X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FForesterUtil.java;h=f144a81684894675f7a3442a03586b1560e9b619;hb=aff0b302cc19e0ee3e73bc4a87884b4591ac5f08;hp=48d973b500c4c6fdaf95c192f82888caf7769b69;hpb=fea4064e24c6cb362b0e033cf7047afd20f5f53f;p=jalview.git diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index 48d973b..f144a81 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -34,6 +34,7 @@ import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.FileReader; import java.io.FileWriter; +import java.io.FilenameFilter; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; @@ -98,7 +99,7 @@ public final class ForesterUtil { public final static String OS_VERSION = System.getProperty( "os.version" ); 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 final static double ZERO_DIFF = 1.0E-12; private static final Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s:\\[\\]]" ); static { final DecimalFormatSymbols dfs = new DecimalFormatSymbols(); @@ -116,6 +117,13 @@ public final class ForesterUtil { } } + final public static String removeFileExtension( final String file_name ) { + if ( file_name.indexOf( "." ) > 0 ) { + return file_name.substring( 0, file_name.lastIndexOf( "." ) ); + } + return file_name; + } + /** * 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, @@ -220,7 +228,8 @@ public final class ForesterUtil { final private static int calculateColorComponent( final double smallercolor_component_x, final double largercolor_component_x, final double x ) { - return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) ); + return ( int ) ( smallercolor_component_x + + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) ); } /** @@ -533,15 +542,16 @@ public final class ForesterUtil { } 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" ) ) { + final String s = mol_seq.toUpperCase(); + if ( s.contains( "L" ) || s.contains( "I" ) || s.contains( "E" ) || s.contains( "H" ) || s.contains( "D" ) + || s.contains( "Q" ) ) { return TYPE.AA; } else { - if ( mol_seq.contains( "T" ) ) { + if ( s.contains( "T" ) ) { return TYPE.DNA; } - else if ( mol_seq.contains( "U" ) ) { + else if ( s.contains( "U" ) ) { return TYPE.RNA; } } @@ -585,6 +595,13 @@ public final class ForesterUtil { return ( ( s == null ) || ( s.length() < 1 ) ); } + final public static boolean isEmptyTrimmed( final String s ) { + if ( s == null ) { + return true; + } + return ( ( s.trim().length() < 1 ) ); + } + /** * Returns true is Domain domain falls in an uninterrupted stretch of * covered positions. @@ -606,6 +623,10 @@ public final class ForesterUtil { return ( ( Math.abs( a - b ) ) < ZERO_DIFF ); } + final public static boolean isEqual( final double a, final double b, final double tolerance ) { + return ( ( Math.abs( a - b ) ) < tolerance ); + } + final public static boolean isEven( final int n ) { return ( n % 2 ) == 0; } @@ -703,6 +724,10 @@ public final class ForesterUtil { return null; } + final public static String isWritableFile( final String s ) { + return isWritableFile( new File( s ) ); + } + /** * Helper for method "stringToColor". *

@@ -734,7 +759,8 @@ public final class ForesterUtil { final public static void map2file( final File file, final Map data, final String entry_separator, - final String data_separator ) throws IOException { + final String data_separator ) + throws IOException { final Writer writer = new BufferedWriter( new FileWriter( file ) ); map2writer( writer, data, entry_separator, data_separator ); writer.close(); @@ -743,7 +769,8 @@ public final class ForesterUtil { final public static void map2writer( final Writer writer, final Map data, final String entry_separator, - final String data_separator ) throws IOException { + final String data_separator ) + throws IOException { boolean first = true; for( final Entry entry : data.entrySet() ) { if ( !first ) { @@ -758,7 +785,8 @@ 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 Object key : map.keySet() ) { sb.append( key.toString() ); @@ -865,6 +893,21 @@ public final class ForesterUtil { else if ( tax_group.equals( TaxonomyGroups.BACTERIA ) ) { return TaxonomyColors.BACTERIA_COLOR; } + else if ( tax_group.equals( TaxonomyGroups.VIRUSES ) ) { + return TaxonomyColors.VIRUSES_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.ALPHAHERPESVIRINAE ) ) { + return TaxonomyColors.ALPHAHERPESVIRINAE_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.BETAHERPESVIRINAE ) ) { + return TaxonomyColors.BETAHERPESVIRINAE_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.GAMMAHERPESVIRINAE ) ) { + return TaxonomyColors.GAMMAHERPESVIRINAE_COLOR; + } + else if ( tax_group.equals( TaxonomyGroups.OTHER ) ) { + return TaxonomyColors.OTHER_COLOR; + } } return null; } @@ -945,6 +988,21 @@ public final class ForesterUtil { else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) { return TaxonomyGroups.BACTERIA; } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) { + return TaxonomyGroups.BACTERIA; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.VIRUSES ) ) { + return TaxonomyGroups.VIRUSES; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALPHAHERPESVIRINAE ) ) { + return TaxonomyGroups.ALPHAHERPESVIRINAE; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.BETAHERPESVIRINAE ) ) { + return TaxonomyGroups.BETAHERPESVIRINAE; + } + else if ( tax.equalsIgnoreCase( TaxonomyGroups.GAMMAHERPESVIRINAE ) ) { + return TaxonomyGroups.GAMMAHERPESVIRINAE; + } return null; } @@ -974,7 +1032,7 @@ 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; } @@ -988,11 +1046,17 @@ public final class ForesterUtil { System.exit( -1 ); } - final public static StringBuffer pad( final double number, final int size, final char pad, final boolean left_pad ) { + final public static StringBuffer pad( final double number, + final int size, + final char pad, + final boolean left_pad ) { return pad( new StringBuffer( number + "" ), size, pad, left_pad ); } - final public static StringBuffer pad( final String string, final int size, final char pad, final boolean left_pad ) { + final public static StringBuffer pad( final String string, + final int size, + final char pad, + final boolean left_pad ) { return pad( new StringBuffer( string ), size, pad, left_pad ); } @@ -1046,7 +1110,9 @@ public final class ForesterUtil { System.err.println( "[" + prg_name + "] > error: " + message ); } - final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) { + final public static void printProgramInformation( final String prg_name, + final String prg_version, + final String date ) { final int l = prg_name.length() + prg_version.length() + date.length() + 4; System.out.println(); System.out.println( prg_name + " " + prg_version + " (" + date + ")" ); @@ -1090,7 +1156,8 @@ public final class ForesterUtil { } if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) { System.out.println(); - System.out.println( "[running on Java " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); + System.out + .println( "[running on Java " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); } System.out.println(); } @@ -1140,12 +1207,14 @@ public final class ForesterUtil { 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 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 ) ) + 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 ) { @@ -1347,7 +1416,7 @@ public final class ForesterUtil { 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 ); @@ -1356,7 +1425,7 @@ 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 ); @@ -1365,7 +1434,7 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error: should not have occured! Please contact program author(s)." ); + + "] > unexpected error: should not have occured! Please contact program author(s)." ); System.err.println( message ); e.printStackTrace( System.err ); System.err.println(); @@ -1418,9 +1487,7 @@ public final class ForesterUtil { return sb.toString(); } - - public final static Phylogeny[] readPhylogeniesFromUrl( final URL url, - final PhylogenyParser parser ) + public final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final PhylogenyParser parser ) throws NoSuchAlgorithmException, IOException, KeyManagementException { if ( url == null ) { throw new IllegalArgumentException( "URL to read from must not be null" ); @@ -1429,8 +1496,8 @@ public final class ForesterUtil { throw new IllegalArgumentException( "parser to use to read from URL must not be null" ); } final URLConnection con; - if ( url.toString().startsWith( "https:" ) ) { - con = TrustManager.makeHttpsURLConnection( url ); + if ( url.toString().startsWith( "https:" ) ) { + con = TrustManager.makeHttpsURLConnection( url ); } else if ( url.toString().startsWith( "http:" ) ) { con = url.openConnection(); @@ -1438,12 +1505,12 @@ public final class ForesterUtil { else { throw new IllegalArgumentException( "Cannot deal with URL: " + url ); } - if ( con == null ) { + if ( con == null ) { throw new IOException( "could not create connection from " + url ); } con.setDefaultUseCaches( false ); final InputStream is = con.getInputStream(); - if ( is == null ) { + if ( is == null ) { throw new IOException( "could not create input stream from " + url ); } final Phylogeny[] trees = ParserBasedPhylogenyFactory.getInstance().create( is, parser ); @@ -1451,11 +1518,193 @@ public final class ForesterUtil { is.close(); } catch ( final Exception e ) { - // ignore + // ignore } return trees; } - + + public final static File getMatchingFile( final File dir, final String prefix, final String suffix ) + throws IOException { + if ( !dir.exists() ) { + throw new IOException( "[" + dir + "] does not exist" ); + } + if ( !dir.isDirectory() ) { + throw new IOException( "[" + dir + "] is not a directory" ); + } + if ( dir.listFiles().length == 0 ) { + throw new IOException( "[" + dir + "] is empty" ); + } + final File files[] = dir.listFiles( new FilenameFilter() { + + @Override + public boolean accept( final File dir, final String name ) { + return ( name.endsWith( suffix ) ); + } + } ); + if ( files.length == 0 ) { + throw new IOException( "no files ending with \"" + suffix + "\" found in [" + dir + "]" ); + } + String my_prefix = prefix; + boolean done = false; + boolean more_than_one = false; + File the_one = null; + do { + int matches = 0; + for( final File file : files ) { + if ( file.getName().startsWith( my_prefix ) ) { + matches++; + if ( matches > 1 ) { + the_one = null; + break; + } + the_one = file; + } + } + if ( matches > 1 ) { + more_than_one = true; + done = true; + } + if ( matches == 1 ) { + done = true; + } + else { + if ( my_prefix.length() <= 1 ) { + throw new IOException( "no file matching \"" + removeFileExtension( prefix ) + + "\" and ending with \"" + suffix + "\" found in [" + dir + "]" ); + } + my_prefix = my_prefix.substring( 0, my_prefix.length() - 1 ); + } + } while ( !done ); + if ( more_than_one ) { + throw new IOException( "multiple files matching \"" + removeFileExtension( prefix ) + + "\" and ending with \"" + suffix + "\" found in [" + dir + "]" ); + } + else if ( the_one != null ) { + } + else { + throw new IOException( "no file matching \"" + removeFileExtension( prefix ) + "\" and ending with \"" + + suffix + "\" found in [" + dir + "]" ); + } + return the_one; + } + + public final static String greatestCommonPrefix( final String a, final String b ) { + final int min_length = Math.min( a.length(), b.length() ); + for( int i = 0; i < min_length; ++i ) { + if ( a.charAt( i ) != b.charAt( i ) ) { + return a.substring( 0, i ); + } + } + return a.substring( 0, min_length ); + } + + public final static boolean isContainsPrefix( final String word, final String prefix, final String separator ) { + if ( ForesterUtil.isEmpty( separator ) ) { + throw new IllegalArgumentException( "separator must not be null or empty" ); + } + final String[] word_ary = word.split( Pattern.quote( separator ) ); + final String[] prefix_ary = prefix.split( Pattern.quote( separator ) ); + if ( word_ary.length < prefix_ary.length ) { + return false; + } + final int prefix_ary_length = prefix_ary.length; + for( int i = 0; i < prefix_ary_length; ++i ) { + if ( !( word_ary[ i ].equals( prefix_ary[ i ] ) ) ) { + return false; + } + } + return true; + } + + public final static String greatestCommonPrefix( final String a, final String b, final String separator ) { + if ( ForesterUtil.isEmpty( separator ) ) { + throw new IllegalArgumentException( "separator must not be null or empty" ); + } + final String[] as = a.split( Pattern.quote( separator ) ); + final String[] bs = b.split( Pattern.quote( separator ) ); + final int min_length = Math.min( as.length, bs.length ); + for( int i = 0; i < min_length; ++i ) { + if ( !( as[ i ].equals( bs[ i ] ) ) ) { + final StringBuilder sb = new StringBuilder(); + boolean first = true; + for( int j = 0; j < i; ++j ) { + if ( first ) { + first = false; + } + else { + sb.append( separator ); + } + sb.append( as[ j ] ); + } + return sb.toString(); + } + } + final StringBuilder sb = new StringBuilder(); + boolean first = true; + for( int j = 0; j < min_length; ++j ) { + if ( first ) { + first = false; + } + else { + sb.append( separator ); + } + sb.append( as[ j ] ); + } + return sb.toString(); + } + + public final static String greatestCommonPrefix( final List strings ) { + if ( strings == null ) { + throw new IllegalArgumentException( "list of strings is null" ); + } + if ( strings.isEmpty() ) { + throw new IllegalArgumentException( "list of strings is empty" ); + } + String common = strings.get( 0 ); + for( int i = 1; i < strings.size(); ++i ) { + common = greatestCommonPrefix( common, strings.get( i ) ); + } + return common; + } + + public final static String greatestCommonPrefix( final List strings, final String separator ) { + if ( ForesterUtil.isEmpty( separator ) ) { + return greatestCommonPrefix( strings ); + } + if ( strings == null ) { + throw new IllegalArgumentException( "list of strings is null" ); + } + if ( strings.isEmpty() ) { + throw new IllegalArgumentException( "list of strings is empty" ); + } + String common = strings.get( 0 ); + for( int i = 1; i < strings.size(); ++i ) { + common = greatestCommonPrefix( common, strings.get( i ), separator ); + } + return common; + } + + public static List spliIntoPrefixes( final String prefix, final String separator ) { + final String[] a = prefix.split( Pattern.quote( separator ) ); + final List l = new ArrayList(); + for( int i = 0; i < a.length; ++i ) { + final StringBuilder sb = new StringBuilder(); + for( int j = 0; j <= i; ++j ) { + sb.append( a[ j ] ); + if ( j < i ) { + sb.append( separator ); + } + } + l.add( sb.toString() ); + } + return l; + } + + public static boolean isLooksLikeFasta( final File file ) throws IOException { + final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase(); + return ( ( !isEmptyTrimmed( first_line ) && first_line.trim().startsWith( ">" ) ) ); + } + private ForesterUtil() { } }