X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterUtil.java;h=84be63a8484b4bd556f7d3d8490be7ea5d5657de;hb=cdad7364d81a04e88c3c7dc998cceede129286f4;hp=eef965f1566b48dc1252ebb732c3a6f4f4ea9d32;hpb=d15038d8870ccccd726ad82ac9a707afb6a7f31e;p=jalview.git diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index eef965f..84be63a 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -41,6 +41,7 @@ import java.io.StringReader; import java.io.Writer; import java.math.BigDecimal; import java.net.URL; +import java.net.URLConnection; import java.text.DateFormat; import java.text.DecimalFormat; import java.text.DecimalFormatSymbols; @@ -74,23 +75,24 @@ import org.forester.surfacing.SurfacingUtil; public final class ForesterUtil { public final static String FILE_SEPARATOR = System.getProperty( "file.separator" ); - public final static String LINE_SEPARATOR = System.getProperty( "line.separator" ); + public static final NumberFormat FORMATTER_06; + public static final NumberFormat FORMATTER_3; + public static final NumberFormat FORMATTER_6; + public static final NumberFormat FORMATTER_9; public final static String JAVA_VENDOR = System.getProperty( "java.vendor" ); public final static String JAVA_VERSION = System.getProperty( "java.version" ); + public final static String LINE_SEPARATOR = System.getProperty( "line.separator" ); + public static final String NCBI_GI = "http://www.ncbi.nlm.nih.gov/protein/gi:"; + public static final String NCBI_NUCCORE = "http://www.ncbi.nlm.nih.gov/nuccore/"; + public static final String NCBI_PROTEIN = "http://www.ncbi.nlm.nih.gov/protein/"; + public static final BigDecimal NULL_BD = new BigDecimal( 0 ); public final static String OS_ARCH = System.getProperty( "os.arch" ); public final static String OS_NAME = System.getProperty( "os.name" ); public final static String OS_VERSION = System.getProperty( "os.version" ); - public final static Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s]" ); - public final static double ZERO_DIFF = 1.0E-9; - public static final BigDecimal NULL_BD = new BigDecimal( 0 ); - public static final NumberFormat FORMATTER_9; - 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 static final String PDB = "http://www.pdb.org/pdb/explore/explore.do?pdbId="; 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 double ZERO_DIFF = 1.0E-9; + private static final Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s:\\[\\]]" ); static { final DecimalFormatSymbols dfs = new DecimalFormatSymbols(); dfs.setDecimalSeparator( '.' ); @@ -104,16 +106,6 @@ 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 ); @@ -121,72 +113,6 @@ 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. @@ -276,6 +202,16 @@ public final class 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 String collapseWhiteSpace( final String s ) { return s.replaceAll( "[\\s]+", " " ); } @@ -424,16 +360,6 @@ public final class ForesterUtil { } } - public static String[] file2array( final File file ) throws IOException { - final List list = file2list( file ); - final String[] ary = new String[ list.size() ]; - int i = 0; - for( final String s : list ) { - ary[ i++ ] = s; - } - return ary; - } - public static String[][] file22dArray( final File file ) throws IOException { final List list = new ArrayList(); final BufferedReader in = new BufferedReader( new FileReader( file ) ); @@ -462,6 +388,16 @@ public final class ForesterUtil { return ary; } + public static String[] file2array( final File file ) throws IOException { + final List list = file2list( file ); + final String[] ary = new String[ list.size() ]; + int i = 0; + for( final String s : list ) { + ary[ i++ ] = 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 ) ); @@ -528,7 +464,9 @@ public final class ForesterUtil { reader = new BufferedReader( new StringReader( source.toString() ) ); } else if ( source instanceof URL ) { - reader = new BufferedReader( new InputStreamReader( ( ( URL ) source ).openStream() ) ); + final URLConnection url_connection = ( ( URL ) source ).openConnection(); + url_connection.setDefaultUseCaches( false ); + reader = new BufferedReader( new InputStreamReader( url_connection.getInputStream() ) ); } else { throw new IllegalArgumentException( "dont know how to read [" + source.getClass() + "]" ); @@ -566,10 +504,6 @@ public final class ForesterUtil { } } - final public static boolean isContainsParanthesesableNhCharacter( final String nh ) { - return PARANTHESESABLE_NH_CHARS_PATTERN.matcher( nh ).find(); - } - final public static boolean isEmpty( final List l ) { if ( ( l == null ) || l.isEmpty() ) { return true; @@ -598,6 +532,23 @@ public final class ForesterUtil { return ( ( s == null ) || ( s.length() < 1 ) ); } + /** + * 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; + } + final public static boolean isEqual( final double a, final double b ) { return ( ( Math.abs( a - b ) ) < ZERO_DIFF ); } @@ -642,6 +593,16 @@ public final class ForesterUtil { } } + 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 boolean isNull( final BigDecimal s ) { return ( ( s == null ) || ( s.compareTo( NULL_BD ) == 0 ) ); } @@ -679,16 +640,6 @@ public final class ForesterUtil { } } - 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 ) { if ( f.isDirectory() ) { return "[" + f + "] is a directory"; @@ -786,6 +737,164 @@ public final class ForesterUtil { } } + 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; + } + final public static BufferedReader obtainReader( final Object source ) throws IOException, FileNotFoundException { BufferedReader reader = null; if ( source instanceof File ) { @@ -817,6 +926,15 @@ public final class ForesterUtil { return reader; } + public final static void outOfMemoryError( final OutOfMemoryError e ) { + System.err.println(); + System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" ); + System.err.println(); + e.printStackTrace( System.err ); + System.err.println(); + System.exit( -1 ); + } + final public static StringBuffer pad( final double number, final int size, final char pad, final boolean left_pad ) { return pad( new StringBuffer( number + "" ), size, pad, left_pad ); } @@ -932,6 +1050,55 @@ public final class ForesterUtil { System.out.println( "[" + prg_name + "] > " + message ); } + /** + * + * 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; + } + final public static String removeSuffix( final String file_name ) { final int i = file_name.lastIndexOf( '.' ); if ( i > 1 ) { @@ -957,18 +1124,11 @@ public final class ForesterUtil { return s; } - final public static String replaceIllegalNhCharacters( final String nh ) { - if ( nh == null ) { - return ""; - } - return nh.trim().replaceAll( "[\\[\\]:]+", "_" ); - } - final public static String replaceIllegalNhxCharacters( final String nhx ) { if ( nhx == null ) { return ""; } - return nhx.trim().replaceAll( "[\\[\\](),:;\\s]+", "_" ); + return nhx.trim().replaceAll( "[\\[\\]']+", "_" ); } final public static double round( final double value, final int decimal_place ) { @@ -1001,6 +1161,35 @@ public final class ForesterUtil { } } + public final static StringBuilder santitizeStringForNH( String data ) { + data = data.replaceAll( "\\s+", " " ).trim(); + final StringBuilder sb = new StringBuilder(); + if ( data.length() > 0 ) { + final boolean single_pars = data.indexOf( '\'' ) > -1; + final boolean double_pars = data.indexOf( '"' ) > -1; + if ( single_pars && double_pars ) { + data = data.replace( '\'', '`' ); + sb.append( '\'' ); + sb.append( data ); + sb.append( '\'' ); + } + else if ( single_pars ) { + sb.append( '"' ); + sb.append( data ); + sb.append( '"' ); + } + else if ( PARANTHESESABLE_NH_CHARS_PATTERN.matcher( data ).find() ) { + sb.append( '\'' ); + sb.append( data ); + sb.append( '\'' ); + } + else { + sb.append( data ); + } + } + return sb; + } + public static boolean seqIsLikelyToBeAa( final String s ) { final String seq = s.toLowerCase(); if ( ( seq.indexOf( 'r' ) > -1 ) || ( seq.indexOf( 'd' ) > -1 ) || ( seq.indexOf( 'e' ) > -1 ) @@ -1059,17 +1248,17 @@ public final class ForesterUtil { return str_array; } - final public static void unexpectedFatalError( final Exception e ) { + final public static void unexpectedFatalError( final Error e ) { System.err.println(); - System.err.println( "unexpected exception: should not have occured! Please contact program author(s)." ); + System.err.println( "unexpected error: should not have occured! Please contact program author(s)." ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); } - final public static void unexpectedFatalError( final Error e ) { + final public static void unexpectedFatalError( final Exception e ) { System.err.println(); - System.err.println( "unexpected error: should not have occured! Please contact program author(s)." ); + System.err.println( "unexpected exception: should not have occured! Please contact program author(s)." ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); @@ -1194,121 +1383,4 @@ public final class ForesterUtil { final String regex = "[\\s;,]+"; return str.split( regex ); } - - public final static void outOfMemoryError( final OutOfMemoryError e ) { - System.err.println(); - System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" ); - System.err.println(); - e.printStackTrace( System.err ); - System.err.println(); - 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; - } - else if ( tax.equalsIgnoreCase( "protostomia" ) ) { - printRel( tax_code, "protostomia" ); - return TaxonomyColors.PROTOSTOMIA_COLOR; - } - else if ( tax.equalsIgnoreCase( "cnidaria" ) ) { - printRel( tax_code, "cnidaria" ); - return TaxonomyColors.CNIDARIA_COLOR; - } - else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( "placozoa" ) ) { - printRel( tax_code, "placozoa" ); - return TaxonomyColors.PLACOZOA_COLOR; - } - else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( "ctenophora" ) ) { - printRel( tax_code, "ctenophora" ); - return TaxonomyColors.CTENOPHORA_COLOR; - } - else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( "porifera" ) ) { - printRel( tax_code, "porifera" ); - return TaxonomyColors.PORIFERA_COLOR; - } - else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( "choanoflagellida" ) ) { - printRel( tax_code, "choanoflagellida" ); - return TaxonomyColors.CHOANOFLAGELLIDA; - } - else if ( tax.toLowerCase().startsWith( "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; - } - else if ( tax.equalsIgnoreCase( "dikarya" ) ) { - printRel( tax_code, "dikarya" ); - return TaxonomyColors.DIKARYA_COLOR; - } - else if ( tax.equalsIgnoreCase( "fungi" ) || tax.equalsIgnoreCase( "other fungi" ) ) { - printRel( tax_code, "other fungi" ); - return TaxonomyColors.OTHER_FUNGI_COLOR; - } - else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) { - printRel( tax_code, "nucleariidae and fonticula group" ); - return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR; - } - else if ( tax.equalsIgnoreCase( "amoebozoa" ) ) { - printRel( tax_code, "amoebozoa" ); - return TaxonomyColors.AMOEBOZOA_COLOR; - } - else if ( tax.equalsIgnoreCase( "embryophyta" ) ) { - printRel( tax_code, "embryophyta" ); - return TaxonomyColors.EMBRYOPHYTA_COLOR; - } - else if ( tax.equalsIgnoreCase( "chlorophyta" ) ) { - printRel( tax_code, "chlorophyta" ); - return TaxonomyColors.CHLOROPHYTA_COLOR; - } - else if ( tax.equalsIgnoreCase( "rhodophyta" ) ) { - printRel( tax_code, "rhodophyta" ); - return TaxonomyColors.RHODOPHYTA_COLOR; - } - else if ( tax.toLowerCase().startsWith( "hacrobia" ) ) { - printRel( tax_code, "hacrobia" ); - return TaxonomyColors.HACROBIA_COLOR; - } - else if ( tax.equalsIgnoreCase( "glaucocystophyceae" ) || tax.equalsIgnoreCase( "glaucophyta" ) ) { - printRel( tax_code, "glaucocystophyceae" ); - return TaxonomyColors.GLAUCOPHYTA_COLOR; - } - else if ( tax.equalsIgnoreCase( "stramenopiles" ) ) { - printRel( tax_code, "stramenopiles" ); - return TaxonomyColors.STRAMENOPILES_COLOR; - } - else if ( tax.equalsIgnoreCase( "alveolata" ) ) { - printRel( tax_code, "alveolata" ); - return TaxonomyColors.ALVEOLATA_COLOR; - } - else if ( tax.equalsIgnoreCase( "rhizaria" ) ) { - printRel( tax_code, "rhizaria" ); - return TaxonomyColors.RHIZARIA_COLOR; - } - else if ( tax.equalsIgnoreCase( "excavata" ) ) { - printRel( tax_code, "excavata" ); - return TaxonomyColors.EXCAVATA_COLOR; - } - else if ( tax.equalsIgnoreCase( "apusozoa" ) ) { - printRel( tax_code, "apusozoa" ); - return TaxonomyColors.APUSOZOA_COLOR; - } - else if ( tax.equalsIgnoreCase( "archaea" ) ) { - printRel( tax_code, "archaea" ); - return TaxonomyColors.ARCHAEA_COLOR; - } - else if ( tax.equalsIgnoreCase( "bacteria" ) ) { - printRel( tax_code, "bacteria" ); - return TaxonomyColors.BACTERIA_COLOR; - } - 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 + "\" );" ); - } }