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( '.' );
public final static Color obtainColorDependingOnTaxonomyGroup( final String tax_group ) {
if ( !ForesterUtil.isEmpty( tax_group ) ) {
- if ( tax_group.equals( "deuterostomia" ) ) {
+ if ( tax_group.equals( TaxonomyGroups.DEUTEROSTOMIA ) ) {
return TaxonomyColors.DEUTEROSTOMIA_COLOR;
}
- else if ( tax_group.equals( "protostomia" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.PROTOSTOMIA ) ) {
return TaxonomyColors.PROTOSTOMIA_COLOR;
}
- else if ( tax_group.equals( "cnidaria" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CNIDARIA ) ) {
return TaxonomyColors.CNIDARIA_COLOR;
}
- else if ( tax_group.equals( "placozoa" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.PLACOZOA ) ) {
return TaxonomyColors.PLACOZOA_COLOR;
}
- else if ( tax_group.equals( "ctenophora" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CTENOPHORA ) ) {
return TaxonomyColors.CTENOPHORA_COLOR;
}
- else if ( tax_group.equals( "porifera" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.PORIFERA ) ) {
return TaxonomyColors.PORIFERA_COLOR;
}
- else if ( tax_group.equals( "choanoflagellida" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
return TaxonomyColors.CHOANOFLAGELLIDA;
}
- else if ( tax_group.equals( "ichthyophonida & filasterea" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA ) ) {
return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
}
- else if ( tax_group.equals( "dikarya" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.DIKARYA ) ) {
return TaxonomyColors.DIKARYA_COLOR;
}
- else if ( tax_group.equalsIgnoreCase( "fungi" ) || tax_group.equalsIgnoreCase( "other fungi" ) ) {
+ else if ( tax_group.equalsIgnoreCase( TaxonomyGroups.FUNGI )
+ || tax_group.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
return TaxonomyColors.OTHER_FUNGI_COLOR;
}
- else if ( tax_group.equals( "nucleariidae and fonticula" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP ) ) {
return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR;
}
- else if ( tax_group.equals( "amoebozoa" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.AMOEBOZOA ) ) {
return TaxonomyColors.AMOEBOZOA_COLOR;
}
- else if ( tax_group.equals( "embryophyta" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.EMBRYOPHYTA ) ) {
return TaxonomyColors.EMBRYOPHYTA_COLOR;
}
- else if ( tax_group.equals( "chlorophyta" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.CHLOROPHYTA ) ) {
return TaxonomyColors.CHLOROPHYTA_COLOR;
}
- else if ( tax_group.equals( "rhodophyta" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.RHODOPHYTA ) ) {
return TaxonomyColors.RHODOPHYTA_COLOR;
}
- else if ( tax_group.equals( "hacrobia" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.HACROBIA ) ) {
return TaxonomyColors.HACROBIA_COLOR;
}
- else if ( tax_group.equals( "glaucocystophyceae" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) ) {
return TaxonomyColors.GLAUCOPHYTA_COLOR;
}
- else if ( tax_group.equals( "stramenopiles" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.STRAMENOPILES ) ) {
return TaxonomyColors.STRAMENOPILES_COLOR;
}
- else if ( tax_group.equals( "alveolata" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.ALVEOLATA ) ) {
return TaxonomyColors.ALVEOLATA_COLOR;
}
- else if ( tax_group.equals( "rhizaria" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.RHIZARIA ) ) {
return TaxonomyColors.RHIZARIA_COLOR;
}
- else if ( tax_group.equals( "excavata" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.EXCAVATA ) ) {
return TaxonomyColors.EXCAVATA_COLOR;
}
- else if ( tax_group.equals( "apusozoa" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.APUSOZOA ) ) {
return TaxonomyColors.APUSOZOA_COLOR;
}
- else if ( tax_group.equals( "archaea" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.ARCHAEA ) ) {
return TaxonomyColors.ARCHAEA_COLOR;
}
- else if ( tax_group.equals( "bacteria" ) ) {
+ else if ( tax_group.equals( TaxonomyGroups.BACTERIA ) ) {
return TaxonomyColors.BACTERIA_COLOR;
}
}
}
public final static String obtainNormalizedTaxonomyGroup( final String tax ) {
- if ( tax.equalsIgnoreCase( "deuterostomia" ) ) {
- return "deuterostomia";
+ if ( tax.equalsIgnoreCase( TaxonomyGroups.DEUTEROSTOMIA ) ) {
+ return TaxonomyGroups.DEUTEROSTOMIA;
}
- else if ( tax.equalsIgnoreCase( "protostomia" ) ) {
- return "protostomia";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.PROTOSTOMIA ) ) {
+ return TaxonomyGroups.PROTOSTOMIA;
}
- else if ( tax.equalsIgnoreCase( "cnidaria" ) ) {
- return "cnidaria";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.CNIDARIA ) ) {
+ return TaxonomyGroups.CNIDARIA;
}
- else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( "placozoa" ) ) {
- return "placozoa";
+ else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( TaxonomyGroups.PLACOZOA ) ) {
+ return TaxonomyGroups.PLACOZOA;
}
- else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( "ctenophora" ) ) {
- return "ctenophora";
+ else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( TaxonomyGroups.CTENOPHORA ) ) {
+ return TaxonomyGroups.CTENOPHORA;
}
- else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( "porifera" ) ) {
- return "porifera";
+ else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( TaxonomyGroups.PORIFERA ) ) {
+ return TaxonomyGroups.PORIFERA;
}
- else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( "choanoflagellida" ) ) {
- return "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" ) ) {
- return "ichthyophonida & filasterea";
+ return TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA;
}
- else if ( tax.equalsIgnoreCase( "dikarya" ) ) {
- return "dikarya";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.DIKARYA ) ) {
+ return TaxonomyGroups.DIKARYA;
}
- else if ( tax.equalsIgnoreCase( "other fungi" ) ) {
- return "other fungi";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.FUNGI ) || tax.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
+ return TaxonomyGroups.OTHER_FUNGI;
}
else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) {
- return "nucleariidae and fonticula group";
+ return TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP;
}
- else if ( tax.equalsIgnoreCase( "amoebozoa" ) ) {
- return "amoebozoa";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.AMOEBOZOA ) ) {
+ return TaxonomyGroups.AMOEBOZOA;
}
- else if ( tax.equalsIgnoreCase( "embryophyta" ) ) {
- return "embryophyta";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.EMBRYOPHYTA ) ) {
+ return TaxonomyGroups.EMBRYOPHYTA;
}
- else if ( tax.equalsIgnoreCase( "chlorophyta" ) ) {
- return "chlorophyta";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.CHLOROPHYTA ) ) {
+ return TaxonomyGroups.CHLOROPHYTA;
}
- else if ( tax.equalsIgnoreCase( "rhodophyta" ) ) {
- return "rhodophyta";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHODOPHYTA ) ) {
+ return TaxonomyGroups.RHODOPHYTA;
}
- else if ( tax.toLowerCase().startsWith( "hacrobia" ) ) {
- return "hacrobia";
+ else if ( tax.toLowerCase().startsWith( TaxonomyGroups.HACROBIA ) ) {
+ return TaxonomyGroups.HACROBIA;
}
- else if ( tax.equalsIgnoreCase( "glaucocystophyceae" ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
- return "glaucocystophyceae";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
+ return TaxonomyGroups.GLAUCOCYSTOPHYCEAE;
}
- else if ( tax.equalsIgnoreCase( "stramenopiles" ) ) {
- return "stramenopiles";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.STRAMENOPILES ) ) {
+ return TaxonomyGroups.STRAMENOPILES;
}
- else if ( tax.equalsIgnoreCase( "alveolata" ) ) {
- return "alveolata";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALVEOLATA ) ) {
+ return TaxonomyGroups.ALVEOLATA;
}
- else if ( tax.equalsIgnoreCase( "rhizaria" ) ) {
- return "rhizaria";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHIZARIA ) ) {
+ return TaxonomyGroups.RHIZARIA;
}
- else if ( tax.equalsIgnoreCase( "excavata" ) ) {
- return "excavata";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.EXCAVATA ) ) {
+ return TaxonomyGroups.EXCAVATA;
}
- else if ( tax.equalsIgnoreCase( "apusozoa" ) ) {
- return "apusozoa";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.APUSOZOA ) ) {
+ return TaxonomyGroups.APUSOZOA;
}
- else if ( tax.equalsIgnoreCase( "archaea" ) ) {
- return "archaea";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.ARCHAEA ) ) {
+ return TaxonomyGroups.ARCHAEA;
}
- else if ( tax.equalsIgnoreCase( "bacteria" ) ) {
- return "bacteria";
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) {
+ return TaxonomyGroups.BACTERIA;
}
return null;
}