X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterUtil.java;h=336c88763124454613da3df163c1535e93f9810a;hb=bc282cbd857f4fb9decdc00b278640bcf146a645;hp=ada203b58d264f2360481492534f929b9ee930cc;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index ada203b..336c887 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -5,7 +5,7 @@ // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved -// +// // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either @@ -15,7 +15,7 @@ // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. -// +// // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA @@ -38,6 +38,7 @@ import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.StringReader; +import java.io.Writer; import java.math.BigDecimal; import java.net.URL; import java.text.DateFormat; @@ -47,32 +48,23 @@ import java.text.NumberFormat; import java.text.ParseException; import java.text.SimpleDateFormat; import java.util.ArrayList; +import java.util.Collection; import java.util.Date; -import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; +import java.util.Map.Entry; import java.util.Set; 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.io.parsers.PhylogenyParser; -import org.forester.io.parsers.nexus.NexusPhylogeniesParser; -import org.forester.io.parsers.nhx.NHXParser; -import org.forester.io.parsers.phyloxml.PhyloXmlParser; -import org.forester.io.parsers.tol.TolParser; -import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Distribution; import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.Taxonomy; -import org.forester.phylogeny.iterators.PhylogenyNodeIterator; public final class ForesterUtil { @@ -103,34 +95,53 @@ public final class ForesterUtil { private ForesterUtil() { } + public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasTaxonomy() ) { + node.getNodeData().setTaxonomy( new Taxonomy() ); + } + } + + public static void ensurePresenceOfSequence( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasSequence() ) { + node.getNodeData().setSequence( new Sequence() ); + } + } + + final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasDistribution() ) { + node.getNodeData().setDistribution( new Distribution( "" ) ); + } + } + + final public static void ensurePresenceOfDate( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasDate() ) { + node.getNodeData().setDate( new org.forester.phylogeny.data.Date() ); + } + } + final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) { if ( sb.length() > 0 ) { sb.append( separator ); } } - final public static boolean isEmpty( final List l ) { - if ( ( l == null ) || l.isEmpty() ) { - return true; - } - for( final Object o : l ) { - if ( o != null ) { - return false; - } - } - return true; + public static boolean isWindowns() { + return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1; } - final public static boolean isEmpty( final Set s ) { - if ( ( s == null ) || s.isEmpty() ) { + final public static String getForesterLibraryInformation() { + return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")"; + } + + 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 ) + || ( seq.indexOf( 'q' ) > -1 ) || ( seq.indexOf( 'h' ) > -1 ) || ( seq.indexOf( 'k' ) > -1 ) + || ( seq.indexOf( 'w' ) > -1 ) || ( seq.indexOf( 's' ) > -1 ) || ( seq.indexOf( 'm' ) > -1 ) + || ( seq.indexOf( 'p' ) > -1 ) || ( seq.indexOf( 'v' ) > -1 ) ) { return true; } - for( final Object o : s ) { - if ( o != null ) { - return false; - } - } - return true; + return false; } /** @@ -260,6 +271,27 @@ public final class ForesterUtil { return s.replaceAll( "[\\s]+", " " ); } + final public static void collection2file( final File file, final Collection data, final String separator ) + throws IOException { + final Writer writer = new BufferedWriter( new FileWriter( file ) ); + collection2writer( writer, data, separator ); + writer.close(); + } + + final public static void collection2writer( final Writer writer, final Collection data, final String separator ) + throws IOException { + boolean first = true; + for( final Object object : data ) { + if ( !first ) { + writer.write( separator ); + } + else { + first = false; + } + writer.write( object.toString() ); + } + } + final public static String colorToHex( final Color color ) { final String rgb = Integer.toHexString( color.getRGB() ); return rgb.substring( 2, rgb.length() ); @@ -305,6 +337,14 @@ public final class ForesterUtil { return new BufferedWriter( new FileWriter( file ) ); } + final public static EasyWriter createEasyWriter( final File file ) throws IOException { + return new EasyWriter( createBufferedWriter( file ) ); + } + + final public static BufferedWriter createEasyWriter( final String name ) throws IOException { + return createEasyWriter( createFileForWriting( name ) ); + } + final public static BufferedWriter createBufferedWriter( final String name ) throws IOException { return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) ); } @@ -317,203 +357,6 @@ public final class ForesterUtil { return file; } - final public static PhylogenyParser createParserDependingFileContents( final File file, - final boolean phyloxml_validate_against_xsd ) - throws FileNotFoundException, IOException { - PhylogenyParser parser = null; - final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase(); - if ( first_line.startsWith( "<" ) ) { - parser = new PhyloXmlParser(); - if ( phyloxml_validate_against_xsd ) { - final ClassLoader cl = PhyloXmlParser.class.getClassLoader(); - final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE ); - if ( xsd_url != null ) { - ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() ); - } - else { - if ( ForesterConstants.RELEASE ) { - throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from [" - + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" ); - } - } - } - } - else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) ) - || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) { - parser = new NexusPhylogeniesParser(); - } - else { - parser = new NHXParser(); - } - return parser; - } - - final public static PhylogenyParser createParserDependingOnFileType( final File file, - final boolean phyloxml_validate_against_xsd ) - throws FileNotFoundException, IOException { - PhylogenyParser parser = null; - parser = createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd ); - if ( parser == null ) { - parser = createParserDependingFileContents( file, phyloxml_validate_against_xsd ); - } - return parser; - } - - /** - * Return null if it can not guess the parser to use based on name suffix. - * - * @param filename - * @return - */ - final public static PhylogenyParser createParserDependingOnSuffix( final String filename, - final boolean phyloxml_validate_against_xsd ) { - PhylogenyParser parser = null; - final String filename_lc = filename.toLowerCase(); - if ( filename_lc.endsWith( ".tol" ) || filename_lc.endsWith( ".tolxml" ) || filename_lc.endsWith( ".tol.zip" ) ) { - parser = new TolParser(); - } - else if ( filename_lc.endsWith( ".xml" ) || filename_lc.endsWith( ".px" ) || filename_lc.endsWith( "phyloxml" ) - || filename_lc.endsWith( ".zip" ) ) { - parser = new PhyloXmlParser(); - if ( phyloxml_validate_against_xsd ) { - final ClassLoader cl = PhyloXmlParser.class.getClassLoader(); - final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE ); - if ( xsd_url != null ) { - ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() ); - } - else { - if ( ForesterConstants.RELEASE ) { - throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from [" - + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" ); - } - } - } - } - else if ( filename_lc.endsWith( ".nexus" ) || filename_lc.endsWith( ".nex" ) || filename_lc.endsWith( ".nx" ) ) { - parser = new NexusPhylogeniesParser(); - } - else if ( filename_lc.endsWith( ".nhx" ) || filename_lc.endsWith( ".nh" ) || filename_lc.endsWith( ".newick" ) ) { - parser = new NHXParser(); - } - return parser; - } - - final public static PhylogenyParser createParserDependingOnUrlContents( final URL url, - final boolean phyloxml_validate_against_xsd ) - throws FileNotFoundException, IOException { - final String lc_filename = url.getFile().toString().toLowerCase(); - PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd ); - if ( ( parser != null ) && lc_filename.endsWith( ".zip" ) ) { - if ( parser instanceof PhyloXmlParser ) { - ( ( PhyloXmlParser ) parser ).setZippedInputstream( true ); - } - else if ( parser instanceof TolParser ) { - ( ( TolParser ) parser ).setZippedInputstream( true ); - } - } - if ( parser == null ) { - final String first_line = getFirstLine( url ).trim().toLowerCase(); - if ( first_line.startsWith( "<" ) ) { - parser = new PhyloXmlParser(); - if ( phyloxml_validate_against_xsd ) { - final ClassLoader cl = PhyloXmlParser.class.getClassLoader(); - final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE ); - if ( xsd_url != null ) { - ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() ); - } - else { - throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from [" - + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" ); - } - } - } - else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) ) - || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) { - parser = new NexusPhylogeniesParser(); - } - else { - parser = new NHXParser(); - } - } - return parser; - } - - final public static void ensurePresenceOfDate( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDate() ) { - node.getNodeData().setDate( new org.forester.phylogeny.data.Date() ); - } - } - - final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDistribution() ) { - node.getNodeData().setDistribution( new Distribution( "" ) ); - } - } - - public static void ensurePresenceOfSequence( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasSequence() ) { - node.getNodeData().setSequence( new Sequence() ); - } - } - - public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasTaxonomy() ) { - node.getNodeData().setTaxonomy( new Taxonomy() ); - } - } - - /** - * Extracts a code if and only if: - * one and only one _, - * shorter than 25, - * no |, - * no ., - * if / present it has to be after the _, - * if PFAM_STYLE_ONLY: / must be present, - * tax code can only contain uppercase letters and numbers, - * and must contain at least one uppercase letter. - * Return null if no code extractable. - * - * @param name - * @param limit_to_five - * @return - */ - public static String extractTaxonomyCodeFromNodeName( final String name, - final boolean limit_to_five, - final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction ) { - if ( ( name.indexOf( "_" ) > 0 ) - && ( name.length() < 25 ) - && ( name.lastIndexOf( "_" ) == name.indexOf( "_" ) ) - && ( name.indexOf( "|" ) < 0 ) - && ( name.indexOf( "." ) < 0 ) - && ( ( taxonomy_extraction != ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name - .indexOf( "/" ) >= 0 ) ) - && ( ( ( name.indexOf( "/" ) ) < 0 ) || ( name.indexOf( "/" ) > name.indexOf( "_" ) ) ) ) { - final String[] s = name.split( "[_/]" ); - if ( s.length > 1 ) { - String str = s[ 1 ]; - if ( limit_to_five ) { - if ( str.length() > 5 ) { - str = str.substring( 0, 5 ); - } - else if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) { - str = str.substring( 0, 3 ); - } - } - final Matcher letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str ); - if ( !letters_and_numbers.matches() ) { - return null; - } - final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str ); - if ( numbers_only.matches() ) { - return null; - } - return str; - } - } - return null; - } - public static void fatalError( final String prg_name, final String message ) { System.err.println(); System.err.println( "[" + prg_name + "] > " + message ); @@ -521,6 +364,16 @@ public final class ForesterUtil { System.exit( -1 ); } + public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) { + final String error = isReadableFile( file ); + if ( !isEmpty( error ) ) { + System.err.println(); + System.err.println( "[" + prg_name + "] > " + error ); + System.err.println(); + System.exit( -1 ); + } + } + public static String[] file2array( final File file ) throws IOException { final List list = file2list( file ); final String[] ary = new String[ list.size() ]; @@ -622,27 +475,6 @@ public final class ForesterUtil { return ForesterUtil.LINE_SEPARATOR; } - /** - * Returns all custom data tag names of this Phylogeny as Hashtable. Tag - * names are keys, values are Boolean set to false. - */ - final public static Hashtable getPropertyRefs( final Phylogeny phylogeny ) { - final Hashtable ht = new Hashtable(); - if ( phylogeny.isEmpty() ) { - return ht; - } - for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode current_node = iter.next(); - if ( current_node.getNodeData().isHasProperties() ) { - final String[] tags = current_node.getNodeData().getProperties().getPropertyRefs(); - for( int i = 0; i < tags.length; ++i ) { - ht.put( tags[ i ], new Boolean( false ) ); - } - } - } - return ht; - } - final public static void increaseCountingMap( final Map counting_map, final String item_name ) { if ( !counting_map.containsKey( item_name ) ) { counting_map.put( item_name, 1 ); @@ -652,23 +484,29 @@ public final class ForesterUtil { } } - final static public boolean isAllNonEmptyInternalLabelsArePositiveNumbers( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isRoot() && !n.isExternal() ) { - if ( !ForesterUtil.isEmpty( n.getName() ) ) { - double d = -1.0; - try { - d = Double.parseDouble( n.getName() ); - } - catch ( final Exception e ) { - d = -1.0; - } - if ( d < 0.0 ) { - return false; - } - } + 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; + } + for( final Object o : l ) { + if ( o != null ) { + return false; + } + } + return true; + } + + final public static boolean isEmpty( final Set s ) { + if ( ( s == null ) || s.isEmpty() ) { + return true; + } + for( final Object o : s ) { + if ( o != null ) { + return false; } } return true; @@ -683,43 +521,7 @@ public final class ForesterUtil { } final public static boolean isEven( final int n ) { - return n % 2 == 0; - } - - final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - if ( it.next().getNodeData().isHasEvent() ) { - return true; - } - } - return false; - } - - /** - * Returns true if at least one branch has a length larger than zero. - * - * - * @param phy - */ - final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - if ( it.next().getDistanceToParent() > 0.0 ) { - return true; - } - } - return false; - } - - final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - if ( it.next().getBranchData().isHasConfidences() ) { - return true; - } - } - return false; + return ( n % 2 ) == 0; } /** @@ -739,10 +541,9 @@ public final class ForesterUtil { if ( ( a.length < 1 ) || ( b.length < 1 ) ) { return false; } - for( int i = 0; i < a.length; ++i ) { - final String ai = a[ i ]; - for( int j = 0; j < b.length; ++j ) { - if ( ( ai != null ) && ( b[ j ] != null ) && ai.equals( b[ j ] ) ) { + for( final String ai : a ) { + for( final String element : b ) { + if ( ( ai != null ) && ( element != null ) && ai.equals( element ) ) { return true; } } @@ -824,6 +625,33 @@ public final class ForesterUtil { return map; } + final public static void map2file( final File file, + final Map data, + final String entry_separator, + final String data_separator ) throws IOException { + final Writer writer = new BufferedWriter( new FileWriter( file ) ); + map2writer( writer, data, entry_separator, data_separator ); + writer.close(); + } + + final public static void map2writer( final Writer writer, + final Map data, + final String entry_separator, + final String data_separator ) throws IOException { + boolean first = true; + for( final Entry entry : data.entrySet() ) { + if ( !first ) { + writer.write( data_separator ); + } + else { + first = false; + } + writer.write( entry.getKey().toString() ); + writer.write( entry_separator ); + writer.write( entry.getValue().toString() ); + } + } + 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(); ) { @@ -930,16 +758,6 @@ public final class ForesterUtil { return Integer.parseInt( str ); } - final public static void postOrderRelabelInternalNodes( final Phylogeny phylogeny, final int starting_number ) { - int i = starting_number; - for( final PhylogenyNodeIterator it = phylogeny.iteratorPostorder(); it.hasNext(); ) { - final PhylogenyNode node = it.next(); - if ( !node.isExternal() ) { - node.setName( String.valueOf( i++ ) ); - } - } - } - final public static void printArray( final Object[] a ) { for( int i = 0; i < a.length; ++i ) { System.out.println( "[" + i + "]=" + a[ i ] ); @@ -953,7 +771,7 @@ public final class ForesterUtil { } final public static void printErrorMessage( final String prg_name, final String message ) { - System.out.println( "[" + prg_name + "] > error: " + message ); + System.err.println( "[" + prg_name + "] > error: " + message ); } final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) { @@ -967,20 +785,29 @@ public final class ForesterUtil { } final public static void printProgramInformation( final String prg_name, + final String desc, final String prg_version, final String date, final String email, - final String www ) { - final int l = prg_name.length() + prg_version.length() + date.length() + 4; + final String www, + final String based_on ) { + String my_prg_name = new String( prg_name ); + if ( !ForesterUtil.isEmpty( desc ) ) { + my_prg_name += ( " - " + desc ); + } + final int l = my_prg_name.length() + prg_version.length() + date.length() + 4; System.out.println(); - System.out.println( prg_name + " " + prg_version + " (" + date + ")" ); + System.out.println( my_prg_name + " " + prg_version + " (" + date + ")" ); for( int i = 0; i < l; ++i ) { System.out.print( "_" ); } System.out.println(); System.out.println(); - System.out.println( "WWW : " + www ); - System.out.println( "Contact: " + email ); + System.out.println( "WWW : " + www ); + System.out.println( "Contact : " + email ); + if ( !ForesterUtil.isEmpty( based_on ) ) { + System.out.println( "Based on: " + based_on ); + } if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) { System.out.println(); System.out.println( "[running on Java " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); @@ -988,6 +815,14 @@ public final class ForesterUtil { System.out.println(); } + final public static void printProgramInformation( final String prg_name, + final String prg_version, + final String date, + final String email, + final String www ) { + printProgramInformation( prg_name, null, prg_version, date, email, www, null ); + } + final public static void printWarningMessage( final String prg_name, final String message ) { System.out.println( "[" + prg_name + "] > warning: " + message ); } @@ -1011,7 +846,7 @@ public final class ForesterUtil { */ final public static String removeWhiteSpace( String s ) { int i; - for( i = 0; i <= s.length() - 1; i++ ) { + for( i = 0; i <= ( s.length() - 1 ); i++ ) { if ( ( s.charAt( i ) == ' ' ) || ( s.charAt( i ) == '\t' ) || ( s.charAt( i ) == '\n' ) || ( s.charAt( i ) == '\r' ) ) { s = s.substring( 0, i ) + s.substring( i + 1 ); @@ -1021,10 +856,6 @@ public final class ForesterUtil { return s; } - final public static boolean isContainsParanthesesableNhCharacter( final String nh ) { - return PARANTHESESABLE_NH_CHARS_PATTERN.matcher( nh ).find(); - } - final public static String replaceIllegalNhCharacters( final String nh ) { if ( nh == null ) { return ""; @@ -1056,6 +887,10 @@ public final class ForesterUtil { return ( int ) ( f + 0.5f ); } + final public static short roundToShort( final double d ) { + return ( short ) ( d + 0.5 ); + } + final public static String sanitizeString( final String s ) { if ( s == null ) { return ""; @@ -1071,117 +906,56 @@ public final class ForesterUtil { } final public static String stringArrayToString( final String[] a ) { - final StringBuffer sb = new StringBuffer(); + return stringArrayToString( a, ", " ); + } + + final public static String stringArrayToString( final String[] a, final String separator ) { + final StringBuilder sb = new StringBuilder(); if ( ( a != null ) && ( a.length > 0 ) ) { - for( int i = 0; i < a.length - 1; ++i ) { - sb.append( a[ i ] + ", " ); + for( int i = 0; i < ( a.length - 1 ); ++i ) { + sb.append( a[ i ] + separator ); } sb.append( a[ a.length - 1 ] ); } return sb.toString(); } - final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) { - double value = -1; - try { - value = Double.parseDouble( n.getName() ); - } - catch ( final NumberFormatException e ) { - throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: " - + e.getLocalizedMessage() ); - } - if ( value >= 0.0 ) { - n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) ); - n.setName( "" ); - } + final public static String[] stringListToArray( final List list ) { + if ( list != null ) { + final String[] str = new String[ list.size() ]; + int i = 0; + for( final String l : list ) { + str[ i++ ] = l; } + return str; } + return null; } - final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isRoot() && !n.isExternal() && !n.getBranchData().isHasConfidences() ) { - if ( !ForesterUtil.isEmpty( n.getName() ) ) { - double d = -1.0; - try { - d = Double.parseDouble( n.getName() ); - } - catch ( final Exception e ) { - d = -1.0; - } - if ( d >= 0.0 ) { - n.getBranchData().addConfidence( new Confidence( d, "" ) ); - n.setName( "" ); - } - } + final public static String stringListToString( final List l, final String separator ) { + final StringBuilder sb = new StringBuilder(); + if ( ( l != null ) && ( l.size() > 0 ) ) { + for( int i = 0; i < ( l.size() - 1 ); ++i ) { + sb.append( l.get( i ) + separator ); } + sb.append( l.get( l.size() - 1 ) ); } + return sb.toString(); } - final static public void transferNodeNameToField( final Phylogeny phy, final PhylogenyNodeField field ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - final String name = n.getName().trim(); - if ( !ForesterUtil.isEmpty( name ) ) { - switch ( field ) { - case TAXONOMY_CODE: - //temp hack - // if ( name.length() > 5 ) { - // n.setName( "" ); - // if ( !n.getNodeData().isHasTaxonomy() ) { - // n.getNodeData().setTaxonomy( new Taxonomy() ); - // } - // n.getNodeData().getTaxonomy().setScientificName( name ); - // break; - // } - // - n.setName( "" ); - PhylogenyMethods.setTaxonomyCode( n, name ); - break; - case TAXONOMY_SCIENTIFIC_NAME: - n.setName( "" ); - if ( !n.getNodeData().isHasTaxonomy() ) { - n.getNodeData().setTaxonomy( new Taxonomy() ); - } - n.getNodeData().getTaxonomy().setScientificName( name ); - break; - case TAXONOMY_COMMON_NAME: - n.setName( "" ); - if ( !n.getNodeData().isHasTaxonomy() ) { - n.getNodeData().setTaxonomy( new Taxonomy() ); - } - n.getNodeData().getTaxonomy().setCommonName( name ); - break; - case SEQUENCE_SYMBOL: - n.setName( "" ); - if ( !n.getNodeData().isHasSequence() ) { - n.getNodeData().setSequence( new Sequence() ); - } - n.getNodeData().getSequence().setSymbol( name ); - break; - case SEQUENCE_NAME: - n.setName( "" ); - if ( !n.getNodeData().isHasSequence() ) { - n.getNodeData().setSequence( new Sequence() ); - } - n.getNodeData().getSequence().setName( name ); - break; - } - } + final public static String[] stringSetToArray( final Set strings ) { + final String[] str_array = new String[ strings.size() ]; + int i = 0; + for( final String e : strings ) { + str_array[ i++ ] = e; } + return str_array; } final public static void unexpectedFatalError( final String prg_name, final Exception e ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error (Should not have occured! Please contact program author(s).)" ); + + "] > Unexpected error. Should not have occured! Please contact program author(s)." ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); @@ -1190,7 +964,7 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final String message ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error. Should not have occured! Please contact program author(s)." ); + + "] > Unexpected error. Should not have occured! Please contact program author(s)." ); System.err.println( message ); System.err.println(); System.exit( -1 ); @@ -1199,7 +973,7 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error. Should not have occured! Please contact program author(s)." ); + + "] > Unexpected error. Should not have occured! Please contact program author(s)." ); System.err.println( message ); e.printStackTrace( System.err ); System.err.println(); @@ -1219,7 +993,7 @@ public final class ForesterUtil { ls = -1; start = i + 1; } - if ( i > start + width - 1 ) { + if ( i > ( ( start + width ) - 1 ) ) { if ( ls != -1 ) { sb.setCharAt( ls, '\n' ); start = ls + 1; @@ -1234,12 +1008,4 @@ public final class ForesterUtil { } return sb.toString(); } - - public static enum PhylogenyNodeField { - CLADE_NAME, TAXONOMY_CODE, TAXONOMY_SCIENTIFIC_NAME, TAXONOMY_COMMON_NAME, SEQUENCE_SYMBOL, SEQUENCE_NAME; - } - - public static enum TAXONOMY_EXTRACTION { - NO, YES, PFAM_STYLE_ONLY; - } }