X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterUtil.java;h=b3eb0f218612e582556885a34eb7a6765930bd1c;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=043df398316acaafb67058ef75e1dab17c596ec0;hpb=ebabb46561f996b5fcd59bd202defd7b189ea5b6;p=jalview.git diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index 043df39..b3eb0f2 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; @@ -41,6 +41,7 @@ import java.io.StringReader; import java.io.Writer; import java.math.BigDecimal; import java.net.URL; +import java.net.URLConnection; import java.text.DateFormat; import java.text.DecimalFormat; import java.text.DecimalFormatSymbols; @@ -50,7 +51,6 @@ import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Collection; import java.util.Date; -import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Map.Entry; @@ -59,29 +59,42 @@ 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.archaeopteryx.Constants; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Distribution; import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.Taxonomy; +import org.forester.protein.BasicProtein; +import org.forester.protein.Domain; +import org.forester.protein.Protein; +import org.forester.sequence.MolecularSequence; +import org.forester.sequence.MolecularSequence.TYPE; +import org.forester.surfacing.SurfacingUtil; public final class ForesterUtil { public final static String FILE_SEPARATOR = System.getProperty( "file.separator" ); - public final static String LINE_SEPARATOR = System.getProperty( "line.separator" ); + public static final NumberFormat FORMATTER_06; + public static final NumberFormat FORMATTER_3; + public static final NumberFormat FORMATTER_6; + public static final NumberFormat FORMATTER_9; public final static String JAVA_VENDOR = System.getProperty( "java.vendor" ); public final static String JAVA_VERSION = System.getProperty( "java.version" ); + public final static String LINE_SEPARATOR = System.getProperty( "line.separator" ); + public static final String NCBI_GI = "http://www.ncbi.nlm.nih.gov/protein/gi:"; + public static final String NCBI_NUCCORE = "http://www.ncbi.nlm.nih.gov/nuccore/"; + public static final String NCBI_PROTEIN = "http://www.ncbi.nlm.nih.gov/protein/"; + public static final BigDecimal NULL_BD = new BigDecimal( 0 ); public final static String OS_ARCH = System.getProperty( "os.arch" ); public final static String OS_NAME = System.getProperty( "os.name" ); public final static String OS_VERSION = System.getProperty( "os.version" ); - public final static Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s]" ); + public static final String PDB = "http://www.pdb.org/pdb/explore/explore.do?pdbId="; + public final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/"; public 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; + private static final Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s:\\[\\]]" ); static { final DecimalFormatSymbols dfs = new DecimalFormatSymbols(); dfs.setDecimalSeparator( '.' ); @@ -92,69 +105,23 @@ public final class ForesterUtil { FORMATTER_3 = new DecimalFormat( "#.###", dfs ); } - private ForesterUtil() { - } - - public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasTaxonomy() ) { - node.getNodeData().setTaxonomy( new Taxonomy() ); - } - } - - public static void ensurePresenceOfSequence( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasSequence() ) { - node.getNodeData().setSequence( new Sequence() ); - } - } - - final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDistribution() ) { - node.getNodeData().setDistribution( new Distribution( "" ) ); - } - } - - final public static void ensurePresenceOfDate( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDate() ) { - node.getNodeData().setDate( new org.forester.phylogeny.data.Date() ); - } - } - final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) { if ( sb.length() > 0 ) { sb.append( separator ); } } - public static boolean isWindowns() { - return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1; - } - - final public static String getForesterLibraryInformation() { - return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")"; - } - - public static boolean seqIsLikelyToBeAa( final String s ) { - final String seq = s.toLowerCase(); - if ( ( seq.indexOf( 'r' ) > -1 ) || ( seq.indexOf( 'd' ) > -1 ) || ( seq.indexOf( 'e' ) > -1 ) - || ( seq.indexOf( 'q' ) > -1 ) || ( seq.indexOf( 'h' ) > -1 ) || ( seq.indexOf( 'k' ) > -1 ) - || ( seq.indexOf( 'w' ) > -1 ) || ( seq.indexOf( 's' ) > -1 ) || ( seq.indexOf( 'm' ) > -1 ) - || ( seq.indexOf( 'p' ) > -1 ) || ( seq.indexOf( 'v' ) > -1 ) ) { - return true; - } - return false; - } - /** * 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 + * the value * @param min - * the smallest value + * the smallest value * @param max - * the largest value + * the largest value * @param minColor * the color for min * @param maxColor @@ -185,15 +152,15 @@ public final class ForesterUtil { * 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 + * the largest value * @param mean - * the mean/median value + * the mean/median value * @param minColor * the color for min * @param maxColor @@ -236,7 +203,7 @@ public final class ForesterUtil { /** * Helper method for calcColor methods. - * + * * @param smallercolor_component_x * color component the smaller color * @param largercolor_component_x @@ -253,8 +220,8 @@ public final class ForesterUtil { /** * Helper method for calcColor methods. - * - * + * + * * @param value * the value * @param larger @@ -267,6 +234,16 @@ public final class ForesterUtil { return ( 255.0 * ( value - smaller ) ) / ( larger - smaller ); } + public static int calculateOverlap( final Domain domain, final List covered_positions ) { + int overlap_count = 0; + for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) { + if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) { + ++overlap_count; + } + } + return overlap_count; + } + final public static String collapseWhiteSpace( final String s ) { return s.replaceAll( "[\\s]+", " " ); } @@ -337,6 +314,10 @@ public final class ForesterUtil { 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 EasyWriter createEasyWriter( final File file ) throws IOException { return new EasyWriter( createBufferedWriter( file ) ); } @@ -345,10 +326,6 @@ public final class ForesterUtil { return createEasyWriter( createFileForWriting( name ) ); } - 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() ) { @@ -357,6 +334,37 @@ public final class ForesterUtil { return file; } + 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() ); + } + } + + public static void fatalError( final String message ) { + System.err.println(); + System.err.println( "error: " + message ); + System.err.println(); + System.exit( -1 ); + } + public static void fatalError( final String prg_name, final String message ) { System.err.println(); System.err.println( "[" + prg_name + "] > " + message ); @@ -364,6 +372,16 @@ public final class ForesterUtil { System.exit( -1 ); } + public static void fatalErrorIfFileNotReadable( final File file ) { + final String error = isReadableFile( file ); + if ( !isEmpty( error ) ) { + System.err.println(); + System.err.println( "error: " + error ); + System.err.println(); + System.exit( -1 ); + } + } + public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) { final String error = isReadableFile( file ); if ( !isEmpty( error ) ) { @@ -374,6 +392,34 @@ public final class ForesterUtil { } } + public static String[][] file22dArray( 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( "#" ) ) { + list.add( str ); + } + } + in.close(); + final String[][] ary = new String[ list.size() ][ 2 ]; + final Pattern pa = Pattern.compile( "(\\S+)\\s+(\\S+)" ); + int i = 0; + for( final String s : list ) { + final Matcher m = pa.matcher( s ); + if ( m.matches() ) { + ary[ i ][ 0 ] = m.group( 1 ); + ary[ i ][ 1 ] = m.group( 2 ); + ++i; + } + else { + throw new IOException( "unexpcted format: " + s ); + } + } + return ary; + } + public static String[] file2array( final File file ) throws IOException { final List list = file2list( file ); final String[] ary = new String[ list.size() ]; @@ -450,7 +496,9 @@ public final class ForesterUtil { reader = new BufferedReader( new StringReader( source.toString() ) ); } else if ( source instanceof URL ) { - reader = new BufferedReader( new InputStreamReader( ( ( URL ) source ).openStream() ) ); + final URLConnection url_connection = ( ( URL ) source ).openConnection(); + url_connection.setDefaultUseCaches( false ); + reader = new BufferedReader( new InputStreamReader( url_connection.getInputStream() ) ); } else { throw new IllegalArgumentException( "dont know how to read [" + source.getClass() + "]" ); @@ -471,10 +519,30 @@ public final class ForesterUtil { return line; } + final public static String getForesterLibraryInformation() { + return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")"; + } + final public static String getLineSeparator() { return ForesterUtil.LINE_SEPARATOR; } + final public static MolecularSequence.TYPE guessMolecularSequenceType( final String mol_seq ) { + if ( mol_seq.contains( "L" ) || mol_seq.contains( "I" ) || mol_seq.contains( "E" ) || mol_seq.contains( "H" ) + || mol_seq.contains( "D" ) || mol_seq.contains( "Q" ) ) { + return TYPE.AA; + } + else { + if ( mol_seq.contains( "T" ) ) { + return TYPE.DNA; + } + else if ( mol_seq.contains( "U" ) ) { + return TYPE.RNA; + } + } + return null; + } + 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 ); @@ -484,10 +552,6 @@ public final class ForesterUtil { } } - final public static boolean isContainsParanthesesableNhCharacter( final String nh ) { - return PARANTHESESABLE_NH_CHARS_PATTERN.matcher( nh ).find(); - } - final public static boolean isEmpty( final List l ) { if ( ( l == null ) || l.isEmpty() ) { return true; @@ -516,6 +580,23 @@ public final class ForesterUtil { return ( ( s == null ) || ( s.length() < 1 ) ); } + /** + * Returns true is Domain domain falls in an uninterrupted stretch of + * covered positions. + * + * @param domain + * @param covered_positions + * @return + */ + public static boolean isEngulfed( final Domain domain, final List covered_positions ) { + for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) { + if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) { + return false; + } + } + return true; + } + final public static boolean isEqual( final double a, final double b ) { return ( ( Math.abs( a - b ) ) < ZERO_DIFF ); } @@ -528,7 +609,7 @@ public final class ForesterUtil { * 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 @@ -560,6 +641,16 @@ public final class ForesterUtil { } } + public final static boolean isMac() { + try { + return OS_NAME.toLowerCase().startsWith( "mac" ); + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e ); + return false; + } + } + final public static boolean isNull( final BigDecimal s ) { return ( ( s == null ) || ( s.compareTo( NULL_BD ) == 0 ) ); } @@ -587,6 +678,16 @@ public final class ForesterUtil { return isReadableFile( new File( s ) ); } + public final static boolean isWindows() { + try { + return OS_NAME.toLowerCase().indexOf( "win" ) > -1; + } + catch ( final Exception e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e ); + return false; + } + } + final public static String isWritableFile( final File f ) { if ( f.isDirectory() ) { return "[" + f + "] is a directory"; @@ -612,7 +713,7 @@ public final class ForesterUtil { return i; } - final public static SortedMap listToSortedCountsMap( final List list ) { + final public static SortedMap listToSortedCountsMap( final List list ) { final SortedMap map = new TreeMap(); for( final Object key : list ) { if ( !map.containsKey( key ) ) { @@ -652,10 +753,9 @@ public final class ForesterUtil { } } - final public static StringBuffer mapToStringBuffer( final Map map, final String key_value_separator ) { + 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(); + for( final Object key : map.keySet() ) { sb.append( key.toString() ); sb.append( key_value_separator ); sb.append( map.get( key ).toString() ); @@ -685,6 +785,164 @@ public final class ForesterUtil { } } + public final static Color obtainColorDependingOnTaxonomyGroup( final String tax_group ) { + if ( !ForesterUtil.isEmpty( tax_group ) ) { + if ( tax_group.equals( TaxonomyGroups.DEUTEROSTOMIA ) ) { + return TaxonomyColors.DEUTEROSTOMIA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.PROTOSTOMIA ) ) { + return TaxonomyColors.PROTOSTOMIA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.CNIDARIA ) ) { + return TaxonomyColors.CNIDARIA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.PLACOZOA ) ) { + return TaxonomyColors.PLACOZOA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.CTENOPHORA ) ) { + return TaxonomyColors.CTENOPHORA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.PORIFERA ) ) { + return TaxonomyColors.PORIFERA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.CHOANOFLAGELLIDA ) ) { + return TaxonomyColors.CHOANOFLAGELLIDA; + } + else if ( tax_group.equals( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA ) ) { + return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA; + } + else if ( tax_group.equals( TaxonomyGroups.DIKARYA ) ) { + return TaxonomyColors.DIKARYA_COLOR; + } + else if ( tax_group.equalsIgnoreCase( TaxonomyGroups.FUNGI ) + || tax_group.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) { + return TaxonomyColors.OTHER_FUNGI_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP ) ) { + return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.AMOEBOZOA ) ) { + return TaxonomyColors.AMOEBOZOA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.EMBRYOPHYTA ) ) { + return TaxonomyColors.EMBRYOPHYTA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.CHLOROPHYTA ) ) { + return TaxonomyColors.CHLOROPHYTA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.RHODOPHYTA ) ) { + return TaxonomyColors.RHODOPHYTA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.HACROBIA ) ) { + return TaxonomyColors.HACROBIA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) ) { + return TaxonomyColors.GLAUCOPHYTA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.STRAMENOPILES ) ) { + return TaxonomyColors.STRAMENOPILES_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.ALVEOLATA ) ) { + return TaxonomyColors.ALVEOLATA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.RHIZARIA ) ) { + return TaxonomyColors.RHIZARIA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.EXCAVATA ) ) { + return TaxonomyColors.EXCAVATA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.APUSOZOA ) ) { + return TaxonomyColors.APUSOZOA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.ARCHAEA ) ) { + return TaxonomyColors.ARCHAEA_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.BACTERIA ) ) { + return TaxonomyColors.BACTERIA_COLOR; + } + } + return null; + } + + public final static String obtainNormalizedTaxonomyGroup( final String tax ) { + if ( tax.equalsIgnoreCase( TaxonomyGroups.DEUTEROSTOMIA ) ) { + return TaxonomyGroups.DEUTEROSTOMIA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.PROTOSTOMIA ) ) { + return TaxonomyGroups.PROTOSTOMIA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.CNIDARIA ) ) { + return TaxonomyGroups.CNIDARIA; + } + else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( TaxonomyGroups.PLACOZOA ) ) { + return TaxonomyGroups.PLACOZOA; + } + else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( TaxonomyGroups.CTENOPHORA ) ) { + return TaxonomyGroups.CTENOPHORA; + } + else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( TaxonomyGroups.PORIFERA ) ) { + return TaxonomyGroups.PORIFERA; + } + else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( TaxonomyGroups.CHOANOFLAGELLIDA ) ) { + return TaxonomyGroups.CHOANOFLAGELLIDA; + } + else if ( tax.toLowerCase().startsWith( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA ) + || tax.toLowerCase().startsWith( "ichthyophonida and filasterea" ) + || tax.toLowerCase().startsWith( "ichthyosporea & filasterea" ) + || tax.toLowerCase().startsWith( "ichthyosporea and filasterea" ) ) { + return TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.DIKARYA ) ) { + return TaxonomyGroups.DIKARYA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.FUNGI ) || tax.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) { + return TaxonomyGroups.OTHER_FUNGI; + } + else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) { + return TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.AMOEBOZOA ) ) { + return TaxonomyGroups.AMOEBOZOA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.EMBRYOPHYTA ) ) { + return TaxonomyGroups.EMBRYOPHYTA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.CHLOROPHYTA ) ) { + return TaxonomyGroups.CHLOROPHYTA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHODOPHYTA ) ) { + return TaxonomyGroups.RHODOPHYTA; + } + else if ( tax.toLowerCase().startsWith( TaxonomyGroups.HACROBIA ) ) { + return TaxonomyGroups.HACROBIA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) || tax.equalsIgnoreCase( "glaucophyta" ) ) { + return TaxonomyGroups.GLAUCOCYSTOPHYCEAE; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.STRAMENOPILES ) ) { + return TaxonomyGroups.STRAMENOPILES; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALVEOLATA ) ) { + return TaxonomyGroups.ALVEOLATA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHIZARIA ) ) { + return TaxonomyGroups.RHIZARIA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.EXCAVATA ) ) { + return TaxonomyGroups.EXCAVATA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.APUSOZOA ) ) { + return TaxonomyGroups.APUSOZOA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.ARCHAEA ) ) { + return TaxonomyGroups.ARCHAEA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) { + return TaxonomyGroups.BACTERIA; + } + return null; + } + final public static BufferedReader obtainReader( final Object source ) throws IOException, FileNotFoundException { BufferedReader reader = null; if ( source instanceof File ) { @@ -711,11 +969,20 @@ public final class ForesterUtil { } else { throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass() - + "] (can only parse objects of type File, InputStream, String, or StringBuffer)" ); + + "] (can only parse objects of type File, InputStream, String, or StringBuffer)" ); } return reader; } + public final static void outOfMemoryError( final OutOfMemoryError e ) { + System.err.println(); + System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" ); + System.err.println(); + e.printStackTrace( System.err ); + System.err.println(); + System.exit( -1 ); + } + final public static StringBuffer pad( final double number, final int size, final char pad, final boolean left_pad ) { return pad( new StringBuffer( number + "" ), size, pad, left_pad ); } @@ -771,7 +1038,7 @@ public final class ForesterUtil { } final public static void printErrorMessage( final String prg_name, final String message ) { - System.out.println( "[" + prg_name + "] > error: " + message ); + System.err.println( "[" + prg_name + "] > error: " + message ); } final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) { @@ -785,6 +1052,14 @@ public final class ForesterUtil { } final public static void printProgramInformation( final String prg_name, + final String prg_version, + final String date, + final String email, + final String www ) { + printProgramInformation( prg_name, null, prg_version, date, email, www, null ); + } + + final public static void printProgramInformation( final String prg_name, final String desc, final String prg_version, final String date, @@ -815,14 +1090,6 @@ public final class ForesterUtil { System.out.println(); } - final public static void printProgramInformation( final String prg_name, - final String prg_version, - final String date, - final String email, - final String www ) { - printProgramInformation( prg_name, null, prg_version, date, email, www, null ); - } - final public static void printWarningMessage( final String prg_name, final String message ) { System.out.println( "[" + prg_name + "] > warning: " + message ); } @@ -831,6 +1098,69 @@ public final class ForesterUtil { System.out.println( "[" + prg_name + "] > " + message ); } + public static List readUrl( final String url_str ) throws IOException { + final URL url = new URL( url_str ); + final URLConnection urlc = url.openConnection(); + //urlc.setRequestProperty( "User-Agent", "" ); + final BufferedReader in = new BufferedReader( new InputStreamReader( urlc.getInputStream() ) ); + String line; + final List result = new ArrayList(); + while ( ( line = in.readLine() ) != null ) { + result.add( line ); + } + in.close(); + return result; + } + + /** + * + * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => + * domain with 0.3 is ignored + * + * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored + * + * + * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ + * ignored + * + * @param max_allowed_overlap + * maximal allowed overlap (inclusive) to be still considered not + * overlapping (zero or negative value to allow any overlap) + * @param remove_engulfed_domains + * to remove domains which are completely engulfed by coverage of + * domains with better support + * @param protein + * @return + */ + public static Protein removeOverlappingDomains( final int max_allowed_overlap, + final boolean remove_engulfed_domains, + final Protein protein ) { + final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies() + .getSpeciesId(), protein.getLength() ); + final List sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein ); + final List covered_positions = new ArrayList(); + for( final Domain domain : sorted ) { + if ( ( ( max_allowed_overlap < 0 ) || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) ) + && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) { + final int covered_positions_size = covered_positions.size(); + for( int i = covered_positions_size; i < domain.getFrom(); ++i ) { + covered_positions.add( false ); + } + final int new_covered_positions_size = covered_positions.size(); + for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) { + if ( i < new_covered_positions_size ) { + covered_positions.set( i, true ); + } + else { + covered_positions.add( true ); + } + } + pruned_protein.addProteinDomain( domain ); + } + } + return pruned_protein; + } + final public static String removeSuffix( final String file_name ) { final int i = file_name.lastIndexOf( '.' ); if ( i > 1 ) { @@ -841,7 +1171,7 @@ public final class ForesterUtil { /** * Removes all white space from String s. - * + * * @return String s with white space removed */ final public static String removeWhiteSpace( String s ) { @@ -856,18 +1186,11 @@ public final class ForesterUtil { return s; } - final public static String replaceIllegalNhCharacters( final String nh ) { - if ( nh == null ) { - return ""; - } - return nh.trim().replaceAll( "[\\[\\]:]+", "_" ); - } - final public static String replaceIllegalNhxCharacters( final String nhx ) { if ( nhx == null ) { return ""; } - return nhx.trim().replaceAll( "[\\[\\](),:;\\s]+", "_" ); + return nhx.trim().replaceAll( "[\\[\\]']+", "_" ); } final public static double round( final double value, final int decimal_place ) { @@ -900,6 +1223,46 @@ public final class ForesterUtil { } } + public final static StringBuilder santitizeStringForNH( String data ) { + data = data.replaceAll( "\\s+", " " ).trim(); + final StringBuilder sb = new StringBuilder(); + if ( data.length() > 0 ) { + final boolean single_pars = data.indexOf( '\'' ) > -1; + final boolean double_pars = data.indexOf( '"' ) > -1; + if ( single_pars && double_pars ) { + data = data.replace( '\'', '`' ); + sb.append( '\'' ); + sb.append( data ); + sb.append( '\'' ); + } + else if ( single_pars ) { + sb.append( '"' ); + sb.append( data ); + sb.append( '"' ); + } + else if ( PARANTHESESABLE_NH_CHARS_PATTERN.matcher( data ).find() ) { + sb.append( '\'' ); + sb.append( data ); + sb.append( '\'' ); + } + else { + sb.append( data ); + } + } + return sb; + } + + public static boolean seqIsLikelyToBeAa( final String s ) { + final String seq = s.toLowerCase(); + if ( ( seq.indexOf( 'r' ) > -1 ) || ( seq.indexOf( 'd' ) > -1 ) || ( seq.indexOf( 'e' ) > -1 ) + || ( seq.indexOf( 'q' ) > -1 ) || ( seq.indexOf( 'h' ) > -1 ) || ( seq.indexOf( 'k' ) > -1 ) + || ( seq.indexOf( 'w' ) > -1 ) || ( seq.indexOf( 's' ) > -1 ) || ( seq.indexOf( 'm' ) > -1 ) + || ( seq.indexOf( 'p' ) > -1 ) || ( seq.indexOf( 'v' ) > -1 ) ) { + return true; + } + return false; + } + final private static String[] splitString( final String str ) { final String regex = "[\\s;,]+"; return str.split( regex ); @@ -952,10 +1315,34 @@ public final class ForesterUtil { return str_array; } + final public static void unexpectedFatalError( final Error e ) { + System.err.println(); + System.err.println( "unexpected error: should not have occured! Please contact program author(s)." ); + e.printStackTrace( System.err ); + System.err.println(); + System.exit( -1 ); + } + + final public static void unexpectedFatalError( final Exception e ) { + System.err.println(); + System.err.println( "unexpected exception: 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 message ) { + System.err.println(); + System.err.println( "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 Exception e ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error (Should not have occured! Please contact program author(s).)" ); + + "] > unexpected error; should not have occured! Please contact program author(s)." ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); @@ -964,7 +1351,7 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final String message ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error. Should not have occured! Please contact program author(s)." ); + + "] > unexpected error: should not have occured! Please contact program author(s)." ); System.err.println( message ); System.err.println(); System.exit( -1 ); @@ -973,13 +1360,30 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error. Should not have occured! Please contact program author(s)." ); + + "] > unexpected error: should not have occured! Please contact program author(s)." ); System.err.println( message ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); } + public final static void updateProgress( final double progress_percentage ) { + final int width = 50; + System.out.print( "\r[" ); + int i = 0; + for( ; i <= ForesterUtil.roundToInt( progress_percentage * width ); i++ ) { + System.out.print( "." ); + } + for( ; i < width; i++ ) { + System.out.print( " " ); + } + System.out.print( "]" ); + } + + public final static void updateProgress( final int i, final DecimalFormat f ) { + System.out.print( "\r[" + f.format( i ) + "]" ); + } + public final static String wordWrap( final String str, final int width ) { final StringBuilder sb = new StringBuilder( str ); int start = 0; @@ -1008,4 +1412,7 @@ public final class ForesterUtil { } return sb.toString(); } + + private ForesterUtil() { + } }