2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.util;
28 import java.awt.Color;
29 import java.io.BufferedReader;
30 import java.io.BufferedWriter;
32 import java.io.FileInputStream;
33 import java.io.FileNotFoundException;
34 import java.io.FileOutputStream;
35 import java.io.FileReader;
36 import java.io.FileWriter;
37 import java.io.FilenameFilter;
38 import java.io.IOException;
39 import java.io.InputStream;
40 import java.io.InputStreamReader;
41 import java.io.StringReader;
42 import java.io.Writer;
43 import java.math.BigDecimal;
45 import java.net.URLConnection;
46 import java.security.KeyManagementException;
47 import java.security.NoSuchAlgorithmException;
48 import java.text.DateFormat;
49 import java.text.DecimalFormat;
50 import java.text.DecimalFormatSymbols;
51 import java.text.NumberFormat;
52 import java.text.ParseException;
53 import java.text.SimpleDateFormat;
54 import java.util.ArrayList;
55 import java.util.Collection;
56 import java.util.Date;
57 import java.util.List;
59 import java.util.Map.Entry;
61 import java.util.SortedMap;
62 import java.util.SortedSet;
63 import java.util.TreeMap;
64 import java.util.TreeSet;
65 import java.util.regex.Matcher;
66 import java.util.regex.Pattern;
68 import org.forester.archaeopteryx.AptxConstants;
69 import org.forester.io.parsers.PhylogenyParser;
70 import org.forester.phylogeny.Phylogeny;
71 import org.forester.phylogeny.PhylogenyNode;
72 import org.forester.phylogeny.data.Distribution;
73 import org.forester.phylogeny.data.Sequence;
74 import org.forester.phylogeny.data.Taxonomy;
75 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
76 import org.forester.protein.BasicProtein;
77 import org.forester.protein.Domain;
78 import org.forester.protein.Protein;
79 import org.forester.sequence.MolecularSequence;
80 import org.forester.sequence.MolecularSequence.TYPE;
81 import org.forester.surfacing.SurfacingUtil;
83 public final class ForesterUtil {
85 public final static String FILE_SEPARATOR = System.getProperty( "file.separator" );
86 public static final NumberFormat FORMATTER_06;
87 public static final NumberFormat FORMATTER_3;
88 public static final NumberFormat FORMATTER_6;
89 public static final NumberFormat FORMATTER_9;
90 public final static String JAVA_VENDOR = System.getProperty( "java.vendor" );
91 public final static String JAVA_VERSION = System.getProperty( "java.version" );
92 public final static String LINE_SEPARATOR = System.getProperty( "line.separator" );
93 public static final String NCBI_GI = "http://www.ncbi.nlm.nih.gov/protein/gi:";
94 public static final String NCBI_NUCCORE = "http://www.ncbi.nlm.nih.gov/nuccore/";
95 public static final String NCBI_PROTEIN = "http://www.ncbi.nlm.nih.gov/protein/";
96 public static final BigDecimal NULL_BD = new BigDecimal( 0 );
97 public final static String OS_ARCH = System.getProperty( "os.arch" );
98 public final static String OS_NAME = System.getProperty( "os.name" );
99 public final static String OS_VERSION = System.getProperty( "os.version" );
100 public static final String PDB = "http://www.pdb.org/pdb/explore/explore.do?pdbId=";
101 public final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/";
102 public final static double ZERO_DIFF = 1.0E-12;
103 private static final Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s:\\[\\]]" );
105 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
106 dfs.setDecimalSeparator( '.' );
107 // dfs.setGroupingSeparator( ( char ) 0 );
108 FORMATTER_9 = new DecimalFormat( "#.#########", dfs );
109 FORMATTER_6 = new DecimalFormat( "#.######", dfs );
110 FORMATTER_06 = new DecimalFormat( "0.######", dfs );
111 FORMATTER_3 = new DecimalFormat( "#.###", dfs );
114 final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
115 if ( sb.length() > 0 ) {
116 sb.append( separator );
120 final public static String removeFileExtension( final String file_name ) {
121 if ( file_name.indexOf( "." ) > 0 ) {
122 return file_name.substring( 0, file_name.lastIndexOf( "." ) );
128 * This calculates a color. If value is equal to min the returned color is
129 * minColor, if value is equal to max the returned color is maxColor,
130 * otherwise a color 'proportional' to value is returned.
144 final public static Color calcColor( double value,
147 final Color minColor,
148 final Color maxColor ) {
155 final double x = ForesterUtil.calculateColorFactor( value, max, min );
156 final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), maxColor.getRed(), x );
157 final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), maxColor.getGreen(), x );
158 final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), maxColor.getBlue(), x );
159 return new Color( red, green, blue );
163 * This calculates a color. If value is equal to min the returned color is
164 * minColor, if value is equal to max the returned color is maxColor, if
165 * value is equal to mean the returned color is meanColor, otherwise a color
166 * 'proportional' to value is returned -- either between min-mean or
176 * the mean/median value
185 final public static Color calcColor( double value,
189 final Color minColor,
190 final Color maxColor,
191 final Color meanColor ) {
198 if ( value < mean ) {
199 final double x = ForesterUtil.calculateColorFactor( value, mean, min );
200 final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), meanColor.getRed(), x );
201 final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), meanColor.getGreen(), x );
202 final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), meanColor.getBlue(), x );
203 return new Color( red, green, blue );
205 else if ( value > mean ) {
206 final double x = ForesterUtil.calculateColorFactor( value, max, mean );
207 final int red = ForesterUtil.calculateColorComponent( meanColor.getRed(), maxColor.getRed(), x );
208 final int green = ForesterUtil.calculateColorComponent( meanColor.getGreen(), maxColor.getGreen(), x );
209 final int blue = ForesterUtil.calculateColorComponent( meanColor.getBlue(), maxColor.getBlue(), x );
210 return new Color( red, green, blue );
218 * Helper method for calcColor methods.
220 * @param smallercolor_component_x
221 * color component the smaller color
222 * @param largercolor_component_x
223 * color component the larger color
226 * @return an int representing a color component
228 final private static int calculateColorComponent( final double smallercolor_component_x,
229 final double largercolor_component_x,
231 return ( int ) ( smallercolor_component_x
232 + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) );
236 * Helper method for calcColor methods.
245 * @return a normalized value between larger and smaller
247 final private static double calculateColorFactor( final double value, final double larger, final double smaller ) {
248 return ( 255.0 * ( value - smaller ) ) / ( larger - smaller );
251 public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
252 int overlap_count = 0;
253 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
254 if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
258 return overlap_count;
261 final public static String collapseWhiteSpace( final String s ) {
262 return s.replaceAll( "[\\s]+", " " );
265 final public static void collection2file( final File file, final Collection<?> data, final String separator )
267 final Writer writer = new BufferedWriter( new FileWriter( file ) );
268 collection2writer( writer, data, separator );
272 final public static void collection2writer( final Writer writer, final Collection<?> data, final String separator )
274 boolean first = true;
275 for( final Object object : data ) {
277 writer.write( separator );
282 writer.write( object.toString() );
286 final public static String colorToHex( final Color color ) {
287 final String rgb = Integer.toHexString( color.getRGB() );
288 return rgb.substring( 2, rgb.length() );
291 synchronized public static void copyFile( final File in, final File out ) throws IOException {
292 final FileInputStream in_s = new FileInputStream( in );
293 final FileOutputStream out_s = new FileOutputStream( out );
295 final byte[] buf = new byte[ 1024 ];
297 while ( ( i = in_s.read( buf ) ) != -1 ) {
298 out_s.write( buf, 0, i );
301 catch ( final IOException e ) {
305 if ( in_s != null ) {
308 if ( out_s != null ) {
314 final public static int countChars( final String str, final char c ) {
316 for( int i = 0; i < str.length(); ++i ) {
317 if ( str.charAt( i ) == c ) {
324 final public static BufferedWriter createBufferedWriter( final File file ) throws IOException {
325 if ( file.exists() ) {
326 throw new IOException( "[" + file + "] already exists" );
328 return new BufferedWriter( new FileWriter( file ) );
331 final public static BufferedWriter createBufferedWriter( final String name ) throws IOException {
332 return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) );
335 final public static EasyWriter createEasyWriter( final File file ) throws IOException {
336 return new EasyWriter( createBufferedWriter( file ) );
339 final public static BufferedWriter createEasyWriter( final String name ) throws IOException {
340 return createEasyWriter( createFileForWriting( name ) );
343 final public static File createFileForWriting( final String name ) throws IOException {
344 final File file = new File( name );
345 if ( file.exists() ) {
346 throw new IOException( "[" + name + "] already exists" );
351 final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
352 if ( !node.getNodeData().isHasDate() ) {
353 node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
357 final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
358 if ( !node.getNodeData().isHasDistribution() ) {
359 node.getNodeData().setDistribution( new Distribution( "" ) );
363 public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
364 if ( !node.getNodeData().isHasSequence() ) {
365 node.getNodeData().setSequence( new Sequence() );
369 public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
370 if ( !node.getNodeData().isHasTaxonomy() ) {
371 node.getNodeData().setTaxonomy( new Taxonomy() );
375 public static void fatalError( final String message ) {
376 System.err.println();
377 System.err.println( "error: " + message );
378 System.err.println();
382 public static void fatalError( final String prg_name, final String message ) {
383 System.err.println();
384 System.err.println( "[" + prg_name + "] > " + message );
385 System.err.println();
389 public static void fatalErrorIfFileNotReadable( final File file ) {
390 final String error = isReadableFile( file );
391 if ( !isEmpty( error ) ) {
392 System.err.println();
393 System.err.println( "error: " + error );
394 System.err.println();
399 public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) {
400 final String error = isReadableFile( file );
401 if ( !isEmpty( error ) ) {
402 System.err.println();
403 System.err.println( "[" + prg_name + "] > " + error );
404 System.err.println();
409 public static String[][] file22dArray( final File file ) throws IOException {
410 final List<String> list = new ArrayList<String>();
411 final BufferedReader in = new BufferedReader( new FileReader( file ) );
413 while ( ( str = in.readLine() ) != null ) {
415 if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
420 final String[][] ary = new String[ list.size() ][ 2 ];
421 final Pattern pa = Pattern.compile( "(\\S+)\\s+(\\S+)" );
423 for( final String s : list ) {
424 final Matcher m = pa.matcher( s );
426 ary[ i ][ 0 ] = m.group( 1 );
427 ary[ i ][ 1 ] = m.group( 2 );
431 throw new IOException( "unexpcted format: " + s );
437 public static String[] file2array( final File file ) throws IOException {
438 final List<String> list = file2list( file );
439 final String[] ary = new String[ list.size() ];
441 for( final String s : list ) {
447 final public static List<String> file2list( final File file ) throws IOException {
448 final List<String> list = new ArrayList<String>();
449 final BufferedReader in = new BufferedReader( new FileReader( file ) );
451 while ( ( str = in.readLine() ) != null ) {
453 if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
454 for( final String s : splitString( str ) ) {
463 final public static SortedSet<String> file2set( final File file ) throws IOException {
464 final SortedSet<String> set = new TreeSet<String>();
465 final BufferedReader in = new BufferedReader( new FileReader( file ) );
467 while ( ( str = in.readLine() ) != null ) {
469 if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
470 for( final String s : splitString( str ) ) {
479 final public static String getCurrentDateTime() {
480 final DateFormat format = new SimpleDateFormat( "yyyy/MM/dd HH:mm:ss" );
481 return format.format( new Date() );
484 final public static String getFileSeparator() {
485 return ForesterUtil.FILE_SEPARATOR;
488 final public static String getFirstLine( final Object source ) throws FileNotFoundException, IOException {
489 BufferedReader reader = null;
490 if ( source instanceof File ) {
491 final File f = ( File ) source;
493 throw new IOException( "[" + f.getAbsolutePath() + "] does not exist" );
495 else if ( !f.isFile() ) {
496 throw new IOException( "[" + f.getAbsolutePath() + "] is not a file" );
498 else if ( !f.canRead() ) {
499 throw new IOException( "[" + f.getAbsolutePath() + "] is not a readable" );
501 reader = new BufferedReader( new FileReader( f ) );
503 else if ( source instanceof InputStream ) {
504 reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) );
506 else if ( source instanceof String ) {
507 reader = new BufferedReader( new StringReader( ( String ) source ) );
509 else if ( source instanceof StringBuffer ) {
510 reader = new BufferedReader( new StringReader( source.toString() ) );
512 else if ( source instanceof URL ) {
513 final URLConnection url_connection = ( ( URL ) source ).openConnection();
514 url_connection.setDefaultUseCaches( false );
515 reader = new BufferedReader( new InputStreamReader( url_connection.getInputStream() ) );
518 throw new IllegalArgumentException( "dont know how to read [" + source.getClass() + "]" );
521 while ( ( line = reader.readLine() ) != null ) {
523 if ( !ForesterUtil.isEmpty( line ) ) {
524 if ( reader != null ) {
530 if ( reader != null ) {
536 final public static String getForesterLibraryInformation() {
537 return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")";
540 final public static String getLineSeparator() {
541 return ForesterUtil.LINE_SEPARATOR;
544 final public static MolecularSequence.TYPE guessMolecularSequenceType( final String mol_seq ) {
545 final String s = mol_seq.toUpperCase();
546 if ( s.contains( "L" ) || s.contains( "I" ) || s.contains( "E" ) || s.contains( "H" ) || s.contains( "D" )
547 || s.contains( "Q" ) ) {
551 if ( s.contains( "T" ) ) {
554 else if ( s.contains( "U" ) ) {
561 final public static void increaseCountingMap( final Map<String, Integer> counting_map, final String item_name ) {
562 if ( !counting_map.containsKey( item_name ) ) {
563 counting_map.put( item_name, 1 );
566 counting_map.put( item_name, counting_map.get( item_name ) + 1 );
570 final public static boolean isEmpty( final List<?> l ) {
571 if ( ( l == null ) || l.isEmpty() ) {
574 for( final Object o : l ) {
582 final public static boolean isEmpty( final Set<?> s ) {
583 if ( ( s == null ) || s.isEmpty() ) {
586 for( final Object o : s ) {
594 final public static boolean isEmpty( final String s ) {
595 return ( ( s == null ) || ( s.length() < 1 ) );
598 final public static boolean isEmptyTrimmed( final String s ) {
602 return ( ( s.trim().length() < 1 ) );
606 * Returns true is Domain domain falls in an uninterrupted stretch of
610 * @param covered_positions
613 public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
614 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
615 if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
622 final public static boolean isEqual( final double a, final double b ) {
623 return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
626 final public static boolean isEqual( final double a, final double b, final double tolerance ) {
627 return ( ( Math.abs( a - b ) ) < tolerance );
630 final public static boolean isEven( final int n ) {
631 return ( n % 2 ) == 0;
635 * This determines whether String[] a and String[] b have at least one
636 * String in common (intersect). Returns false if at least one String[] is
640 * a String[] b a String[]
641 * @return true if both a and b or not empty or null and contain at least
642 * one element in common false otherwise
644 final public static boolean isIntersecting( final String[] a, final String[] b ) {
645 if ( ( a == null ) || ( b == null ) ) {
648 if ( ( a.length < 1 ) || ( b.length < 1 ) ) {
651 for( final String ai : a ) {
652 for( final String element : b ) {
653 if ( ( ai != null ) && ( element != null ) && ai.equals( element ) ) {
661 final public static double isLargerOrEqualToZero( final double d ) {
670 public final static boolean isMac() {
672 return OS_NAME.toLowerCase().startsWith( "mac" );
674 catch ( final Exception e ) {
675 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "minor error: " + e );
680 final public static boolean isNull( final BigDecimal s ) {
681 return ( ( s == null ) || ( s.compareTo( NULL_BD ) == 0 ) );
684 final public static String isReadableFile( final File f ) {
686 return "file [" + f + "] does not exist";
688 if ( f.isDirectory() ) {
689 return "[" + f + "] is a directory";
692 return "[" + f + "] is not a file";
694 if ( !f.canRead() ) {
695 return "file [" + f + "] is not readable";
697 if ( f.length() < 1 ) {
698 return "file [" + f + "] is empty";
703 final public static String isReadableFile( final String s ) {
704 return isReadableFile( new File( s ) );
707 public final static boolean isWindows() {
709 return OS_NAME.toLowerCase().indexOf( "win" ) > -1;
711 catch ( final Exception e ) {
712 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "minor error: " + e );
717 final public static String isWritableFile( final File f ) {
718 if ( f.isDirectory() ) {
719 return "[" + f + "] is a directory";
722 return "[" + f + "] already exists";
727 final public static String isWritableFile( final String s ) {
728 return isWritableFile( new File( s ) );
732 * Helper for method "stringToColor".
734 * (Last modified: 12/20/03)
736 final public static int limitRangeForColor( int i ) {
746 final public static SortedMap<Object, Integer> listToSortedCountsMap( final List<?> list ) {
747 final SortedMap<Object, Integer> map = new TreeMap<Object, Integer>();
748 for( final Object key : list ) {
749 if ( !map.containsKey( key ) ) {
753 map.put( key, map.get( key ) + 1 );
759 final public static void map2file( final File file,
760 final Map<?, ?> data,
761 final String entry_separator,
762 final String data_separator )
764 final Writer writer = new BufferedWriter( new FileWriter( file ) );
765 map2writer( writer, data, entry_separator, data_separator );
769 final public static void map2writer( final Writer writer,
770 final Map<?, ?> data,
771 final String entry_separator,
772 final String data_separator )
774 boolean first = true;
775 for( final Entry<?, ?> entry : data.entrySet() ) {
777 writer.write( data_separator );
782 writer.write( entry.getKey().toString() );
783 writer.write( entry_separator );
784 writer.write( entry.getValue().toString() );
788 final public static StringBuffer mapToStringBuffer( final Map<Object, Object> map,
789 final String key_value_separator ) {
790 final StringBuffer sb = new StringBuffer();
791 for( final Object key : map.keySet() ) {
792 sb.append( key.toString() );
793 sb.append( key_value_separator );
794 sb.append( map.get( key ).toString() );
795 sb.append( ForesterUtil.getLineSeparator() );
800 final public static String normalizeString( final String s,
802 final boolean left_pad,
803 final char pad_char ) {
804 if ( s.length() > length ) {
805 return s.substring( 0, length );
808 final StringBuffer pad = new StringBuffer( length - s.length() );
809 for( int i = 0; i < ( length - s.length() ); ++i ) {
810 pad.append( pad_char );
821 public final static Color obtainColorDependingOnTaxonomyGroup( final String tax_group ) {
822 if ( !ForesterUtil.isEmpty( tax_group ) ) {
823 if ( tax_group.equals( TaxonomyGroups.DEUTEROSTOMIA ) ) {
824 return TaxonomyColors.DEUTEROSTOMIA_COLOR;
826 else if ( tax_group.equals( TaxonomyGroups.PROTOSTOMIA ) ) {
827 return TaxonomyColors.PROTOSTOMIA_COLOR;
829 else if ( tax_group.equals( TaxonomyGroups.CNIDARIA ) ) {
830 return TaxonomyColors.CNIDARIA_COLOR;
832 else if ( tax_group.equals( TaxonomyGroups.PLACOZOA ) ) {
833 return TaxonomyColors.PLACOZOA_COLOR;
835 else if ( tax_group.equals( TaxonomyGroups.CTENOPHORA ) ) {
836 return TaxonomyColors.CTENOPHORA_COLOR;
838 else if ( tax_group.equals( TaxonomyGroups.PORIFERA ) ) {
839 return TaxonomyColors.PORIFERA_COLOR;
841 else if ( tax_group.equals( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
842 return TaxonomyColors.CHOANOFLAGELLIDA;
844 else if ( tax_group.equals( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA ) ) {
845 return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
847 else if ( tax_group.equals( TaxonomyGroups.DIKARYA ) ) {
848 return TaxonomyColors.DIKARYA_COLOR;
850 else if ( tax_group.equalsIgnoreCase( TaxonomyGroups.FUNGI )
851 || tax_group.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
852 return TaxonomyColors.OTHER_FUNGI_COLOR;
854 else if ( tax_group.equals( TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP ) ) {
855 return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR;
857 else if ( tax_group.equals( TaxonomyGroups.AMOEBOZOA ) ) {
858 return TaxonomyColors.AMOEBOZOA_COLOR;
860 else if ( tax_group.equals( TaxonomyGroups.EMBRYOPHYTA ) ) {
861 return TaxonomyColors.EMBRYOPHYTA_COLOR;
863 else if ( tax_group.equals( TaxonomyGroups.CHLOROPHYTA ) ) {
864 return TaxonomyColors.CHLOROPHYTA_COLOR;
866 else if ( tax_group.equals( TaxonomyGroups.RHODOPHYTA ) ) {
867 return TaxonomyColors.RHODOPHYTA_COLOR;
869 else if ( tax_group.equals( TaxonomyGroups.HACROBIA ) ) {
870 return TaxonomyColors.HACROBIA_COLOR;
872 else if ( tax_group.equals( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) ) {
873 return TaxonomyColors.GLAUCOPHYTA_COLOR;
875 else if ( tax_group.equals( TaxonomyGroups.STRAMENOPILES ) ) {
876 return TaxonomyColors.STRAMENOPILES_COLOR;
878 else if ( tax_group.equals( TaxonomyGroups.ALVEOLATA ) ) {
879 return TaxonomyColors.ALVEOLATA_COLOR;
881 else if ( tax_group.equals( TaxonomyGroups.RHIZARIA ) ) {
882 return TaxonomyColors.RHIZARIA_COLOR;
884 else if ( tax_group.equals( TaxonomyGroups.EXCAVATA ) ) {
885 return TaxonomyColors.EXCAVATA_COLOR;
887 else if ( tax_group.equals( TaxonomyGroups.APUSOZOA ) ) {
888 return TaxonomyColors.APUSOZOA_COLOR;
890 else if ( tax_group.equals( TaxonomyGroups.ARCHAEA ) ) {
891 return TaxonomyColors.ARCHAEA_COLOR;
893 else if ( tax_group.equals( TaxonomyGroups.BACTERIA ) ) {
894 return TaxonomyColors.BACTERIA_COLOR;
896 else if ( tax_group.equals( TaxonomyGroups.VIRUSES ) ) {
897 return TaxonomyColors.VIRUSES_COLOR;
899 else if ( tax_group.equals( TaxonomyGroups.ALPHAHERPESVIRINAE ) ) {
900 return TaxonomyColors.ALPHAHERPESVIRINAE_COLOR;
902 else if ( tax_group.equals( TaxonomyGroups.BETAHERPESVIRINAE ) ) {
903 return TaxonomyColors.BETAHERPESVIRINAE_COLOR;
905 else if ( tax_group.equals( TaxonomyGroups.GAMMAHERPESVIRINAE ) ) {
906 return TaxonomyColors.GAMMAHERPESVIRINAE_COLOR;
908 else if ( tax_group.equals( TaxonomyGroups.OTHER ) ) {
909 return TaxonomyColors.OTHER_COLOR;
915 public final static String obtainNormalizedTaxonomyGroup( final String tax ) {
916 if ( tax.equalsIgnoreCase( TaxonomyGroups.DEUTEROSTOMIA ) ) {
917 return TaxonomyGroups.DEUTEROSTOMIA;
919 else if ( tax.equalsIgnoreCase( TaxonomyGroups.PROTOSTOMIA ) ) {
920 return TaxonomyGroups.PROTOSTOMIA;
922 else if ( tax.equalsIgnoreCase( TaxonomyGroups.CNIDARIA ) ) {
923 return TaxonomyGroups.CNIDARIA;
925 else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( TaxonomyGroups.PLACOZOA ) ) {
926 return TaxonomyGroups.PLACOZOA;
928 else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( TaxonomyGroups.CTENOPHORA ) ) {
929 return TaxonomyGroups.CTENOPHORA;
931 else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( TaxonomyGroups.PORIFERA ) ) {
932 return TaxonomyGroups.PORIFERA;
934 else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
935 return TaxonomyGroups.CHOANOFLAGELLIDA;
937 else if ( tax.toLowerCase().startsWith( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA )
938 || tax.toLowerCase().startsWith( "ichthyophonida and filasterea" )
939 || tax.toLowerCase().startsWith( "ichthyosporea & filasterea" )
940 || tax.toLowerCase().startsWith( "ichthyosporea and filasterea" ) ) {
941 return TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA;
943 else if ( tax.equalsIgnoreCase( TaxonomyGroups.DIKARYA ) ) {
944 return TaxonomyGroups.DIKARYA;
946 else if ( tax.equalsIgnoreCase( TaxonomyGroups.FUNGI ) || tax.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
947 return TaxonomyGroups.OTHER_FUNGI;
949 else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) {
950 return TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP;
952 else if ( tax.equalsIgnoreCase( TaxonomyGroups.AMOEBOZOA ) ) {
953 return TaxonomyGroups.AMOEBOZOA;
955 else if ( tax.equalsIgnoreCase( TaxonomyGroups.EMBRYOPHYTA ) ) {
956 return TaxonomyGroups.EMBRYOPHYTA;
958 else if ( tax.equalsIgnoreCase( TaxonomyGroups.CHLOROPHYTA ) ) {
959 return TaxonomyGroups.CHLOROPHYTA;
961 else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHODOPHYTA ) ) {
962 return TaxonomyGroups.RHODOPHYTA;
964 else if ( tax.toLowerCase().startsWith( TaxonomyGroups.HACROBIA ) ) {
965 return TaxonomyGroups.HACROBIA;
967 else if ( tax.equalsIgnoreCase( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
968 return TaxonomyGroups.GLAUCOCYSTOPHYCEAE;
970 else if ( tax.equalsIgnoreCase( TaxonomyGroups.STRAMENOPILES ) ) {
971 return TaxonomyGroups.STRAMENOPILES;
973 else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALVEOLATA ) ) {
974 return TaxonomyGroups.ALVEOLATA;
976 else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHIZARIA ) ) {
977 return TaxonomyGroups.RHIZARIA;
979 else if ( tax.equalsIgnoreCase( TaxonomyGroups.EXCAVATA ) ) {
980 return TaxonomyGroups.EXCAVATA;
982 else if ( tax.equalsIgnoreCase( TaxonomyGroups.APUSOZOA ) ) {
983 return TaxonomyGroups.APUSOZOA;
985 else if ( tax.equalsIgnoreCase( TaxonomyGroups.ARCHAEA ) ) {
986 return TaxonomyGroups.ARCHAEA;
988 else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) {
989 return TaxonomyGroups.BACTERIA;
991 else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) {
992 return TaxonomyGroups.BACTERIA;
994 else if ( tax.equalsIgnoreCase( TaxonomyGroups.VIRUSES ) ) {
995 return TaxonomyGroups.VIRUSES;
997 else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALPHAHERPESVIRINAE ) ) {
998 return TaxonomyGroups.ALPHAHERPESVIRINAE;
1000 else if ( tax.equalsIgnoreCase( TaxonomyGroups.BETAHERPESVIRINAE ) ) {
1001 return TaxonomyGroups.BETAHERPESVIRINAE;
1003 else if ( tax.equalsIgnoreCase( TaxonomyGroups.GAMMAHERPESVIRINAE ) ) {
1004 return TaxonomyGroups.GAMMAHERPESVIRINAE;
1009 final public static BufferedReader obtainReader( final Object source ) throws IOException, FileNotFoundException {
1010 BufferedReader reader = null;
1011 if ( source instanceof File ) {
1012 final File f = ( File ) source;
1013 if ( !f.exists() ) {
1014 throw new IOException( "\"" + f.getAbsolutePath() + "\" does not exist" );
1016 else if ( !f.isFile() ) {
1017 throw new IOException( "\"" + f.getAbsolutePath() + "\" is not a file" );
1019 else if ( !f.canRead() ) {
1020 throw new IOException( "\"" + f.getAbsolutePath() + "\" is not a readable" );
1022 reader = new BufferedReader( new FileReader( f ) );
1024 else if ( source instanceof InputStream ) {
1025 reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) );
1027 else if ( source instanceof String ) {
1028 reader = new BufferedReader( new StringReader( ( String ) source ) );
1030 else if ( source instanceof StringBuffer ) {
1031 reader = new BufferedReader( new StringReader( source.toString() ) );
1034 throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass()
1035 + "] (can only parse objects of type File, InputStream, String, or StringBuffer)" );
1040 public final static void outOfMemoryError( final OutOfMemoryError e ) {
1041 System.err.println();
1042 System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
1043 System.err.println();
1044 e.printStackTrace( System.err );
1045 System.err.println();
1049 final public static StringBuffer pad( final double number,
1052 final boolean left_pad ) {
1053 return pad( new StringBuffer( number + "" ), size, pad, left_pad );
1056 final public static StringBuffer pad( final String string,
1059 final boolean left_pad ) {
1060 return pad( new StringBuffer( string ), size, pad, left_pad );
1063 final public static StringBuffer pad( final StringBuffer string,
1066 final boolean left_pad ) {
1067 final StringBuffer padding = new StringBuffer();
1068 final int s = size - string.length();
1070 return new StringBuffer( string.substring( 0, size ) );
1072 for( int i = 0; i < s; ++i ) {
1073 padding.append( pad );
1076 return padding.append( string );
1079 return string.append( padding );
1083 final public static double parseDouble( final String str ) throws ParseException {
1084 if ( ForesterUtil.isEmpty( str ) ) {
1087 return Double.parseDouble( str );
1090 final public static int parseInt( final String str ) throws ParseException {
1091 if ( ForesterUtil.isEmpty( str ) ) {
1094 return Integer.parseInt( str );
1097 final public static void printArray( final Object[] a ) {
1098 for( int i = 0; i < a.length; ++i ) {
1099 System.out.println( "[" + i + "]=" + a[ i ] );
1103 final public static void printCountingMap( final Map<String, Integer> counting_map ) {
1104 for( final String key : counting_map.keySet() ) {
1105 System.out.println( key + ": " + counting_map.get( key ) );
1109 final public static void printErrorMessage( final String prg_name, final String message ) {
1110 System.err.println( "[" + prg_name + "] > error: " + message );
1113 final public static void printProgramInformation( final String prg_name,
1114 final String prg_version,
1115 final String date ) {
1116 final int l = prg_name.length() + prg_version.length() + date.length() + 4;
1117 System.out.println();
1118 System.out.println( prg_name + " " + prg_version + " (" + date + ")" );
1119 for( int i = 0; i < l; ++i ) {
1120 System.out.print( "_" );
1122 System.out.println();
1125 final public static void printProgramInformation( final String prg_name,
1126 final String prg_version,
1129 final String www ) {
1130 printProgramInformation( prg_name, null, prg_version, date, email, www, null );
1133 final public static void printProgramInformation( final String prg_name,
1135 final String prg_version,
1139 final String based_on ) {
1140 String my_prg_name = new String( prg_name );
1141 if ( !ForesterUtil.isEmpty( desc ) ) {
1142 my_prg_name += ( " - " + desc );
1144 final int l = my_prg_name.length() + prg_version.length() + date.length() + 4;
1145 System.out.println();
1146 System.out.println( my_prg_name + " " + prg_version + " (" + date + ")" );
1147 for( int i = 0; i < l; ++i ) {
1148 System.out.print( "_" );
1150 System.out.println();
1151 System.out.println();
1152 System.out.println( "WWW : " + www );
1153 System.out.println( "Contact : " + email );
1154 if ( !ForesterUtil.isEmpty( based_on ) ) {
1155 System.out.println( "Based on: " + based_on );
1157 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
1158 System.out.println();
1160 .println( "[running on Java " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
1162 System.out.println();
1165 final public static void printWarningMessage( final String prg_name, final String message ) {
1166 System.out.println( "[" + prg_name + "] > warning: " + message );
1169 final public static void programMessage( final String prg_name, final String message ) {
1170 System.out.println( "[" + prg_name + "] > " + message );
1173 public static List<String> readUrl( final String url_str ) throws IOException {
1174 final URL url = new URL( url_str );
1175 final URLConnection urlc = url.openConnection();
1176 //urlc.setRequestProperty( "User-Agent", "" );
1177 final BufferedReader in = new BufferedReader( new InputStreamReader( urlc.getInputStream() ) );
1179 final List<String> result = new ArrayList<String>();
1180 while ( ( line = in.readLine() ) != null ) {
1189 * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1190 * domain with 0.3 is ignored
1192 * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1195 * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1198 * @param max_allowed_overlap
1199 * maximal allowed overlap (inclusive) to be still considered not
1200 * overlapping (zero or negative value to allow any overlap)
1201 * @param remove_engulfed_domains
1202 * to remove domains which are completely engulfed by coverage of
1203 * domains with better support
1207 public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1208 final boolean remove_engulfed_domains,
1209 final Protein protein ) {
1210 final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(),
1211 protein.getSpecies().getSpeciesId(),
1212 protein.getLength() );
1213 final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1214 final List<Boolean> covered_positions = new ArrayList<Boolean>();
1215 for( final Domain domain : sorted ) {
1216 if ( ( ( max_allowed_overlap < 0 )
1217 || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1218 && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1219 final int covered_positions_size = covered_positions.size();
1220 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1221 covered_positions.add( false );
1223 final int new_covered_positions_size = covered_positions.size();
1224 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1225 if ( i < new_covered_positions_size ) {
1226 covered_positions.set( i, true );
1229 covered_positions.add( true );
1232 pruned_protein.addProteinDomain( domain );
1235 return pruned_protein;
1238 final public static String removeSuffix( final String file_name ) {
1239 final int i = file_name.lastIndexOf( '.' );
1241 return file_name.substring( 0, i );
1247 * Removes all white space from String s.
1249 * @return String s with white space removed
1251 final public static String removeWhiteSpace( String s ) {
1253 for( i = 0; i <= ( s.length() - 1 ); i++ ) {
1254 if ( ( s.charAt( i ) == ' ' ) || ( s.charAt( i ) == '\t' ) || ( s.charAt( i ) == '\n' )
1255 || ( s.charAt( i ) == '\r' ) ) {
1256 s = s.substring( 0, i ) + s.substring( i + 1 );
1263 final public static String replaceIllegalNhxCharacters( final String nhx ) {
1264 if ( nhx == null ) {
1267 return nhx.trim().replaceAll( "[\\[\\]']+", "_" );
1270 final public static double round( final double value, final int decimal_place ) {
1271 BigDecimal bd = new BigDecimal( value );
1272 bd = bd.setScale( decimal_place, BigDecimal.ROUND_HALF_UP );
1273 return bd.doubleValue();
1277 * Rounds d to an int.
1279 final public static int roundToInt( final double d ) {
1280 return ( int ) ( d + 0.5 );
1283 final public static int roundToInt( final float f ) {
1284 return ( int ) ( f + 0.5f );
1287 final public static short roundToShort( final double d ) {
1288 return ( short ) ( d + 0.5 );
1291 final public static String sanitizeString( final String s ) {
1300 public final static StringBuilder santitizeStringForNH( String data ) {
1301 data = data.replaceAll( "\\s+", " " ).trim();
1302 final StringBuilder sb = new StringBuilder();
1303 if ( data.length() > 0 ) {
1304 final boolean single_pars = data.indexOf( '\'' ) > -1;
1305 final boolean double_pars = data.indexOf( '"' ) > -1;
1306 if ( single_pars && double_pars ) {
1307 data = data.replace( '\'', '`' );
1312 else if ( single_pars ) {
1317 else if ( PARANTHESESABLE_NH_CHARS_PATTERN.matcher( data ).find() ) {
1329 public static boolean seqIsLikelyToBeAa( final String s ) {
1330 final String seq = s.toLowerCase();
1331 if ( ( seq.indexOf( 'r' ) > -1 ) || ( seq.indexOf( 'd' ) > -1 ) || ( seq.indexOf( 'e' ) > -1 )
1332 || ( seq.indexOf( 'q' ) > -1 ) || ( seq.indexOf( 'h' ) > -1 ) || ( seq.indexOf( 'k' ) > -1 )
1333 || ( seq.indexOf( 'w' ) > -1 ) || ( seq.indexOf( 's' ) > -1 ) || ( seq.indexOf( 'm' ) > -1 )
1334 || ( seq.indexOf( 'p' ) > -1 ) || ( seq.indexOf( 'v' ) > -1 ) ) {
1340 final private static String[] splitString( final String str ) {
1341 final String regex = "[\\s;,]+";
1342 return str.split( regex );
1345 final public static String stringArrayToString( final String[] a ) {
1346 return stringArrayToString( a, ", " );
1349 final public static String stringArrayToString( final String[] a, final String separator ) {
1350 final StringBuilder sb = new StringBuilder();
1351 if ( ( a != null ) && ( a.length > 0 ) ) {
1352 for( int i = 0; i < ( a.length - 1 ); ++i ) {
1353 sb.append( a[ i ] + separator );
1355 sb.append( a[ a.length - 1 ] );
1357 return sb.toString();
1360 final public static String[] stringListToArray( final List<String> list ) {
1361 if ( list != null ) {
1362 final String[] str = new String[ list.size() ];
1364 for( final String l : list ) {
1372 final public static String stringListToString( final List<String> l, final String separator ) {
1373 final StringBuilder sb = new StringBuilder();
1374 if ( ( l != null ) && ( l.size() > 0 ) ) {
1375 for( int i = 0; i < ( l.size() - 1 ); ++i ) {
1376 sb.append( l.get( i ) + separator );
1378 sb.append( l.get( l.size() - 1 ) );
1380 return sb.toString();
1383 final public static String[] stringSetToArray( final Set<String> strings ) {
1384 final String[] str_array = new String[ strings.size() ];
1386 for( final String e : strings ) {
1387 str_array[ i++ ] = e;
1392 final public static void unexpectedFatalError( final Error e ) {
1393 System.err.println();
1394 System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
1395 e.printStackTrace( System.err );
1396 System.err.println();
1400 final public static void unexpectedFatalError( final Exception e ) {
1401 System.err.println();
1402 System.err.println( "unexpected exception: should not have occured! Please contact program author(s)." );
1403 e.printStackTrace( System.err );
1404 System.err.println();
1408 final public static void unexpectedFatalError( final String message ) {
1409 System.err.println();
1410 System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
1411 System.err.println( message );
1412 System.err.println();
1416 final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
1417 System.err.println();
1418 System.err.println( "[" + prg_name
1419 + "] > unexpected error; should not have occured! Please contact program author(s)." );
1420 e.printStackTrace( System.err );
1421 System.err.println();
1425 final public static void unexpectedFatalError( final String prg_name, final String message ) {
1426 System.err.println();
1427 System.err.println( "[" + prg_name
1428 + "] > unexpected error: should not have occured! Please contact program author(s)." );
1429 System.err.println( message );
1430 System.err.println();
1434 final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) {
1435 System.err.println();
1436 System.err.println( "[" + prg_name
1437 + "] > unexpected error: should not have occured! Please contact program author(s)." );
1438 System.err.println( message );
1439 e.printStackTrace( System.err );
1440 System.err.println();
1444 public final static void updateProgress( final double progress_percentage ) {
1445 final int width = 50;
1446 System.out.print( "\r[" );
1448 for( ; i <= ForesterUtil.roundToInt( progress_percentage * width ); i++ ) {
1449 System.out.print( "." );
1451 for( ; i < width; i++ ) {
1452 System.out.print( " " );
1454 System.out.print( "]" );
1457 public final static void updateProgress( final int i, final DecimalFormat f ) {
1458 System.out.print( "\r[" + f.format( i ) + "]" );
1461 public final static String wordWrap( final String str, final int width ) {
1462 final StringBuilder sb = new StringBuilder( str );
1466 while ( i < sb.length() ) {
1467 if ( sb.charAt( i ) == ' ' ) {
1470 if ( sb.charAt( i ) == '\n' ) {
1474 if ( i > ( ( start + width ) - 1 ) ) {
1476 sb.setCharAt( ls, '\n' );
1481 sb.insert( i, '\n' );
1487 return sb.toString();
1490 public final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final PhylogenyParser parser )
1491 throws NoSuchAlgorithmException, IOException, KeyManagementException {
1492 if ( url == null ) {
1493 throw new IllegalArgumentException( "URL to read from must not be null" );
1495 else if ( parser == null ) {
1496 throw new IllegalArgumentException( "parser to use to read from URL must not be null" );
1498 final URLConnection con;
1499 if ( url.toString().startsWith( "https:" ) ) {
1500 con = TrustManager.makeHttpsURLConnection( url );
1502 else if ( url.toString().startsWith( "http:" ) ) {
1503 con = url.openConnection();
1506 throw new IllegalArgumentException( "Cannot deal with URL: " + url );
1508 if ( con == null ) {
1509 throw new IOException( "could not create connection from " + url );
1511 con.setDefaultUseCaches( false );
1512 final InputStream is = con.getInputStream();
1514 throw new IOException( "could not create input stream from " + url );
1516 final Phylogeny[] trees = ParserBasedPhylogenyFactory.getInstance().create( is, parser );
1520 catch ( final Exception e ) {
1526 public final static File getMatchingFile( final File dir, final String prefix, final String suffix )
1527 throws IOException {
1528 if ( !dir.exists() ) {
1529 throw new IOException( "[" + dir + "] does not exist" );
1531 if ( !dir.isDirectory() ) {
1532 throw new IOException( "[" + dir + "] is not a directory" );
1534 if ( dir.listFiles().length == 0 ) {
1535 throw new IOException( "[" + dir + "] is empty" );
1537 final File files[] = dir.listFiles( new FilenameFilter() {
1540 public boolean accept( final File dir, final String name ) {
1541 return ( name.endsWith( suffix ) );
1544 if ( files.length == 0 ) {
1545 throw new IOException( "no files ending with \"" + suffix + "\" found in [" + dir + "]" );
1547 String my_prefix = prefix;
1548 boolean done = false;
1549 boolean more_than_one = false;
1550 File the_one = null;
1553 for( final File file : files ) {
1554 if ( file.getName().startsWith( my_prefix ) ) {
1556 if ( matches > 1 ) {
1563 if ( matches > 1 ) {
1564 more_than_one = true;
1567 if ( matches == 1 ) {
1571 if ( my_prefix.length() <= 1 ) {
1572 throw new IOException( "no file matching \"" + removeFileExtension( prefix )
1573 + "\" and ending with \"" + suffix + "\" found in [" + dir + "]" );
1575 my_prefix = my_prefix.substring( 0, my_prefix.length() - 1 );
1578 if ( more_than_one ) {
1579 throw new IOException( "multiple files matching \"" + removeFileExtension( prefix )
1580 + "\" and ending with \"" + suffix + "\" found in [" + dir + "]" );
1582 else if ( the_one != null ) {
1585 throw new IOException( "no file matching \"" + removeFileExtension( prefix ) + "\" and ending with \""
1586 + suffix + "\" found in [" + dir + "]" );
1591 public final static String greatestCommonPrefix( final String a, final String b ) {
1592 final int min_length = Math.min( a.length(), b.length() );
1593 for( int i = 0; i < min_length; ++i ) {
1594 if ( a.charAt( i ) != b.charAt( i ) ) {
1595 return a.substring( 0, i );
1598 return a.substring( 0, min_length );
1601 public final static boolean isContainsPrefix( final String word, final String prefix, final String separator ) {
1602 if ( ForesterUtil.isEmpty( separator ) ) {
1603 throw new IllegalArgumentException( "separator must not be null or empty" );
1605 final String[] word_ary = word.split( Pattern.quote( separator ) );
1606 final String[] prefix_ary = prefix.split( Pattern.quote( separator ) );
1607 if ( word_ary.length < prefix_ary.length ) {
1610 final int prefix_ary_length = prefix_ary.length;
1611 for( int i = 0; i < prefix_ary_length; ++i ) {
1612 if ( !( word_ary[ i ].equals( prefix_ary[ i ] ) ) ) {
1619 public final static String greatestCommonPrefix( final String a, final String b, final String separator ) {
1620 if ( ForesterUtil.isEmpty( separator ) ) {
1621 throw new IllegalArgumentException( "separator must not be null or empty" );
1623 final String[] as = a.split( Pattern.quote( separator ) );
1624 final String[] bs = b.split( Pattern.quote( separator ) );
1625 final int min_length = Math.min( as.length, bs.length );
1626 for( int i = 0; i < min_length; ++i ) {
1627 if ( !( as[ i ].equals( bs[ i ] ) ) ) {
1628 final StringBuilder sb = new StringBuilder();
1629 boolean first = true;
1630 for( int j = 0; j < i; ++j ) {
1635 sb.append( separator );
1637 sb.append( as[ j ] );
1639 return sb.toString();
1642 final StringBuilder sb = new StringBuilder();
1643 boolean first = true;
1644 for( int j = 0; j < min_length; ++j ) {
1649 sb.append( separator );
1651 sb.append( as[ j ] );
1653 return sb.toString();
1656 public final static String greatestCommonPrefix( final List<String> strings ) {
1657 if ( strings == null ) {
1658 throw new IllegalArgumentException( "list of strings is null" );
1660 if ( strings.isEmpty() ) {
1661 throw new IllegalArgumentException( "list of strings is empty" );
1663 String common = strings.get( 0 );
1664 for( int i = 1; i < strings.size(); ++i ) {
1665 common = greatestCommonPrefix( common, strings.get( i ) );
1670 public final static String greatestCommonPrefix( final List<String> strings, final String separator ) {
1671 if ( ForesterUtil.isEmpty( separator ) ) {
1672 return greatestCommonPrefix( strings );
1674 if ( strings == null ) {
1675 throw new IllegalArgumentException( "list of strings is null" );
1677 if ( strings.isEmpty() ) {
1678 throw new IllegalArgumentException( "list of strings is empty" );
1680 String common = strings.get( 0 );
1681 for( int i = 1; i < strings.size(); ++i ) {
1682 common = greatestCommonPrefix( common, strings.get( i ), separator );
1687 public static List<String> spliIntoPrefixes( final String prefix, final String separator ) {
1688 final String[] a = prefix.split( Pattern.quote( separator ) );
1689 final List<String> l = new ArrayList<String>();
1690 for( int i = 0; i < a.length; ++i ) {
1691 final StringBuilder sb = new StringBuilder();
1692 for( int j = 0; j <= i; ++j ) {
1693 sb.append( a[ j ] );
1695 sb.append( separator );
1698 l.add( sb.toString() );
1703 public static boolean isLooksLikeFasta( final File file ) throws IOException {
1704 final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
1705 return ( ( !isEmptyTrimmed( first_line ) && first_line.trim().startsWith( ">" ) ) );
1708 private ForesterUtil() {