import org.forester.phylogeny.data.Distribution;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
+import org.forester.protein.BasicProtein;
+import org.forester.protein.Domain;
+import org.forester.protein.Protein;
+import org.forester.surfacing.SurfacingUtil;
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 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, 153, 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 GLAUCOPHYTA_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 static final Color APUSOZOA_COLOR = new Color( 204, 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 );
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
private ForesterUtil() {
}
+ public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
+ int overlap_count = 0;
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
+ ++overlap_count;
+ }
+ }
+ return overlap_count;
+ }
+
final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
if ( sb.length() > 0 ) {
sb.append( separator );
}
/**
+ *
+ * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
+ * domain with 0.3 is ignored
+ *
+ * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
+ *
+ *
+ * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
+ * ignored
+ *
+ * @param max_allowed_overlap
+ * maximal allowed overlap (inclusive) to be still considered not
+ * overlapping (zero or negative value to allow any overlap)
+ * @param remove_engulfed_domains
+ * to remove domains which are completely engulfed by coverage of
+ * domains with better support
+ * @param protein
+ * @return
+ */
+ public static Protein removeOverlappingDomains( final int max_allowed_overlap,
+ final boolean remove_engulfed_domains,
+ final Protein protein ) {
+ final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
+ .getSpeciesId(), protein.getLength() );
+ final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
+ final List<Boolean> covered_positions = new ArrayList<Boolean>();
+ for( final Domain domain : sorted ) {
+ if ( ( ( max_allowed_overlap < 0 ) || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
+ && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
+ final int covered_positions_size = covered_positions.size();
+ for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
+ covered_positions.add( false );
+ }
+ final int new_covered_positions_size = covered_positions.size();
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( i < new_covered_positions_size ) {
+ covered_positions.set( i, true );
+ }
+ else {
+ covered_positions.add( true );
+ }
+ }
+ pruned_protein.addProteinDomain( domain );
+ }
+ }
+ return pruned_protein;
+ }
+
+ /**
+ * Returns true is Domain domain falls in an uninterrupted stretch of
+ * covered positions.
+ *
+ * @param domain
+ * @param covered_positions
+ * @return
+ */
+ public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
+ for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
+ if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
* This calculates a color. If value is equal to min the returned color is
* minColor, if value is equal to max the returned color is maxColor,
* otherwise a color 'proportional' to value is returned.
System.err.println();
System.exit( -1 );
}
+
+ public final static Color obtainColorDependingOnTaxonomyGroup( final String tax ) {
+ if ( tax.equalsIgnoreCase( "deuterostomia" ) ) {
+ return DEUTEROSTOMIA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "protostomia" ) ) {
+ return PROTOSTOMIA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "metazoa" ) ) {
+ return METAZOA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "holozoa" ) ) {
+ return HOLOZOA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "fungi" ) ) {
+ return FUNGI_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "holomycota" ) ) {
+ return HOLOMYCOTA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "amoebozoa" ) ) {
+ return AMOEBOZOA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "viridiplantae" ) ) {
+ return VIRIDPLANTAE_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "rhodophyta" ) ) {
+ return RHODOPHYTA_COLOR;
+ }
+ else if ( tax.toLowerCase().startsWith( "hacrobia" ) ) {
+ return HACROBIA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "glaucocystophyceae" ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
+ return GLAUCOPHYTA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "stramenopiles" ) ) {
+ return STRAMENOPILES_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "alveolata" ) ) {
+ return ALVEOLATA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "rhizaria" ) ) {
+ return RHIZARIA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "excavata" ) ) {
+ return EXCAVATA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "apusozoa" ) ) {
+ return APUSOZOA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "archaea" ) ) {
+ return ARCHAEA_COLOR;
+ }
+ else if ( tax.equalsIgnoreCase( "bacteria" ) ) {
+ return BACTERIA_COLOR;
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff