X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterUtil.java;h=7492f1e6e957c639e8ddec0f6c18095b78ca4319;hb=5ea47511ea9c077b4b4709bed68ac31d6eee0477;hp=b819971f4cff7c89b13c6a9ddc6a3c218304bf33;hpb=41ea5973f93687513d29e5b7cad1abff8f3adb4b;p=jalview.git

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index b819971..7492f1e 100644
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -91,6 +91,7 @@ public final class ForesterUtil {
     public static final String       NCBI_NUCCORE                     = "http://www.ncbi.nlm.nih.gov/nuccore/";
     public final static String       UNIPROT_KB                       = "http://www.uniprot.org/uniprot/";
     public static final String       NCBI_GI                          = "http://www.ncbi.nlm.nih.gov/protein/gi:";
+    public static final String       PDB                              = "http://www.pdb.org/pdb/explore/explore.do?pdbId=";
     static {
         final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
         dfs.setDecimalSeparator( '.' );
@@ -1204,107 +1205,161 @@ public final class ForesterUtil {
         System.exit( -1 );
     }
 
-    public final static Color obtainColorDependingOnTaxonomyGroup( final String tax, final String tax_code ) {
-        if ( tax.equalsIgnoreCase( "deuterostomia" ) ) {
-            printRel( tax_code, "deuterostomia" );
-            return TaxonomyColors.DEUTEROSTOMIA_COLOR;
+    public final static Color obtainColorDependingOnTaxonomyGroup( final String tax_group ) {
+        if ( !ForesterUtil.isEmpty( tax_group ) ) {
+            if ( tax_group.equals( TaxonomyGroups.DEUTEROSTOMIA ) ) {
+                return TaxonomyColors.DEUTEROSTOMIA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.PROTOSTOMIA ) ) {
+                return TaxonomyColors.PROTOSTOMIA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.CNIDARIA ) ) {
+                return TaxonomyColors.CNIDARIA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.PLACOZOA ) ) {
+                return TaxonomyColors.PLACOZOA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.CTENOPHORA ) ) {
+                return TaxonomyColors.CTENOPHORA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.PORIFERA ) ) {
+                return TaxonomyColors.PORIFERA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
+                return TaxonomyColors.CHOANOFLAGELLIDA;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA ) ) {
+                return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.DIKARYA ) ) {
+                return TaxonomyColors.DIKARYA_COLOR;
+            }
+            else if ( tax_group.equalsIgnoreCase( TaxonomyGroups.FUNGI )
+                    || tax_group.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
+                return TaxonomyColors.OTHER_FUNGI_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP ) ) {
+                return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.AMOEBOZOA ) ) {
+                return TaxonomyColors.AMOEBOZOA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.EMBRYOPHYTA ) ) {
+                return TaxonomyColors.EMBRYOPHYTA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.CHLOROPHYTA ) ) {
+                return TaxonomyColors.CHLOROPHYTA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.RHODOPHYTA ) ) {
+                return TaxonomyColors.RHODOPHYTA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.HACROBIA ) ) {
+                return TaxonomyColors.HACROBIA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) ) {
+                return TaxonomyColors.GLAUCOPHYTA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.STRAMENOPILES ) ) {
+                return TaxonomyColors.STRAMENOPILES_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.ALVEOLATA ) ) {
+                return TaxonomyColors.ALVEOLATA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.RHIZARIA ) ) {
+                return TaxonomyColors.RHIZARIA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.EXCAVATA ) ) {
+                return TaxonomyColors.EXCAVATA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.APUSOZOA ) ) {
+                return TaxonomyColors.APUSOZOA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.ARCHAEA ) ) {
+                return TaxonomyColors.ARCHAEA_COLOR;
+            }
+            else if ( tax_group.equals( TaxonomyGroups.BACTERIA ) ) {
+                return TaxonomyColors.BACTERIA_COLOR;
+            }
         }
-        else if ( tax.equalsIgnoreCase( "protostomia" ) ) {
-            printRel( tax_code, "protostomia" );
-            return TaxonomyColors.PROTOSTOMIA_COLOR;
+        return null;
+    }
+
+    public final static String obtainNormalizedTaxonomyGroup( final String tax ) {
+        if ( tax.equalsIgnoreCase( TaxonomyGroups.DEUTEROSTOMIA ) ) {
+            return TaxonomyGroups.DEUTEROSTOMIA;
+        }
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.PROTOSTOMIA ) ) {
+            return TaxonomyGroups.PROTOSTOMIA;
         }
-        else if ( tax.equalsIgnoreCase( "cnidaria" ) ) {
-            printRel( tax_code, "cnidaria" );
-            return TaxonomyColors.CNIDARIA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.CNIDARIA ) ) {
+            return TaxonomyGroups.CNIDARIA;
         }
-        else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( "placozoa" ) ) {
-            printRel( tax_code, "placozoa" );
-            return TaxonomyColors.PLACOZOA_COLOR;
+        else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( TaxonomyGroups.PLACOZOA ) ) {
+            return TaxonomyGroups.PLACOZOA;
         }
-        else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( "ctenophora" ) ) {
-            printRel( tax_code, "ctenophora" );
-            return TaxonomyColors.CTENOPHORA_COLOR;
+        else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( TaxonomyGroups.CTENOPHORA ) ) {
+            return TaxonomyGroups.CTENOPHORA;
         }
-        else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( "porifera" ) ) {
-            printRel( tax_code, "porifera" );
-            return TaxonomyColors.PORIFERA_COLOR;
+        else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( TaxonomyGroups.PORIFERA ) ) {
+            return TaxonomyGroups.PORIFERA;
         }
-        else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( "choanoflagellida" ) ) {
-            printRel( tax_code, "choanoflagellida" );
-            return TaxonomyColors.CHOANOFLAGELLIDA;
+        else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
+            return TaxonomyGroups.CHOANOFLAGELLIDA;
         }
-        else if ( tax.toLowerCase().startsWith( "ichthyophonida & filasterea" )
+        else if ( tax.toLowerCase().startsWith( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA )
                 || tax.toLowerCase().startsWith( "ichthyophonida and filasterea" )
                 || tax.toLowerCase().startsWith( "ichthyosporea & filasterea" )
                 || tax.toLowerCase().startsWith( "ichthyosporea and filasterea" ) ) {
-            printRel( tax_code, "ichthyophonida & filasterea" );
-            return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
+            return TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA;
         }
-        else if ( tax.equalsIgnoreCase( "fungi" ) ) {
-            printRel( tax_code, "fungi" );
-            return TaxonomyColors.FUNGI_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.DIKARYA ) ) {
+            return TaxonomyGroups.DIKARYA;
+        }
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.FUNGI ) || tax.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
+            return TaxonomyGroups.OTHER_FUNGI;
         }
         else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) {
-            printRel( tax_code, "nucleariidae and fonticula group" );
-            return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR;
+            return TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP;
         }
-        else if ( tax.equalsIgnoreCase( "amoebozoa" ) ) {
-            printRel( tax_code, "amoebozoa" );
-            return TaxonomyColors.AMOEBOZOA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.AMOEBOZOA ) ) {
+            return TaxonomyGroups.AMOEBOZOA;
         }
-        else if ( tax.equalsIgnoreCase( "embryophyta" ) ) {
-            printRel( tax_code, "embryophyta" );
-            return TaxonomyColors.EMBRYOPHYTA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.EMBRYOPHYTA ) ) {
+            return TaxonomyGroups.EMBRYOPHYTA;
         }
-        else if ( tax.equalsIgnoreCase( "chlorophyta" ) ) {
-            printRel( tax_code, "chlorophyta" );
-            return TaxonomyColors.CHLOROPHYTA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.CHLOROPHYTA ) ) {
+            return TaxonomyGroups.CHLOROPHYTA;
         }
-        else if ( tax.equalsIgnoreCase( "rhodophyta" ) ) {
-            printRel( tax_code, "rhodophyta" );
-            return TaxonomyColors.RHODOPHYTA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHODOPHYTA ) ) {
+            return TaxonomyGroups.RHODOPHYTA;
         }
-        else if ( tax.toLowerCase().startsWith( "hacrobia" ) ) {
-            printRel( tax_code, "hacrobia" );
-            return TaxonomyColors.HACROBIA_COLOR;
+        else if ( tax.toLowerCase().startsWith( TaxonomyGroups.HACROBIA ) ) {
+            return TaxonomyGroups.HACROBIA;
         }
-        else if ( tax.equalsIgnoreCase( "glaucocystophyceae" ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
-            printRel( tax_code, "glaucocystophyceae" );
-            return TaxonomyColors.GLAUCOPHYTA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
+            return TaxonomyGroups.GLAUCOCYSTOPHYCEAE;
         }
-        else if ( tax.equalsIgnoreCase( "stramenopiles" ) ) {
-            printRel( tax_code, "stramenopiles" );
-            return TaxonomyColors.STRAMENOPILES_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.STRAMENOPILES ) ) {
+            return TaxonomyGroups.STRAMENOPILES;
         }
-        else if ( tax.equalsIgnoreCase( "alveolata" ) ) {
-            printRel( tax_code, "alveolata" );
-            return TaxonomyColors.ALVEOLATA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALVEOLATA ) ) {
+            return TaxonomyGroups.ALVEOLATA;
         }
-        else if ( tax.equalsIgnoreCase( "rhizaria" ) ) {
-            printRel( tax_code, "rhizaria" );
-            return TaxonomyColors.RHIZARIA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHIZARIA ) ) {
+            return TaxonomyGroups.RHIZARIA;
         }
-        else if ( tax.equalsIgnoreCase( "excavata" ) ) {
-            printRel( tax_code, "excavata" );
-            return TaxonomyColors.EXCAVATA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.EXCAVATA ) ) {
+            return TaxonomyGroups.EXCAVATA;
         }
-        else if ( tax.equalsIgnoreCase( "apusozoa" ) ) {
-            printRel( tax_code, "apusozoa" );
-            return TaxonomyColors.APUSOZOA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.APUSOZOA ) ) {
+            return TaxonomyGroups.APUSOZOA;
         }
-        else if ( tax.equalsIgnoreCase( "archaea" ) ) {
-            printRel( tax_code, "archaea" );
-            return TaxonomyColors.ARCHAEA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.ARCHAEA ) ) {
+            return TaxonomyGroups.ARCHAEA;
         }
-        else if ( tax.equalsIgnoreCase( "bacteria" ) ) {
-            printRel( tax_code, "bacteria" );
-            return TaxonomyColors.BACTERIA_COLOR;
+        else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) {
+            return TaxonomyGroups.BACTERIA;
         }
         return null;
     }
-
-    private final static void printRel( final String tax_code, final String group ) {
-        //System.out.println( tax_code + "->" + group );
-        System.out.println( "_default_taxcode_taxgroup_map.put( \"" + tax_code + "\", \"" + group + "\" );" );
-    }
 }