {
         return _default_taxcode_taxgroup_map.get( code );
     }
+    
+    public static int getTaxIdFromFakeTaxCode( final String code ) {
+       return FAKE_CODE_TO_ID_MAP.get( code );
+    }
+    
+    public static boolean isHasTaxIdFromFakeTaxCode( final String code ) {
+        return FAKE_CODE_TO_ID_MAP.containsKey( code );
+     }
+    
     private final static Map<String, String> _default_taxcode_taxgroup_map = new HashMap<String, String>();
     static {
         _default_taxcode_taxgroup_map.put( "HUMAN", "deuterostomia" );
@@ -534,4 +543,37 @@ final class TaxonomyUtil {
         _default_taxcode_taxgroup_map.put( "HELPH", "bacteria" );
         _default_taxcode_taxgroup_map.put( "AQUAE", "bacteria" );
     }
+    
+    private final static Map<String,Integer> FAKE_CODE_TO_ID_MAP = new  HashMap<String,Integer>();
+
+    static {
+        FAKE_CODE_TO_ID_MAP.put( "CTEXX", 283909);
+        FAKE_CODE_TO_ID_MAP.put( "HMAXX", 6085);
+        FAKE_CODE_TO_ID_MAP.put( "SARXX", 72019);
+        FAKE_CODE_TO_ID_MAP.put( "AALXX", 398408);
+        FAKE_CODE_TO_ID_MAP.put( "PFIXX", 83344);
+        FAKE_CODE_TO_ID_MAP.put( "MPSXX", 692275);
+        FAKE_CODE_TO_ID_MAP.put( "BCOXX", 430998);
+        FAKE_CODE_TO_ID_MAP.put( "APPXX", 178873);
+        FAKE_CODE_TO_ID_MAP.put( "APMXX", 46634);
+        FAKE_CODE_TO_ID_MAP.put( "APSXX", 1042127);
+        FAKE_CODE_TO_ID_MAP.put( "CPUXX", 80637);
+        FAKE_CODE_TO_ID_MAP.put( "JARXX", 202697);
+        FAKE_CODE_TO_ID_MAP.put( "FPIXX", 40483);
+        FAKE_CODE_TO_ID_MAP.put( "PPLXX", 104341);
+        FAKE_CODE_TO_ID_MAP.put( "MVNXX", 1069443);
+        FAKE_CODE_TO_ID_MAP.put( "CREXX", 61392);
+        FAKE_CODE_TO_ID_MAP.put( "FALXX", 691883);
+        FAKE_CODE_TO_ID_MAP.put( "CCLXX", 85681);
+        FAKE_CODE_TO_ID_MAP.put( "ORCXX", 385169);
+        FAKE_CODE_TO_ID_MAP.put( "ASCXX", 763042);
+        FAKE_CODE_TO_ID_MAP.put( "CSUXX", 574566);
+        FAKE_CODE_TO_ID_MAP.put( "OTRXX", 1172189);
+        FAKE_CODE_TO_ID_MAP.put( "FCYXX", 186039);
+        FAKE_CODE_TO_ID_MAP.put( "AKEXX", 702273);
+        FAKE_CODE_TO_ID_MAP.put( "SAGXX", 876976);
+        FAKE_CODE_TO_ID_MAP.put( "ALIXX", 87102);
+        FAKE_CODE_TO_ID_MAP.put( "TTRXX", 529818);
+
+    }
 }

diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
index c379607..692f8dd 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
@@ -26,7 +26,9 @@
 package org.forester.ws.seqdb;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.forester.util.ForesterUtil;
 
@@ -45,7 +47,9 @@ public final class UniProtTaxonomy {
     public final static String CELLULAR_ORGANISMS = "cellular organisms";
     public final static String VIRUSES            = "Viruses";
     public static final String X                  = "x";
-
+    
+  
+    
     public UniProtTaxonomy( final String line ) {
         final String[] items = line.split( "\t" );
         if ( items.length < 5 ) {
@@ -158,6 +162,11 @@ public final class UniProtTaxonomy {
         return _synonym;
     }
 
+    
+   
+    
+    
+    
     public final static UniProtTaxonomy createSpecialFromScientificName( final String sn ) {
         final List<String> lineage = new ArrayList<String>();
         final String code = "";