// 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;
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.phylogeny.PhylogenyNode;
public static final NumberFormat FORMATTER_6;
public static final NumberFormat FORMATTER_06;
public static final NumberFormat FORMATTER_3;
+ public static final String NCBI_PROTEIN = "http://www.ncbi.nlm.nih.gov/protein/";
+ public static final String NCBI_NUCCORE = "http://www.ncbi.nlm.nih.gov/nuccore/";
+ public final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/";
+ public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern
+ .compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]([A-Z][0-9][A-Z0-9]{3}[0-9])(?:\\b|_)" );
+ public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern
+ .compile( "\\b(?:[A-Z0-9]{2,5}|(?:[A-Z][0-9][A-Z0-9]{3}[0-9]))_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)\\b" );
+ public static final String NCBI_GI = "http://www.ncbi.nlm.nih.gov/protein/gi:";
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
private ForesterUtil() {
}
- public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
+ public static String extractRefSeqAccessorAccessor( final PhylogenyNode node ) {
+ String v = null;
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !isEmpty( seq.getSymbol() ) ) {
+ v = SequenceIdParser.parseRefSeqAccessor( seq.getSymbol() );
+ }
+ if ( isEmpty( v ) && !isEmpty( seq.getName() ) ) {
+ v = SequenceIdParser.parseRefSeqAccessor( seq.getName() );
+ }
+ if ( isEmpty( v ) && ( node.getNodeData().getSequence().getAccession() != null )
+ && !isEmpty( seq.getAccession().getValue() ) ) {
+ v = SequenceIdParser.parseRefSeqAccessor( seq.getAccession().getValue() );
+ }
}
+ if ( isEmpty( v ) && !isEmpty( node.getName() ) ) {
+ v = SequenceIdParser.parseRefSeqAccessor( node.getName() );
+ }
+ return v;
}
- public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasSequence() ) {
- node.getNodeData().setSequence( new Sequence() );
+ public static String extractGenbankAccessor( final PhylogenyNode node ) {
+ String v = null;
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !isEmpty( seq.getSymbol() ) ) {
+ v = SequenceIdParser.parseGenbankAccessor( seq.getSymbol() );
+ }
+ if ( isEmpty( v ) && !isEmpty( seq.getName() ) ) {
+ v = SequenceIdParser.parseGenbankAccessor( seq.getName() );
+ }
+ if ( isEmpty( v ) && ( node.getNodeData().getSequence().getAccession() != null )
+ && !isEmpty( seq.getAccession().getValue() ) ) {
+ v = SequenceIdParser.parseGenbankAccessor( seq.getAccession().getValue() );
+ }
+ }
+ if ( isEmpty( v ) && !isEmpty( node.getName() ) ) {
+ v = SequenceIdParser.parseGenbankAccessor( node.getName() );
}
+ return v;
}
- final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDistribution() ) {
- node.getNodeData().setDistribution( new Distribution( "" ) );
+ public static String extractGInumber( final PhylogenyNode node ) {
+ String v = null;
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( isEmpty( v ) && !isEmpty( seq.getName() ) ) {
+ v = SequenceIdParser.parseGInumber( seq.getName() );
+ }
+ if ( isEmpty( v ) && ( node.getNodeData().getSequence().getAccession() != null )
+ && !isEmpty( seq.getAccession().getValue() ) ) {
+ v = SequenceIdParser.parseGInumber( seq.getAccession().getValue() );
+ }
+ }
+ if ( isEmpty( v ) && !isEmpty( node.getName() ) ) {
+ v = SequenceIdParser.parseGInumber( node.getName() );
}
+ return v;
}
- final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDate() ) {
- node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
+ public static String extractUniProtKbProteinSeqIdentifier( final PhylogenyNode node ) {
+ String upkb = null;
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ Matcher m;
+ if ( !isEmpty( seq.getSymbol() ) ) {
+ m = UNIPROT_KB_PATTERN_1.matcher( seq.getSymbol() );
+ if ( m.find() ) {
+ upkb = m.group( 1 );
+ }
+ else {
+ m = UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() );
+ if ( m.find() ) {
+ upkb = m.group();
+ }
+ }
+ }
+ if ( isEmpty( upkb ) && !isEmpty( seq.getName() ) ) {
+ m = UNIPROT_KB_PATTERN_1.matcher( seq.getName() );
+ if ( m.find() ) {
+ upkb = m.group( 1 );
+ }
+ else {
+ m = UNIPROT_KB_PATTERN_2.matcher( seq.getName() );
+ if ( m.find() ) {
+ upkb = m.group();
+ }
+ }
+ }
+ if ( isEmpty( upkb ) && ( node.getNodeData().getSequence().getAccession() != null )
+ && !isEmpty( seq.getAccession().getValue() ) ) {
+ m = UNIPROT_KB_PATTERN_1.matcher( seq.getAccession().getValue() );
+ if ( m.find() ) {
+ upkb = m.group( 1 );
+ }
+ else {
+ m = UNIPROT_KB_PATTERN_2.matcher( seq.getAccession().getValue() );
+ if ( m.find() ) {
+ upkb = m.group();
+ }
+ }
+ }
}
+ if ( isEmpty( upkb ) && !isEmpty( node.getName() ) ) {
+ final Matcher m1 = UNIPROT_KB_PATTERN_1.matcher( node.getName() );
+ if ( m1.find() ) {
+ upkb = m1.group( 1 );
+ }
+ else {
+ final Matcher m2 = UNIPROT_KB_PATTERN_2.matcher( node.getName() );
+ if ( m2.find() ) {
+ upkb = m2.group();
+ }
+ }
+ }
+ return upkb;
}
final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char 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,
}
}
- /**
- * Helper method for calcColor methods.
- *
- * @param smallercolor_component_x
- * color component the smaller color
- * @param largercolor_component_x
- * color component the larger color
- * @param x
- * factor
- * @return an int representing a color component
- */
- final private static int calculateColorComponent( final double smallercolor_component_x,
- final double largercolor_component_x,
- final double x ) {
- return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) );
- }
-
- /**
- * Helper method for calcColor methods.
- *
- *
- * @param value
- * the value
- * @param larger
- * the largest value
- * @param smaller
- * the smallest value
- * @return a normalized value between larger and smaller
- */
- final private static double calculateColorFactor( final double value, final double larger, final double smaller ) {
- return ( 255.0 * ( value - smaller ) ) / ( larger - smaller );
- }
-
final public static String collapseWhiteSpace( final String s ) {
return s.replaceAll( "[\\s]+", " " );
}
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 ) );
}
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() ) {
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 );
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 ) ) {
return line;
}
+ final public static String getForesterLibraryInformation() {
+ return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")";
+ }
+
final public static String getLineSeparator() {
return ForesterUtil.LINE_SEPARATOR;
}
return isReadableFile( new File( s ) );
}
+ public static boolean isWindowns() {
+ return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1;
+ }
+
final public static String isWritableFile( final File f ) {
if ( f.isDirectory() ) {
return "[" + f + "] is a directory";
}
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,
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 );
}
}
}
- final private static String[] splitString( final String str ) {
- final String regex = "[\\s;,]+";
- return str.split( regex );
+ 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 public static String stringArrayToString( final String[] a ) {
return str_array;
}
+ 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 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 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 );
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 );
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;
}
return sb.toString();
}
+
+ /**
+ * Helper method for calcColor methods.
+ *
+ * @param smallercolor_component_x
+ * color component the smaller color
+ * @param largercolor_component_x
+ * color component the larger color
+ * @param x
+ * factor
+ * @return an int representing a color component
+ */
+ final private static int calculateColorComponent( final double smallercolor_component_x,
+ final double largercolor_component_x,
+ final double x ) {
+ return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) );
+ }
+
+ /**
+ * Helper method for calcColor methods.
+ *
+ *
+ * @param value
+ * the value
+ * @param larger
+ * the largest value
+ * @param smaller
+ * the smallest value
+ * @return a normalized value between larger and smaller
+ */
+ final private static double calculateColorFactor( final double value, final double larger, final double smaller ) {
+ return ( 255.0 * ( value - smaller ) ) / ( larger - smaller );
+ }
+
+ final private static String[] splitString( final String str ) {
+ final String regex = "[\\s;,]+";
+ return str.split( regex );
+ }
+
+ 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 );
+ }
}
git://source.jalview.org / jalview.git / blobdiff