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.IOException;
38 import java.io.InputStream;
39 import java.io.InputStreamReader;
40 import java.io.StringReader;
41 import java.io.Writer;
42 import java.math.BigDecimal;
44 import java.text.DateFormat;
45 import java.text.DecimalFormat;
46 import java.text.DecimalFormatSymbols;
47 import java.text.NumberFormat;
48 import java.text.ParseException;
49 import java.text.SimpleDateFormat;
50 import java.util.ArrayList;
51 import java.util.Collection;
52 import java.util.Date;
53 import java.util.Iterator;
54 import java.util.List;
56 import java.util.Map.Entry;
58 import java.util.SortedMap;
59 import java.util.SortedSet;
60 import java.util.TreeMap;
61 import java.util.TreeSet;
62 import java.util.regex.Pattern;
64 import org.forester.phylogeny.PhylogenyNode;
65 import org.forester.phylogeny.data.Distribution;
66 import org.forester.phylogeny.data.Sequence;
67 import org.forester.phylogeny.data.Taxonomy;
69 public final class ForesterUtil {
71 public final static String FILE_SEPARATOR = System.getProperty( "file.separator" );
72 public final static String LINE_SEPARATOR = System.getProperty( "line.separator" );
73 public final static String JAVA_VENDOR = System.getProperty( "java.vendor" );
74 public final static String JAVA_VERSION = System.getProperty( "java.version" );
75 public final static String OS_ARCH = System.getProperty( "os.arch" );
76 public final static String OS_NAME = System.getProperty( "os.name" );
77 public final static String OS_VERSION = System.getProperty( "os.version" );
78 public final static Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s]" );
79 public final static double ZERO_DIFF = 1.0E-9;
80 public static final BigDecimal NULL_BD = new BigDecimal( 0 );
81 public static final NumberFormat FORMATTER_9;
82 public static final NumberFormat FORMATTER_6;
83 public static final NumberFormat FORMATTER_06;
84 public static final NumberFormat FORMATTER_3;
86 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
87 dfs.setDecimalSeparator( '.' );
88 // dfs.setGroupingSeparator( ( char ) 0 );
89 FORMATTER_9 = new DecimalFormat( "#.#########", dfs );
90 FORMATTER_6 = new DecimalFormat( "#.######", dfs );
91 FORMATTER_06 = new DecimalFormat( "0.######", dfs );
92 FORMATTER_3 = new DecimalFormat( "#.###", dfs );
95 private ForesterUtil() {
98 final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
99 if ( sb.length() > 0 ) {
100 sb.append( separator );
105 * This calculates a color. If value is equal to min the returned color is
106 * minColor, if value is equal to max the returned color is maxColor,
107 * otherwise a color 'proportional' to value is returned.
121 final public static Color calcColor( double value,
124 final Color minColor,
125 final Color maxColor ) {
132 final double x = ForesterUtil.calculateColorFactor( value, max, min );
133 final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), maxColor.getRed(), x );
134 final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), maxColor.getGreen(), x );
135 final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), maxColor.getBlue(), x );
136 return new Color( red, green, blue );
140 * This calculates a color. If value is equal to min the returned color is
141 * minColor, if value is equal to max the returned color is maxColor, if
142 * value is equal to mean the returned color is meanColor, otherwise a color
143 * 'proportional' to value is returned -- either between min-mean or
153 * the mean/median value
162 final public static Color calcColor( double value,
166 final Color minColor,
167 final Color maxColor,
168 final Color meanColor ) {
175 if ( value < mean ) {
176 final double x = ForesterUtil.calculateColorFactor( value, mean, min );
177 final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), meanColor.getRed(), x );
178 final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), meanColor.getGreen(), x );
179 final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), meanColor.getBlue(), x );
180 return new Color( red, green, blue );
182 else if ( value > mean ) {
183 final double x = ForesterUtil.calculateColorFactor( value, max, mean );
184 final int red = ForesterUtil.calculateColorComponent( meanColor.getRed(), maxColor.getRed(), x );
185 final int green = ForesterUtil.calculateColorComponent( meanColor.getGreen(), maxColor.getGreen(), x );
186 final int blue = ForesterUtil.calculateColorComponent( meanColor.getBlue(), maxColor.getBlue(), x );
187 return new Color( red, green, blue );
194 final public static String collapseWhiteSpace( final String s ) {
195 return s.replaceAll( "[\\s]+", " " );
198 final public static void collection2file( final File file, final Collection<?> data, final String separator )
200 final Writer writer = new BufferedWriter( new FileWriter( file ) );
201 collection2writer( writer, data, separator );
205 final public static void collection2writer( final Writer writer, final Collection<?> data, final String separator )
207 boolean first = true;
208 for( final Object object : data ) {
210 writer.write( separator );
215 writer.write( object.toString() );
219 final public static String colorToHex( final Color color ) {
220 final String rgb = Integer.toHexString( color.getRGB() );
221 return rgb.substring( 2, rgb.length() );
224 synchronized public static void copyFile( final File in, final File out ) throws IOException {
225 final FileInputStream in_s = new FileInputStream( in );
226 final FileOutputStream out_s = new FileOutputStream( out );
228 final byte[] buf = new byte[ 1024 ];
230 while ( ( i = in_s.read( buf ) ) != -1 ) {
231 out_s.write( buf, 0, i );
234 catch ( final IOException e ) {
238 if ( in_s != null ) {
241 if ( out_s != null ) {
247 final public static int countChars( final String str, final char c ) {
249 for( int i = 0; i < str.length(); ++i ) {
250 if ( str.charAt( i ) == c ) {
257 final public static BufferedWriter createBufferedWriter( final File file ) throws IOException {
258 if ( file.exists() ) {
259 throw new IOException( "[" + file + "] already exists" );
261 return new BufferedWriter( new FileWriter( file ) );
264 final public static BufferedWriter createBufferedWriter( final String name ) throws IOException {
265 return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) );
268 final public static EasyWriter createEasyWriter( final File file ) throws IOException {
269 return new EasyWriter( createBufferedWriter( file ) );
272 final public static BufferedWriter createEasyWriter( final String name ) throws IOException {
273 return createEasyWriter( createFileForWriting( name ) );
276 final public static File createFileForWriting( final String name ) throws IOException {
277 final File file = new File( name );
278 if ( file.exists() ) {
279 throw new IOException( "[" + name + "] already exists" );
284 final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
285 if ( !node.getNodeData().isHasDate() ) {
286 node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
290 final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
291 if ( !node.getNodeData().isHasDistribution() ) {
292 node.getNodeData().setDistribution( new Distribution( "" ) );
296 public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
297 if ( !node.getNodeData().isHasSequence() ) {
298 node.getNodeData().setSequence( new Sequence() );
302 public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
303 if ( !node.getNodeData().isHasTaxonomy() ) {
304 node.getNodeData().setTaxonomy( new Taxonomy() );
308 public static void fatalError( final String message ) {
309 System.err.println();
310 System.err.println( "error: " + message );
311 System.err.println();
315 public static void fatalError( final String prg_name, final String message ) {
316 System.err.println();
317 System.err.println( "[" + prg_name + "] > " + message );
318 System.err.println();
322 public static void fatalErrorIfFileNotReadable( final File file ) {
323 final String error = isReadableFile( file );
324 if ( !isEmpty( error ) ) {
325 System.err.println();
326 System.err.println( "error: " + error );
327 System.err.println();
332 public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) {
333 final String error = isReadableFile( file );
334 if ( !isEmpty( error ) ) {
335 System.err.println();
336 System.err.println( "[" + prg_name + "] > " + error );
337 System.err.println();
342 public static String[] file2array( final File file ) throws IOException {
343 final List<String> list = file2list( file );
344 final String[] ary = new String[ list.size() ];
346 for( final String s : list ) {
352 final public static List<String> file2list( final File file ) throws IOException {
353 final List<String> list = new ArrayList<String>();
354 final BufferedReader in = new BufferedReader( new FileReader( file ) );
356 while ( ( str = in.readLine() ) != null ) {
358 if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
359 for( final String s : splitString( str ) ) {
368 final public static SortedSet<String> file2set( final File file ) throws IOException {
369 final SortedSet<String> set = new TreeSet<String>();
370 final BufferedReader in = new BufferedReader( new FileReader( file ) );
372 while ( ( str = in.readLine() ) != null ) {
374 if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
375 for( final String s : splitString( str ) ) {
384 final public static String getCurrentDateTime() {
385 final DateFormat format = new SimpleDateFormat( "yyyy/MM/dd HH:mm:ss" );
386 return format.format( new Date() );
389 final public static String getFileSeparator() {
390 return ForesterUtil.FILE_SEPARATOR;
393 final public static String getFirstLine( final Object source ) throws FileNotFoundException, IOException {
394 BufferedReader reader = null;
395 if ( source instanceof File ) {
396 final File f = ( File ) source;
398 throw new IOException( "[" + f.getAbsolutePath() + "] does not exist" );
400 else if ( !f.isFile() ) {
401 throw new IOException( "[" + f.getAbsolutePath() + "] is not a file" );
403 else if ( !f.canRead() ) {
404 throw new IOException( "[" + f.getAbsolutePath() + "] is not a readable" );
406 reader = new BufferedReader( new FileReader( f ) );
408 else if ( source instanceof InputStream ) {
409 reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) );
411 else if ( source instanceof String ) {
412 reader = new BufferedReader( new StringReader( ( String ) source ) );
414 else if ( source instanceof StringBuffer ) {
415 reader = new BufferedReader( new StringReader( source.toString() ) );
417 else if ( source instanceof URL ) {
418 reader = new BufferedReader( new InputStreamReader( ( ( URL ) source ).openStream() ) );
421 throw new IllegalArgumentException( "dont know how to read [" + source.getClass() + "]" );
424 while ( ( line = reader.readLine() ) != null ) {
426 if ( !ForesterUtil.isEmpty( line ) ) {
427 if ( reader != null ) {
433 if ( reader != null ) {
439 final public static String getForesterLibraryInformation() {
440 return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")";
443 final public static String getLineSeparator() {
444 return ForesterUtil.LINE_SEPARATOR;
447 final public static void increaseCountingMap( final Map<String, Integer> counting_map, final String item_name ) {
448 if ( !counting_map.containsKey( item_name ) ) {
449 counting_map.put( item_name, 1 );
452 counting_map.put( item_name, counting_map.get( item_name ) + 1 );
456 final public static boolean isContainsParanthesesableNhCharacter( final String nh ) {
457 return PARANTHESESABLE_NH_CHARS_PATTERN.matcher( nh ).find();
460 final public static boolean isEmpty( final List<?> l ) {
461 if ( ( l == null ) || l.isEmpty() ) {
464 for( final Object o : l ) {
472 final public static boolean isEmpty( final Set<?> s ) {
473 if ( ( s == null ) || s.isEmpty() ) {
476 for( final Object o : s ) {
484 final public static boolean isEmpty( final String s ) {
485 return ( ( s == null ) || ( s.length() < 1 ) );
488 final public static boolean isEqual( final double a, final double b ) {
489 return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
492 final public static boolean isEven( final int n ) {
493 return ( n % 2 ) == 0;
497 * This determines whether String[] a and String[] b have at least one
498 * String in common (intersect). Returns false if at least one String[] is
502 * a String[] b a String[]
503 * @return true if both a and b or not empty or null and contain at least
504 * one element in common false otherwise
506 final public static boolean isIntersecting( final String[] a, final String[] b ) {
507 if ( ( a == null ) || ( b == null ) ) {
510 if ( ( a.length < 1 ) || ( b.length < 1 ) ) {
513 for( final String ai : a ) {
514 for( final String element : b ) {
515 if ( ( ai != null ) && ( element != null ) && ai.equals( element ) ) {
523 final public static double isLargerOrEqualToZero( final double d ) {
532 final public static boolean isNull( final BigDecimal s ) {
533 return ( ( s == null ) || ( s.compareTo( NULL_BD ) == 0 ) );
536 final public static String isReadableFile( final File f ) {
538 return "file [" + f + "] does not exist";
540 if ( f.isDirectory() ) {
541 return "[" + f + "] is a directory";
544 return "[" + f + "] is not a file";
546 if ( !f.canRead() ) {
547 return "file [" + f + "] is not readable";
549 if ( f.length() < 1 ) {
550 return "file [" + f + "] is empty";
555 final public static String isReadableFile( final String s ) {
556 return isReadableFile( new File( s ) );
559 public static boolean isWindowns() {
560 return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1;
563 final public static String isWritableFile( final File f ) {
564 if ( f.isDirectory() ) {
565 return "[" + f + "] is a directory";
568 return "[" + f + "] already exists";
574 * Helper for method "stringToColor".
576 * (Last modified: 12/20/03)
578 final public static int limitRangeForColor( int i ) {
588 final public static SortedMap<Object, Integer> listToSortedCountsMap( final List list ) {
589 final SortedMap<Object, Integer> map = new TreeMap<Object, Integer>();
590 for( final Object key : list ) {
591 if ( !map.containsKey( key ) ) {
595 map.put( key, map.get( key ) + 1 );
601 final public static void map2file( final File file,
602 final Map<?, ?> data,
603 final String entry_separator,
604 final String data_separator ) throws IOException {
605 final Writer writer = new BufferedWriter( new FileWriter( file ) );
606 map2writer( writer, data, entry_separator, data_separator );
610 final public static void map2writer( final Writer writer,
611 final Map<?, ?> data,
612 final String entry_separator,
613 final String data_separator ) throws IOException {
614 boolean first = true;
615 for( final Entry<?, ?> entry : data.entrySet() ) {
617 writer.write( data_separator );
622 writer.write( entry.getKey().toString() );
623 writer.write( entry_separator );
624 writer.write( entry.getValue().toString() );
628 final public static StringBuffer mapToStringBuffer( final Map map, final String key_value_separator ) {
629 final StringBuffer sb = new StringBuffer();
630 for( final Iterator iter = map.keySet().iterator(); iter.hasNext(); ) {
631 final Object key = iter.next();
632 sb.append( key.toString() );
633 sb.append( key_value_separator );
634 sb.append( map.get( key ).toString() );
635 sb.append( ForesterUtil.getLineSeparator() );
640 final public static String normalizeString( final String s,
642 final boolean left_pad,
643 final char pad_char ) {
644 if ( s.length() > length ) {
645 return s.substring( 0, length );
648 final StringBuffer pad = new StringBuffer( length - s.length() );
649 for( int i = 0; i < ( length - s.length() ); ++i ) {
650 pad.append( pad_char );
661 final public static BufferedReader obtainReader( final Object source ) throws IOException, FileNotFoundException {
662 BufferedReader reader = null;
663 if ( source instanceof File ) {
664 final File f = ( File ) source;
666 throw new IOException( "\"" + f.getAbsolutePath() + "\" does not exist" );
668 else if ( !f.isFile() ) {
669 throw new IOException( "\"" + f.getAbsolutePath() + "\" is not a file" );
671 else if ( !f.canRead() ) {
672 throw new IOException( "\"" + f.getAbsolutePath() + "\" is not a readable" );
674 reader = new BufferedReader( new FileReader( f ) );
676 else if ( source instanceof InputStream ) {
677 reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) );
679 else if ( source instanceof String ) {
680 reader = new BufferedReader( new StringReader( ( String ) source ) );
682 else if ( source instanceof StringBuffer ) {
683 reader = new BufferedReader( new StringReader( source.toString() ) );
686 throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass()
687 + "] (can only parse objects of type File, InputStream, String, or StringBuffer)" );
692 final public static StringBuffer pad( final double number, final int size, final char pad, final boolean left_pad ) {
693 return pad( new StringBuffer( number + "" ), size, pad, left_pad );
696 final public static StringBuffer pad( final String string, final int size, final char pad, final boolean left_pad ) {
697 return pad( new StringBuffer( string ), size, pad, left_pad );
700 final public static StringBuffer pad( final StringBuffer string,
703 final boolean left_pad ) {
704 final StringBuffer padding = new StringBuffer();
705 final int s = size - string.length();
707 return new StringBuffer( string.substring( 0, size ) );
709 for( int i = 0; i < s; ++i ) {
710 padding.append( pad );
713 return padding.append( string );
716 return string.append( padding );
720 final public static double parseDouble( final String str ) throws ParseException {
721 if ( ForesterUtil.isEmpty( str ) ) {
724 return Double.parseDouble( str );
727 final public static int parseInt( final String str ) throws ParseException {
728 if ( ForesterUtil.isEmpty( str ) ) {
731 return Integer.parseInt( str );
734 final public static void printArray( final Object[] a ) {
735 for( int i = 0; i < a.length; ++i ) {
736 System.out.println( "[" + i + "]=" + a[ i ] );
740 final public static void printCountingMap( final Map<String, Integer> counting_map ) {
741 for( final String key : counting_map.keySet() ) {
742 System.out.println( key + ": " + counting_map.get( key ) );
746 final public static void printErrorMessage( final String prg_name, final String message ) {
747 System.err.println( "[" + prg_name + "] > error: " + message );
750 final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) {
751 final int l = prg_name.length() + prg_version.length() + date.length() + 4;
752 System.out.println();
753 System.out.println( prg_name + " " + prg_version + " (" + date + ")" );
754 for( int i = 0; i < l; ++i ) {
755 System.out.print( "_" );
757 System.out.println();
760 final public static void printProgramInformation( final String prg_name,
761 final String prg_version,
765 printProgramInformation( prg_name, null, prg_version, date, email, www, null );
768 final public static void printProgramInformation( final String prg_name,
770 final String prg_version,
774 final String based_on ) {
775 String my_prg_name = new String( prg_name );
776 if ( !ForesterUtil.isEmpty( desc ) ) {
777 my_prg_name += ( " - " + desc );
779 final int l = my_prg_name.length() + prg_version.length() + date.length() + 4;
780 System.out.println();
781 System.out.println( my_prg_name + " " + prg_version + " (" + date + ")" );
782 for( int i = 0; i < l; ++i ) {
783 System.out.print( "_" );
785 System.out.println();
786 System.out.println();
787 System.out.println( "WWW : " + www );
788 System.out.println( "Contact : " + email );
789 if ( !ForesterUtil.isEmpty( based_on ) ) {
790 System.out.println( "Based on: " + based_on );
792 if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
793 System.out.println();
794 System.out.println( "[running on Java " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
796 System.out.println();
799 final public static void printWarningMessage( final String prg_name, final String message ) {
800 System.out.println( "[" + prg_name + "] > warning: " + message );
803 final public static void programMessage( final String prg_name, final String message ) {
804 System.out.println( "[" + prg_name + "] > " + message );
807 final public static String removeSuffix( final String file_name ) {
808 final int i = file_name.lastIndexOf( '.' );
810 return file_name.substring( 0, i );
816 * Removes all white space from String s.
818 * @return String s with white space removed
820 final public static String removeWhiteSpace( String s ) {
822 for( i = 0; i <= ( s.length() - 1 ); i++ ) {
823 if ( ( s.charAt( i ) == ' ' ) || ( s.charAt( i ) == '\t' ) || ( s.charAt( i ) == '\n' )
824 || ( s.charAt( i ) == '\r' ) ) {
825 s = s.substring( 0, i ) + s.substring( i + 1 );
832 final public static String replaceIllegalNhCharacters( final String nh ) {
836 return nh.trim().replaceAll( "[\\[\\]:]+", "_" );
839 final public static String replaceIllegalNhxCharacters( final String nhx ) {
843 return nhx.trim().replaceAll( "[\\[\\](),:;\\s]+", "_" );
846 final public static double round( final double value, final int decimal_place ) {
847 BigDecimal bd = new BigDecimal( value );
848 bd = bd.setScale( decimal_place, BigDecimal.ROUND_HALF_UP );
849 return bd.doubleValue();
853 * Rounds d to an int.
855 final public static int roundToInt( final double d ) {
856 return ( int ) ( d + 0.5 );
859 final public static int roundToInt( final float f ) {
860 return ( int ) ( f + 0.5f );
863 final public static short roundToShort( final double d ) {
864 return ( short ) ( d + 0.5 );
867 final public static String sanitizeString( final String s ) {
876 public static boolean seqIsLikelyToBeAa( final String s ) {
877 final String seq = s.toLowerCase();
878 if ( ( seq.indexOf( 'r' ) > -1 ) || ( seq.indexOf( 'd' ) > -1 ) || ( seq.indexOf( 'e' ) > -1 )
879 || ( seq.indexOf( 'q' ) > -1 ) || ( seq.indexOf( 'h' ) > -1 ) || ( seq.indexOf( 'k' ) > -1 )
880 || ( seq.indexOf( 'w' ) > -1 ) || ( seq.indexOf( 's' ) > -1 ) || ( seq.indexOf( 'm' ) > -1 )
881 || ( seq.indexOf( 'p' ) > -1 ) || ( seq.indexOf( 'v' ) > -1 ) ) {
887 final public static String stringArrayToString( final String[] a ) {
888 return stringArrayToString( a, ", " );
891 final public static String stringArrayToString( final String[] a, final String separator ) {
892 final StringBuilder sb = new StringBuilder();
893 if ( ( a != null ) && ( a.length > 0 ) ) {
894 for( int i = 0; i < ( a.length - 1 ); ++i ) {
895 sb.append( a[ i ] + separator );
897 sb.append( a[ a.length - 1 ] );
899 return sb.toString();
902 final public static String[] stringListToArray( final List<String> list ) {
903 if ( list != null ) {
904 final String[] str = new String[ list.size() ];
906 for( final String l : list ) {
914 final public static String stringListToString( final List<String> l, final String separator ) {
915 final StringBuilder sb = new StringBuilder();
916 if ( ( l != null ) && ( l.size() > 0 ) ) {
917 for( int i = 0; i < ( l.size() - 1 ); ++i ) {
918 sb.append( l.get( i ) + separator );
920 sb.append( l.get( l.size() - 1 ) );
922 return sb.toString();
925 final public static String[] stringSetToArray( final Set<String> strings ) {
926 final String[] str_array = new String[ strings.size() ];
928 for( final String e : strings ) {
929 str_array[ i++ ] = e;
934 final public static void unexpectedFatalError( final Exception e ) {
935 System.err.println();
936 System.err.println( "unexpected exception: should not have occured! Please contact program author(s)." );
937 e.printStackTrace( System.err );
938 System.err.println();
942 final public static void unexpectedFatalError( final Error e ) {
943 System.err.println();
944 System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
945 e.printStackTrace( System.err );
946 System.err.println();
950 final public static void unexpectedFatalError( final String message ) {
951 System.err.println();
952 System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
953 System.err.println( message );
954 System.err.println();
958 final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
959 System.err.println();
960 System.err.println( "[" + prg_name
961 + "] > unexpected error; should not have occured! Please contact program author(s)." );
962 e.printStackTrace( System.err );
963 System.err.println();
967 final public static void unexpectedFatalError( final String prg_name, final String message ) {
968 System.err.println();
969 System.err.println( "[" + prg_name
970 + "] > unexpected error: should not have occured! Please contact program author(s)." );
971 System.err.println( message );
972 System.err.println();
976 final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) {
977 System.err.println();
978 System.err.println( "[" + prg_name
979 + "] > unexpected error: should not have occured! Please contact program author(s)." );
980 System.err.println( message );
981 e.printStackTrace( System.err );
982 System.err.println();
986 public final static void updateProgress( final double progress_percentage ) {
987 final int width = 50;
988 System.out.print( "\r[" );
990 for( ; i <= ForesterUtil.roundToInt( progress_percentage * width ); i++ ) {
991 System.out.print( "." );
993 for( ; i < width; i++ ) {
994 System.out.print( " " );
996 System.out.print( "]" );
999 public final static String wordWrap( final String str, final int width ) {
1000 final StringBuilder sb = new StringBuilder( str );
1004 while ( i < sb.length() ) {
1005 if ( sb.charAt( i ) == ' ' ) {
1008 if ( sb.charAt( i ) == '\n' ) {
1012 if ( i > ( ( start + width ) - 1 ) ) {
1014 sb.setCharAt( ls, '\n' );
1019 sb.insert( i, '\n' );
1025 return sb.toString();
1029 * Helper method for calcColor methods.
1031 * @param smallercolor_component_x
1032 * color component the smaller color
1033 * @param largercolor_component_x
1034 * color component the larger color
1037 * @return an int representing a color component
1039 final private static int calculateColorComponent( final double smallercolor_component_x,
1040 final double largercolor_component_x,
1042 return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) );
1046 * Helper method for calcColor methods.
1054 * the smallest value
1055 * @return a normalized value between larger and smaller
1057 final private static double calculateColorFactor( final double value, final double larger, final double smaller ) {
1058 return ( 255.0 * ( value - smaller ) ) / ( larger - smaller );
1061 final private static String[] splitString( final String str ) {
1062 final String regex = "[\\s;,]+";
1063 return str.split( regex );
1066 public final static void outOfMemoryError( final OutOfMemoryError e ) {
1067 System.err.println();
1068 System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
1069 System.err.println();
1070 e.printStackTrace( System.err );
1071 System.err.println();