import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
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 final static Color DEUTEROSTOMIA_COLOR = new Color( 255, 0, 0 );
- public final static Color PROTOSTOMIA_COLOR = new Color( 204, 0, 0 );
- public final static Color METAZOA_COLOR = new Color( 204, 0, 102 );
- public final static Color HOLOZOA_COLOR = new Color( 127, 0, 255 );
- public final static Color FUNGI_COLOR = new Color( 255, 128, 0 );
- public final static Color HOLOMYCOTA_COLOR = new Color( 204, 102, 0 );
- public final static Color AMOEBOZOA_COLOR = new Color( 255, 0, 255 );
- public final static Color VIRIDPLANTAE_COLOR = new Color( 0, 255, 0 );
- public final static Color RHODOPHYTA_COLOR = new Color( 0, 153, 76 );
- public final static Color HACROBIA_COLOR = new Color( 0, 102, 51 );
- public final static Color STRAMENOPILES_COLOR = new Color( 0, 0, 255 );
- public final static Color ALVEOLATA_COLOR = new Color( 0, 128, 255 );
- public final static Color RHIZARIA_COLOR = new Color( 0, 255, 255 );
- public final static Color EXCAVATA_COLOR = new Color( 204, 204, 0 );
- public final static Color ARCHAEA_COLOR = new Color( 160, 160, 160 );
- public final static Color BACTERIA_COLOR = new Color( 64, 64, 64 );
+ public static final String PDB = "http://www.pdb.org/pdb/explore/explore.do?pdbId=";
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
return i;
}
- final public static SortedMap<Object, Integer> listToSortedCountsMap( final List list ) {
+ final public static SortedMap<Object, Integer> listToSortedCountsMap( final List<?> list ) {
final SortedMap<Object, Integer> map = new TreeMap<Object, Integer>();
for( final Object key : list ) {
if ( !map.containsKey( key ) ) {
}
}
- final public static StringBuffer mapToStringBuffer( final Map map, final String key_value_separator ) {
+ final public static StringBuffer mapToStringBuffer( final Map<Object, Object> map, final String key_value_separator ) {
final StringBuffer sb = new StringBuffer();
- for( final Iterator iter = map.keySet().iterator(); iter.hasNext(); ) {
- final Object key = iter.next();
+ for( final Object key : map.keySet() ) {
sb.append( key.toString() );
sb.append( key_value_separator );
sb.append( map.get( key ).toString() );
System.err.println();
System.exit( -1 );
}
+
+ 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;
+ }
+ }
+ 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( TaxonomyGroups.CNIDARIA ) ) {
+ return TaxonomyGroups.CNIDARIA;
+ }
+ else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( TaxonomyGroups.PLACOZOA ) ) {
+ return TaxonomyGroups.PLACOZOA;
+ }
+ else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( TaxonomyGroups.CTENOPHORA ) ) {
+ return TaxonomyGroups.CTENOPHORA;
+ }
+ else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( TaxonomyGroups.PORIFERA ) ) {
+ return TaxonomyGroups.PORIFERA;
+ }
+ else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
+ return TaxonomyGroups.CHOANOFLAGELLIDA;
+ }
+ 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 TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA;
+ }
+ 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" ) ) {
+ return TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.AMOEBOZOA ) ) {
+ return TaxonomyGroups.AMOEBOZOA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.EMBRYOPHYTA ) ) {
+ return TaxonomyGroups.EMBRYOPHYTA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.CHLOROPHYTA ) ) {
+ return TaxonomyGroups.CHLOROPHYTA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHODOPHYTA ) ) {
+ return TaxonomyGroups.RHODOPHYTA;
+ }
+ else if ( tax.toLowerCase().startsWith( TaxonomyGroups.HACROBIA ) ) {
+ return TaxonomyGroups.HACROBIA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
+ return TaxonomyGroups.GLAUCOCYSTOPHYCEAE;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.STRAMENOPILES ) ) {
+ return TaxonomyGroups.STRAMENOPILES;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALVEOLATA ) ) {
+ return TaxonomyGroups.ALVEOLATA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHIZARIA ) ) {
+ return TaxonomyGroups.RHIZARIA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.EXCAVATA ) ) {
+ return TaxonomyGroups.EXCAVATA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.APUSOZOA ) ) {
+ return TaxonomyGroups.APUSOZOA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.ARCHAEA ) ) {
+ return TaxonomyGroups.ARCHAEA;
+ }
+ else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) {
+ return TaxonomyGroups.BACTERIA;
+ }
+ return null;
+ }
}