From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 18 Nov 2013 18:29:52 +0000 (+0000)
Subject: cleanup
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fd93d9051360270863585a005a90e1ee307b314b;p=jalview.git

cleanup
---

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index d0df4c7..52b5fdf 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 {
 
@@ -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 );
     }
 
diff --git a/forester/java/src/org/forester/util/TaxonomyUtil.java b/forester/java/src/org/forester/util/TaxonomyUtil.java
index 38c8da2..df45c1d 100644
--- a/forester/java/src/org/forester/util/TaxonomyUtil.java
+++ b/forester/java/src/org/forester/util/TaxonomyUtil.java
@@ -9,16 +9,15 @@ public final class TaxonomyUtil {
     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 );
+        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>();
+    }
+    private final static Map<String, String>  _default_taxcode_taxgroup_map = new HashMap<String, String>();
     static {
         _default_taxcode_taxgroup_map.put( "HUMAN", "deuterostomia" );
         _default_taxcode_taxgroup_map.put( "HOMSA", "deuterostomia" );
@@ -543,37 +542,34 @@ public 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>();
-
+    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);
-
+        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 692f8dd..c379607 100644
--- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
@@ -26,9 +26,7 @@
 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;
 
@@ -47,9 +45,7 @@ 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 ) {
@@ -162,11 +158,6 @@ public final class UniProtTaxonomy {
         return _synonym;
     }
 
-    
-   
-    
-    
-    
     public final static UniProtTaxonomy createSpecialFromScientificName( final String sn ) {
         final List<String> lineage = new ArrayList<String>();
         final String code = "";