in progress

diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
index 600f00f..c373104 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
+++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java
@@ -60,7 +60,7 @@ import org.forester.util.ForesterUtil;
 
 public final class NHXParser implements PhylogenyParser {
 
-    public static final boolean                              LIMIT_SPECIES_NAMES_TO_FIVE_CHARS = true;
+    public static final boolean                              LIMIT_SPECIES_NAMES_TO_FIVE_CHARS = false;
     public static final PhylogenyMethods.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION_DEFAULT       = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
     final static private boolean                             GUESS_ROOTEDNESS_DEFAULT          = true;
     final static private boolean                             GUESS_IF_SUPPORT_VALUES           = true;

diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
index 8d65e24..a1f842e 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
+++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java
@@ -234,7 +234,7 @@ public final class ParserUtils {
             final String[] s = name.split( "[_/]" );
             if ( s.length > 1 ) {
                 String str = s[ 1 ];
-                if ( !limit_to_five || ( str.length() < 6 ) ) {
+                if ( ( str.length() < 6 ) || ( !limit_to_five && ( str.length() < 7 ) ) ) {
                     if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
                         str = str.substring( 0, 3 );
                     }

diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java b/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
index 22c46c7..d83d183 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
+++ b/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
@@ -41,6 +41,8 @@ import org.forester.util.ForesterUtil;
 
 public final class UniProtWsTools {
 
+    private static final boolean ALLOW_TAXONOMY_CODE_HACKS = true; //TODO turn off for final realease!
+
     public enum Db {
         UNKNOWN, UNIPROT;
     }
@@ -116,10 +118,10 @@ public final class UniProtWsTools {
             throws IOException {
         // Hack!  Craniata? .. 
         if ( sn.equals( "Drosophila" ) ) {
-            return hack( UniProtTaxonomy.DROSOPHILA_GENUS );
+            return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS );
         }
         else if ( sn.equals( "Xenopus" ) ) {
-            return hack( UniProtTaxonomy.XENOPUS_GENUS );
+            return uniProtTaxonomyToList( UniProtTaxonomy.XENOPUS_GENUS );
         }
         // else if ( sn.equals( "Nucleariidae and Fonticula group" ) ) {
         //     return hack( UniProtTaxonomy.NUCLEARIIDAE_AND_FONTICULA );
@@ -156,13 +158,12 @@ public final class UniProtWsTools {
     public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String code,
                                                                        final int max_taxonomies_return )
             throws IOException {
-        String my_code = new String( code );
-        // Hacks!
-        if ( my_code.equals( "FUGRU" ) ) {
-            my_code = "TAKRU";
-        }
-        else if ( my_code.equals( "CAP" ) ) {
-            return hack( UniProtTaxonomy.CAPITELLA_TELATA_SPECIES );
+        final String my_code = new String( code );
+        if ( ALLOW_TAXONOMY_CODE_HACKS ) {
+            final List<UniProtTaxonomy> l = resolveFakeTaxonomyCodes( max_taxonomies_return, my_code );
+            if ( l != null ) {
+                return l;
+            }
         }
         final List<String> result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return );
         if ( result.size() > 0 ) {
@@ -171,6 +172,82 @@ public final class UniProtWsTools {
         return null;
     }
 
+    private static List<UniProtTaxonomy> resolveFakeTaxonomyCodes( final int max_taxonomies_return, final String code )
+            throws IOException {
+        if ( code.equals( "CAP" ) ) {
+            return getTaxonomiesFromId( "283909", max_taxonomies_return );
+        }
+        else if ( code.equals( "FUGRU" ) ) {
+            return getTaxonomiesFromId( "31033", max_taxonomies_return );
+        }
+        else if ( code.equals( "GIALA" ) ) {
+            return getTaxonomiesFromId( "5741", max_taxonomies_return );
+        }
+        else if ( code.equals( "TRIVE" ) ) {
+            return getTaxonomiesFromId( "413071", max_taxonomies_return );
+        }
+        else if ( code.equals( "CAPOWC" ) ) {
+            return getTaxonomiesFromId( "192875", max_taxonomies_return );
+        }
+        else if ( code.equals( "SPHARC" ) ) {
+            return getTaxonomiesFromId( "667725", max_taxonomies_return );
+        }
+        else if ( code.equals( "AGABB" ) ) {
+            return getTaxonomiesFromId( "597362", max_taxonomies_return );
+        }
+        else if ( code.equals( "BAUCOM" ) ) {
+            return getTaxonomiesFromId( "430998", max_taxonomies_return );
+        }
+        else if ( code.equals( "DICSQU" ) ) {
+            return getTaxonomiesFromId( "114155", max_taxonomies_return );
+        }
+        else if ( code.equals( "FOMPIN" ) ) {
+            return getTaxonomiesFromId( "40483", max_taxonomies_return );
+        }
+        else if ( code.equals( "HYDMA" ) ) {
+            return getTaxonomiesFromId( "6085", max_taxonomies_return );
+        }
+        else if ( code.equals( "MYCFI" ) ) {
+            return getTaxonomiesFromId( "83344", max_taxonomies_return );
+        }
+        else if ( code.equals( "OIDMAI" ) ) {
+            return getTaxonomiesFromId( "78148", max_taxonomies_return );
+        }
+        else if ( code.equals( "OSTRC" ) ) {
+            return getTaxonomiesFromId( "385169", max_taxonomies_return );
+        }
+        else if ( code.equals( "POSPL" ) ) {
+            return getTaxonomiesFromId( "104341", max_taxonomies_return );
+        }
+        else if ( code.equals( "SAICOM" ) ) {
+            return getTaxonomiesFromId( "5606", max_taxonomies_return );
+        }
+        else if ( code.equals( "SERLA" ) ) {
+            return getTaxonomiesFromId( "85982", max_taxonomies_return );
+        }
+        else if ( code.equals( "SPORO" ) ) {
+            return getTaxonomiesFromId( "40563", max_taxonomies_return );
+        }
+        else if ( code.equals( "ACRALC" ) ) {
+            return getTaxonomiesFromId( "398408", max_taxonomies_return );
+        }
+        else if ( code.equals( "THITER" ) ) {
+            return getTaxonomiesFromId( "35720", max_taxonomies_return );
+        }
+        else if ( code.equals( "MYCTHE" ) ) {
+            return getTaxonomiesFromId( "78579", max_taxonomies_return );
+        }
+        else if ( code.equals( "CONPUT" ) ) {
+            return getTaxonomiesFromId( "80637", max_taxonomies_return );
+        }
+        else if ( code.equals( "WOLCOC" ) ) {
+            return getTaxonomiesFromId( "81056", max_taxonomies_return );
+        }
+        else {
+            return null;
+        }
+    }
+
     private static List<String> getTaxonomyStringFromCommonName( final String cn, final int max_lines_to_return )
             throws IOException {
         return queryUniprot( "taxonomy/?query=common%3a%22" + encode( cn ) + "%22&format=tab", max_lines_to_return );
@@ -191,7 +268,7 @@ public final class UniProtWsTools {
         return queryUniprot( "taxonomy/?query=mnemonic%3a%22" + encode( code ) + "%22&format=tab", max_lines_to_return );
     }
 
-    private static List<UniProtTaxonomy> hack( final UniProtTaxonomy tax ) {
+    private static List<UniProtTaxonomy> uniProtTaxonomyToList( final UniProtTaxonomy tax ) {
         final List<UniProtTaxonomy> l = new ArrayList<UniProtTaxonomy>();
         l.add( tax );
         return l;