// $Id: // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // 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 // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // 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 // // Contact: phylosoft @ gmail . com // WWW: www.phylosoft.org/forester package org.forester.util; import java.awt.Color; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.StringReader; import java.math.BigDecimal; import java.net.URL; import java.text.DateFormat; import java.text.DecimalFormat; import java.text.DecimalFormatSymbols; import java.text.NumberFormat; import java.text.ParseException; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Date; import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; 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.phyloxml.PhyloXmlUtil; import org.forester.io.parsers.tol.TolParser; import org.forester.io.parsers.util.PhylogenyParserException; 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.Identifier; import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; 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 final static String JAVA_VENDOR = System.getProperty( "java.vendor" ); public final static String JAVA_VERSION = System.getProperty( "java.version" ); 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; static { final DecimalFormatSymbols dfs = new DecimalFormatSymbols(); dfs.setDecimalSeparator( '.' ); // dfs.setGroupingSeparator( ( char ) 0 ); FORMATTER_9 = new DecimalFormat( "#.#########", dfs ); FORMATTER_6 = new DecimalFormat( "#.######", dfs ); FORMATTER_06 = new DecimalFormat( "0.######", dfs ); FORMATTER_3 = new DecimalFormat( "#.###", dfs ); } private ForesterUtil() { } public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny[] trees = factory.create( file, parser ); if ( ( trees == null ) || ( trees.length == 0 ) ) { throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file ); } return trees; } 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; } 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; } /** * 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. * * @param value * the value * @param min * the smallest value * @param max * the largest value * @param minColor * the color for min * @param maxColor * the color for max * @return a Color */ final public static Color calcColor( double value, final double min, final double max, final Color minColor, final Color maxColor ) { if ( value < min ) { value = min; } if ( value > max ) { value = max; } final double x = ForesterUtil.calculateColorFactor( value, max, min ); final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), maxColor.getRed(), x ); final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), maxColor.getGreen(), x ); final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), maxColor.getBlue(), x ); return new Color( red, green, blue ); } /** * 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, if * value is equal to mean the returned color is meanColor, otherwise a color * 'proportional' to value is returned -- either between min-mean or * mean-max * * @param value * the value * @param min * the smallest value * @param max * the largest value * @param mean * the mean/median value * @param minColor * the color for min * @param maxColor * the color for max * @param meanColor * the color for mean * @return a Color */ final public static Color calcColor( double value, final double min, final double max, final double mean, final Color minColor, final Color maxColor, final Color meanColor ) { if ( value < min ) { value = min; } if ( value > max ) { value = max; } if ( value < mean ) { final double x = ForesterUtil.calculateColorFactor( value, mean, min ); final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), meanColor.getRed(), x ); final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), meanColor.getGreen(), x ); final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), meanColor.getBlue(), x ); return new Color( red, green, blue ); } else if ( value > mean ) { final double x = ForesterUtil.calculateColorFactor( value, max, mean ); final int red = ForesterUtil.calculateColorComponent( meanColor.getRed(), maxColor.getRed(), x ); final int green = ForesterUtil.calculateColorComponent( meanColor.getGreen(), maxColor.getGreen(), x ); final int blue = ForesterUtil.calculateColorComponent( meanColor.getBlue(), maxColor.getBlue(), x ); return new Color( red, green, blue ); } else { return meanColor; } } /** * Helper method for calcColor methods. * * @param smallercolor_component_x * color component the smaller color * @param largercolor_component_x * color component the larger color * @param x * factor * @return an int representing a color component */ final private static int calculateColorComponent( final double smallercolor_component_x, final double largercolor_component_x, final double x ) { return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) ); } /** * Helper method for calcColor methods. * * * @param value * the value * @param larger * the largest value * @param smaller * the smallest value * @return a normalized value between larger and smaller */ final private static double calculateColorFactor( final double value, final double larger, final double smaller ) { return ( 255.0 * ( value - smaller ) ) / ( larger - smaller ); } final public static String collapseWhiteSpace( final String s ) { return s.replaceAll( "[\\s]+", " " ); } final public static String colorToHex( final Color color ) { final String rgb = Integer.toHexString( color.getRGB() ); return rgb.substring( 2, rgb.length() ); } synchronized public static void copyFile( final File in, final File out ) throws IOException { final FileInputStream in_s = new FileInputStream( in ); final FileOutputStream out_s = new FileOutputStream( out ); try { final byte[] buf = new byte[ 1024 ]; int i = 0; while ( ( i = in_s.read( buf ) ) != -1 ) { out_s.write( buf, 0, i ); } } catch ( final IOException e ) { throw e; } finally { if ( in_s != null ) { in_s.close(); } if ( out_s != null ) { out_s.close(); } } } final public static int countChars( final String str, final char c ) { int count = 0; for( int i = 0; i < str.length(); ++i ) { if ( str.charAt( i ) == c ) { ++count; } } return count; } final public static BufferedWriter createBufferedWriter( final File file ) throws IOException { if ( file.exists() ) { throw new IOException( "[" + file + "] already exists" ); } return new BufferedWriter( new FileWriter( file ) ); } final public static BufferedWriter createBufferedWriter( final String name ) throws IOException { return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) ); } final public static File createFileForWriting( final String name ) throws IOException { final File file = new File( name ); if ( file.exists() ) { throw new IOException( "[" + name + "] already exists" ); } 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 ); 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() ]; 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 ) ); String str; while ( ( str = in.readLine() ) != null ) { str = str.trim(); if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) { for( final String s : splitString( str ) ) { list.add( s ); } } } in.close(); return list; } final public static SortedSet file2set( final File file ) throws IOException { final SortedSet set = new TreeSet(); final BufferedReader in = new BufferedReader( new FileReader( file ) ); String str; while ( ( str = in.readLine() ) != null ) { str = str.trim(); if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) { for( final String s : splitString( str ) ) { set.add( s ); } } } in.close(); return set; } final public static String getCurrentDateTime() { final DateFormat format = new SimpleDateFormat( "yyyy/MM/dd HH:mm:ss" ); return format.format( new Date() ); } final public static String getFileSeparator() { return ForesterUtil.FILE_SEPARATOR; } final public static String getFirstLine( final Object source ) throws FileNotFoundException, IOException { BufferedReader reader = null; if ( source instanceof File ) { final File f = ( File ) source; if ( !f.exists() ) { throw new IOException( "[" + f.getAbsolutePath() + "] does not exist" ); } else if ( !f.isFile() ) { throw new IOException( "[" + f.getAbsolutePath() + "] is not a file" ); } else if ( !f.canRead() ) { throw new IOException( "[" + f.getAbsolutePath() + "] is not a readable" ); } reader = new BufferedReader( new FileReader( f ) ); } else if ( source instanceof InputStream ) { reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) ); } else if ( source instanceof String ) { reader = new BufferedReader( new StringReader( ( String ) source ) ); } else if ( source instanceof StringBuffer ) { reader = new BufferedReader( new StringReader( source.toString() ) ); } else if ( source instanceof URL ) { reader = new BufferedReader( new InputStreamReader( ( ( URL ) source ).openStream() ) ); } else { throw new IllegalArgumentException( "dont know how to read [" + source.getClass() + "]" ); } String line; while ( ( line = reader.readLine() ) != null ) { line = line.trim(); if ( !ForesterUtil.isEmpty( line ) ) { if ( reader != null ) { reader.close(); } return line; } } if ( reader != null ) { reader.close(); } return line; } final public static String getLineSeparator() { 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 ); } else { counting_map.put( item_name, counting_map.get( item_name ) + 1 ); } } 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; } } } } return true; } final public static boolean isEmpty( final String s ) { return ( ( s == null ) || ( s.length() < 1 ) ); } final public static boolean isEqual( final double a, final double b ) { return ( ( Math.abs( a - b ) ) < ZERO_DIFF ); } 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; } /** * This determines whether String[] a and String[] b have at least one * String in common (intersect). Returns false if at least one String[] is * null or empty. * * @param a * a String[] b a String[] * @return true if both a and b or not empty or null and contain at least * one element in common false otherwise */ final public static boolean isIntersecting( final String[] a, final String[] b ) { if ( ( a == null ) || ( b == null ) ) { return false; } 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 ] ) ) { return true; } } } return false; } final public static double isLargerOrEqualToZero( final double d ) { if ( d > 0.0 ) { return d; } else { return 0.0; } } final public static boolean isNull( final BigDecimal s ) { return ( ( s == null ) || ( s.compareTo( NULL_BD ) == 0 ) ); } final public static String isReadableFile( final File f ) { if ( !f.exists() ) { return "file [" + f + "] does not exist"; } if ( f.isDirectory() ) { return "[" + f + "] is a directory"; } if ( !f.isFile() ) { return "[" + f + "] is not a file"; } if ( !f.canRead() ) { return "file [" + f + "] is not readable"; } if ( f.length() < 1 ) { return "file [" + f + "] is empty"; } return null; } final public static String isReadableFile( final String s ) { return isReadableFile( new File( s ) ); } final public static String isWritableFile( final File f ) { if ( f.isDirectory() ) { return "[" + f + "] is a directory"; } if ( f.exists() ) { return "[" + f + "] already exists"; } return null; } /** * Helper for method "stringToColor". *

* (Last modified: 12/20/03) */ final public static int limitRangeForColor( int i ) { if ( i > 255 ) { i = 255; } else if ( i < 0 ) { i = 0; } return i; } final public static SortedMap listToSortedCountsMap( final List list ) { final SortedMap map = new TreeMap(); for( final Object key : list ) { if ( !map.containsKey( key ) ) { map.put( key, 1 ); } else { map.put( key, map.get( key ) + 1 ); } } return map; } 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(); sb.append( key.toString() ); sb.append( key_value_separator ); sb.append( map.get( key ).toString() ); sb.append( ForesterUtil.getLineSeparator() ); } return sb; } final public static String normalizeString( final String s, final int length, final boolean left_pad, final char pad_char ) { if ( s.length() > length ) { return s.substring( 0, length ); } else { final StringBuffer pad = new StringBuffer( length - s.length() ); for( int i = 0; i < ( length - s.length() ); ++i ) { pad.append( pad_char ); } if ( left_pad ) { return pad + s; } else { return s + pad; } } } final public static BufferedReader obtainReader( final Object source ) throws IOException, FileNotFoundException { BufferedReader reader = null; if ( source instanceof File ) { final File f = ( File ) source; if ( !f.exists() ) { throw new IOException( "\"" + f.getAbsolutePath() + "\" does not exist" ); } else if ( !f.isFile() ) { throw new IOException( "\"" + f.getAbsolutePath() + "\" is not a file" ); } else if ( !f.canRead() ) { throw new IOException( "\"" + f.getAbsolutePath() + "\" is not a readable" ); } reader = new BufferedReader( new FileReader( f ) ); } else if ( source instanceof InputStream ) { reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) ); } else if ( source instanceof String ) { reader = new BufferedReader( new StringReader( ( String ) source ) ); } else if ( source instanceof StringBuffer ) { reader = new BufferedReader( new StringReader( source.toString() ) ); } else { throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass() + "] (can only parse objects of type File, InputStream, String, or StringBuffer)" ); } return reader; } 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 ); } final public static StringBuffer pad( final String string, final int size, final char pad, final boolean left_pad ) { return pad( new StringBuffer( string ), size, pad, left_pad ); } final public static StringBuffer pad( final StringBuffer string, final int size, final char pad, final boolean left_pad ) { final StringBuffer padding = new StringBuffer(); final int s = size - string.length(); if ( s < 1 ) { return new StringBuffer( string.substring( 0, size ) ); } for( int i = 0; i < s; ++i ) { padding.append( pad ); } if ( left_pad ) { return padding.append( string ); } else { return string.append( padding ); } } final public static double parseDouble( final String str ) throws ParseException { if ( ForesterUtil.isEmpty( str ) ) { return 0.0; } return Double.parseDouble( str ); } final public static int parseInt( final String str ) throws ParseException { if ( ForesterUtil.isEmpty( str ) ) { return 0; } 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 ] ); } } final public static void printCountingMap( final Map counting_map ) { for( final String key : counting_map.keySet() ) { System.out.println( key + ": " + counting_map.get( key ) ); } } final public static void printErrorMessage( final String prg_name, final String message ) { System.out.println( "[" + prg_name + "] > error: " + message ); } final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) { final int l = prg_name.length() + prg_version.length() + date.length() + 4; System.out.println(); System.out.println( prg_name + " " + prg_version + " (" + date + ")" ); for( int i = 0; i < l; ++i ) { System.out.print( "_" ); } 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 ) { final int l = prg_name.length() + prg_version.length() + date.length() + 4; System.out.println(); System.out.println( 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 ); 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 + "]" ); } System.out.println(); } final public static void printWarningMessage( final String prg_name, final String message ) { System.out.println( "[" + prg_name + "] > warning: " + message ); } final public static void programMessage( final String prg_name, final String message ) { System.out.println( "[" + prg_name + "] > " + message ); } final public static String removeSuffix( final String file_name ) { final int i = file_name.lastIndexOf( '.' ); if ( i > 1 ) { return file_name.substring( 0, i ); } return file_name; } /** * Removes all white space from String s. * * @return String s with white space removed */ final public static String removeWhiteSpace( String s ) { int 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 ); i--; } } 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 ""; } return nh.trim().replaceAll( "[\\[\\]:]+", "_" ); } final public static String replaceIllegalNhxCharacters( final String nhx ) { if ( nhx == null ) { return ""; } return nhx.trim().replaceAll( "[\\[\\](),:;\\s]+", "_" ); } final public static double round( final double value, final int decimal_place ) { BigDecimal bd = new BigDecimal( value ); bd = bd.setScale( decimal_place, BigDecimal.ROUND_HALF_UP ); return bd.doubleValue(); } /** * Rounds d to an int. */ final public static int roundToInt( final double d ) { return ( int ) ( d + 0.5 ); } final public static int roundToInt( final float f ) { return ( int ) ( f + 0.5f ); } final public static String sanitizeString( final String s ) { if ( s == null ) { return ""; } else { return s.trim(); } } final private static String[] splitString( final String str ) { final String regex = "[\\s;,]+"; return str.split( regex ); } final public static String stringArrayToString( final String[] a ) { final StringBuffer sb = new StringBuffer(); if ( ( a != null ) && ( a.length > 0 ) ) { for( int i = 0; i < a.length - 1; ++i ) { sb.append( a[ i ] + ", " ); } 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 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 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; case TAXONOMY_ID_UNIPROT_1: { if ( !n.getNodeData().isHasTaxonomy() ) { n.getNodeData().setTaxonomy( new Taxonomy() ); } String id = name; final int i = name.indexOf( '_' ); if ( i > 0 ) { id = name.substring( 0, i ); } else { n.setName( "" ); } n.getNodeData().getTaxonomy() .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); break; } case TAXONOMY_ID_UNIPROT_2: { if ( !n.getNodeData().isHasTaxonomy() ) { n.getNodeData().setTaxonomy( new Taxonomy() ); } String id = name; final int i = name.indexOf( '_' ); if ( i > 0 ) { id = name.substring( i + 1, name.length() ); } else { n.setName( "" ); } n.getNodeData().getTaxonomy() .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); break; } } } } } 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).)" ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); } 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)." ); System.err.println( message ); System.err.println(); System.exit( -1 ); } 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)." ); System.err.println( message ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); } public final static String wordWrap( final String str, final int width ) { final StringBuilder sb = new StringBuilder( str ); int start = 0; int ls = -1; int i = 0; while ( i < sb.length() ) { if ( sb.charAt( i ) == ' ' ) { ls = i; } if ( sb.charAt( i ) == '\n' ) { ls = -1; start = i + 1; } if ( i > start + width - 1 ) { if ( ls != -1 ) { sb.setCharAt( ls, '\n' ); start = ls + 1; ls = -1; } else { sb.insert( i, '\n' ); start = i + 1; } } i++; } return sb.toString(); } public static enum PhylogenyNodeField { CLADE_NAME, TAXONOMY_CODE, TAXONOMY_SCIENTIFIC_NAME, TAXONOMY_COMMON_NAME, SEQUENCE_SYMBOL, SEQUENCE_NAME, TAXONOMY_ID_UNIPROT_1, TAXONOMY_ID_UNIPROT_2; } public static enum TAXONOMY_EXTRACTION { NO, YES, PFAM_STYLE_ONLY; } }