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( '.' );
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 + "\" );" );
- }
}
git://source.jalview.org / jalview.git / blobdiff