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=ba1af65e1ae72cca9735ad85a6d4f008524ef814;hpb=baa7e9117411d330ce57667fdc4a60086ef0951e;p=jalview.git diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index ba1af65..7492f1e 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; @@ -50,7 +50,6 @@ import java.text.SimpleDateFormat; 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; @@ -59,12 +58,18 @@ import java.util.SortedMap; import java.util.SortedSet; import java.util.TreeMap; import java.util.TreeSet; +import java.util.regex.Matcher; import java.util.regex.Pattern; +import org.forester.archaeopteryx.Constants; import org.forester.phylogeny.PhylogenyNode; 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 { @@ -82,6 +87,11 @@ public final class ForesterUtil { public static final NumberFormat FORMATTER_6; public static final NumberFormat FORMATTER_06; public static final NumberFormat FORMATTER_3; + public static final String NCBI_PROTEIN = "http://www.ncbi.nlm.nih.gov/protein/"; + 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( '.' ); @@ -95,6 +105,16 @@ public final class ForesterUtil { private ForesterUtil() { } + public static int calculateOverlap( final Domain domain, final List 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 ); @@ -102,6 +122,72 @@ public final class ForesterUtil { } /** + * + * 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 sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein ); + final List covered_positions = new ArrayList(); + 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 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. @@ -349,6 +435,34 @@ public final class ForesterUtil { return ary; } + public static String[][] file22dArray( final File file ) throws IOException { + final List list = new ArrayList(); + final BufferedReader in = new BufferedReader( new FileReader( file ) ); + String str; + while ( ( str = in.readLine() ) != null ) { + str = str.trim(); + if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) { + list.add( str ); + } + } + in.close(); + final String[][] ary = new String[ list.size() ][ 2 ]; + final Pattern pa = Pattern.compile( "(\\S+)\\s+(\\S+)" ); + int i = 0; + for( final String s : list ) { + final Matcher m = pa.matcher( s ); + if ( m.matches() ) { + ary[ i ][ 0 ] = m.group( 1 ); + ary[ i ][ 1 ] = m.group( 2 ); + ++i; + } + else { + throw new IOException( "unexpcted format: " + s ); + } + } + return ary; + } + final public static List file2list( final File file ) throws IOException { final List list = new ArrayList(); final BufferedReader in = new BufferedReader( new FileReader( file ) ); @@ -556,8 +670,24 @@ public final class ForesterUtil { return isReadableFile( new File( s ) ); } - public static boolean isWindowns() { - return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1; + public final static boolean isWindows() { + try { + return OS_NAME.toLowerCase().indexOf( "win" ) > -1; + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e ); + return false; + } + } + + public final static boolean isMac() { + try { + return OS_NAME.toLowerCase().startsWith( "mac" ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e ); + return false; + } } final public static String isWritableFile( final File f ) { @@ -585,7 +715,7 @@ public final class ForesterUtil { return i; } - final public static SortedMap listToSortedCountsMap( final List list ) { + final public static SortedMap listToSortedCountsMap( final List list ) { final SortedMap map = new TreeMap(); for( final Object key : list ) { if ( !map.containsKey( key ) ) { @@ -625,10 +755,9 @@ public final class ForesterUtil { } } - final public static StringBuffer mapToStringBuffer( final Map map, final String key_value_separator ) { + final public static StringBuffer mapToStringBuffer( final Map 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() ); @@ -938,7 +1067,7 @@ public final class ForesterUtil { System.err.println(); System.exit( -1 ); } - + final public static void unexpectedFatalError( final Error e ) { System.err.println(); System.err.println( "unexpected error: should not have occured! Please contact program author(s)." ); @@ -996,6 +1125,10 @@ public final class ForesterUtil { System.out.print( "]" ); } + public final static void updateProgress( final int i, final DecimalFormat f ) { + System.out.print( "\r[" + f.format( i ) + "]" ); + } + public final static String wordWrap( final String str, final int width ) { final StringBuilder sb = new StringBuilder( str ); int start = 0; @@ -1071,4 +1204,162 @@ public final class ForesterUtil { 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; + } }