import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
+import java.io.Writer;
import java.math.BigDecimal;
import java.net.URL;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Date;
-import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
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.io.parsers.PhylogenyParser;
-import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
-import org.forester.io.parsers.nhx.NHXParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
-import org.forester.io.parsers.tol.TolParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Distribution;
-import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
public final class ForesterUtil {
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 );
}
}
- final public static boolean isEmpty( final List<?> l ) {
- if ( ( l == null ) || l.isEmpty() ) {
- return true;
- }
- for( final Object o : l ) {
- if ( o != null ) {
- return false;
- }
- }
- return true;
+ public static boolean isWindowns() {
+ return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1;
}
- final public static boolean isEmpty( final Set<?> s ) {
- if ( ( s == null ) || s.isEmpty() ) {
+ 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;
}
- for( final Object o : s ) {
- if ( o != null ) {
- return false;
- }
- }
- return true;
+ return false;
}
/**
return s.replaceAll( "[\\s]+", " " );
}
+ final public static void collection2file( final File file, final Collection<?> data, final String separator )
+ throws IOException {
+ final Writer writer = new BufferedWriter( new FileWriter( file ) );
+ collection2writer( writer, data, separator );
+ writer.close();
+ }
+
+ final public static void collection2writer( final Writer writer, final Collection<?> data, final String separator )
+ throws IOException {
+ boolean first = true;
+ for( final Object object : data ) {
+ if ( !first ) {
+ writer.write( separator );
+ }
+ else {
+ first = false;
+ }
+ writer.write( object.toString() );
+ }
+ }
+
final public static String colorToHex( final Color color ) {
final String rgb = Integer.toHexString( color.getRGB() );
return rgb.substring( 2, rgb.length() );
return new BufferedWriter( new FileWriter( file ) );
}
+ final public static EasyWriter createEasyWriter( final File file ) throws IOException {
+ return new EasyWriter( createBufferedWriter( file ) );
+ }
+
+ final public static BufferedWriter createEasyWriter( final String name ) throws IOException {
+ return createEasyWriter( createFileForWriting( name ) );
+ }
+
final public static BufferedWriter createBufferedWriter( final String name ) throws IOException {
return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) );
}
return file;
}
- final public static PhylogenyParser createParserDependingFileContents( final File file,
- final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
- PhylogenyParser parser = null;
- final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
- if ( first_line.startsWith( "<" ) ) {
- parser = new PhyloXmlParser();
- if ( phyloxml_validate_against_xsd ) {
- final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
- final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
- if ( xsd_url != null ) {
- ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
- }
- else {
- if ( ForesterConstants.RELEASE ) {
- throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
- + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
- }
- }
- }
- }
- else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
- || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
- parser = new NexusPhylogeniesParser();
- }
- else {
- parser = new NHXParser();
- }
- return parser;
- }
-
- final public static PhylogenyParser createParserDependingOnFileType( final File file,
- final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
- PhylogenyParser parser = null;
- parser = createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd );
- if ( parser == null ) {
- parser = createParserDependingFileContents( file, phyloxml_validate_against_xsd );
- }
- return parser;
- }
-
- /**
- * Return null if it can not guess the parser to use based on name suffix.
- *
- * @param filename
- * @return
- */
- final public static PhylogenyParser createParserDependingOnSuffix( final String filename,
- final boolean phyloxml_validate_against_xsd ) {
- PhylogenyParser parser = null;
- final String filename_lc = filename.toLowerCase();
- if ( filename_lc.endsWith( ".tol" ) || filename_lc.endsWith( ".tolxml" ) || filename_lc.endsWith( ".tol.zip" ) ) {
- parser = new TolParser();
- }
- else if ( filename_lc.endsWith( ".xml" ) || filename_lc.endsWith( ".px" ) || filename_lc.endsWith( "phyloxml" )
- || filename_lc.endsWith( ".zip" ) ) {
- parser = new PhyloXmlParser();
- if ( phyloxml_validate_against_xsd ) {
- final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
- final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
- if ( xsd_url != null ) {
- ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
- }
- else {
- if ( ForesterConstants.RELEASE ) {
- throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
- + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
- }
- }
- }
- }
- else if ( filename_lc.endsWith( ".nexus" ) || filename_lc.endsWith( ".nex" ) || filename_lc.endsWith( ".nx" ) ) {
- parser = new NexusPhylogeniesParser();
- }
- else if ( filename_lc.endsWith( ".nhx" ) || filename_lc.endsWith( ".nh" ) || filename_lc.endsWith( ".newick" ) ) {
- parser = new NHXParser();
- }
- return parser;
- }
-
- final public static PhylogenyParser createParserDependingOnUrlContents( final URL url,
- final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
- final String lc_filename = url.getFile().toString().toLowerCase();
- PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd );
- if ( ( parser != null ) && lc_filename.endsWith( ".zip" ) ) {
- if ( parser instanceof PhyloXmlParser ) {
- ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
- }
- else if ( parser instanceof TolParser ) {
- ( ( TolParser ) parser ).setZippedInputstream( true );
- }
- }
- if ( parser == null ) {
- final String first_line = getFirstLine( url ).trim().toLowerCase();
- if ( first_line.startsWith( "<" ) ) {
- parser = new PhyloXmlParser();
- if ( phyloxml_validate_against_xsd ) {
- final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
- final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
- if ( xsd_url != null ) {
- ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
- }
- else {
- throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
- + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
- }
- }
- }
- else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
- || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
- parser = new NexusPhylogeniesParser();
- }
- else {
- parser = new NHXParser();
- }
- }
- return parser;
- }
-
- 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() );
- }
- }
-
- /**
- * Extracts a code if and only if:
- * one and only one _,
- * shorter than 25,
- * no |,
- * no .,
- * if / present it has to be after the _,
- * if PFAM_STYLE_ONLY: / must be present,
- * tax code can only contain uppercase letters and numbers,
- * and must contain at least one uppercase letter.
- * Return null if no code extractable.
- *
- * @param name
- * @param limit_to_five
- * @return
- */
- public static String extractTaxonomyCodeFromNodeName( final String name,
- final boolean limit_to_five,
- final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction ) {
- if ( ( name.indexOf( "_" ) > 0 )
- && ( name.length() < 25 )
- && ( name.lastIndexOf( "_" ) == name.indexOf( "_" ) )
- && ( name.indexOf( "|" ) < 0 )
- && ( name.indexOf( "." ) < 0 )
- && ( ( taxonomy_extraction != ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name
- .indexOf( "/" ) >= 0 ) )
- && ( ( ( name.indexOf( "/" ) ) < 0 ) || ( name.indexOf( "/" ) > name.indexOf( "_" ) ) ) ) {
- final String[] s = name.split( "[_/]" );
- if ( s.length > 1 ) {
- String str = s[ 1 ];
- if ( limit_to_five ) {
- if ( str.length() > 5 ) {
- str = str.substring( 0, 5 );
- }
- else if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
- str = str.substring( 0, 3 );
- }
- }
- final Matcher letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str );
- if ( !letters_and_numbers.matches() ) {
- return null;
- }
- final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str );
- if ( numbers_only.matches() ) {
- return null;
- }
- return str;
- }
- }
- return null;
- }
-
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 String prg_name, final File file ) {
+ final String error = isReadableFile( file );
+ if ( !isEmpty( error ) ) {
+ System.err.println();
+ System.err.println( "[" + prg_name + "] > " + error );
+ System.err.println();
+ System.exit( -1 );
+ }
+ }
+
public static String[] file2array( final File file ) throws IOException {
final List<String> list = file2list( file );
final String[] ary = new String[ list.size() ];
return ForesterUtil.LINE_SEPARATOR;
}
- /**
- * Returns all custom data tag names of this Phylogeny as Hashtable. Tag
- * names are keys, values are Boolean set to false.
- */
- final public static Hashtable<String, Boolean> getPropertyRefs( final Phylogeny phylogeny ) {
- final Hashtable<String, Boolean> ht = new Hashtable<String, Boolean>();
- if ( phylogeny.isEmpty() ) {
- return ht;
- }
- for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode current_node = iter.next();
- if ( current_node.getNodeData().isHasProperties() ) {
- final String[] tags = current_node.getNodeData().getProperties().getPropertyRefs();
- for( int i = 0; i < tags.length; ++i ) {
- ht.put( tags[ i ], new Boolean( false ) );
- }
- }
- }
- return ht;
- }
-
final public static void increaseCountingMap( final Map<String, Integer> counting_map, final String item_name ) {
if ( !counting_map.containsKey( item_name ) ) {
counting_map.put( item_name, 1 );
}
}
- final static public boolean isAllNonEmptyInternalLabelsArePositiveNumbers( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isRoot() && !n.isExternal() ) {
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- double d = -1.0;
- try {
- d = Double.parseDouble( n.getName() );
- }
- catch ( final Exception e ) {
- d = -1.0;
- }
- if ( d < 0.0 ) {
- return false;
- }
- }
+ 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;
+ }
+ for( final Object o : l ) {
+ if ( o != null ) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ final public static boolean isEmpty( final Set<?> s ) {
+ if ( ( s == null ) || s.isEmpty() ) {
+ return true;
+ }
+ for( final Object o : s ) {
+ if ( o != null ) {
+ return false;
}
}
return true;
}
final public static boolean isEven( final int n ) {
- return n % 2 == 0;
- }
-
- final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getNodeData().isHasEvent() ) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Returns true if at least one branch has a length larger than zero.
- *
- *
- * @param phy
- */
- final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getDistanceToParent() > 0.0 ) {
- return true;
- }
- }
- return false;
- }
-
- final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getBranchData().isHasConfidences() ) {
- return true;
- }
- }
- return false;
+ return ( n % 2 ) == 0;
}
/**
if ( ( a.length < 1 ) || ( b.length < 1 ) ) {
return false;
}
- for( int i = 0; i < a.length; ++i ) {
- final String ai = a[ i ];
- for( int j = 0; j < b.length; ++j ) {
- if ( ( ai != null ) && ( b[ j ] != null ) && ai.equals( b[ j ] ) ) {
+ for( final String ai : a ) {
+ for( final String element : b ) {
+ if ( ( ai != null ) && ( element != null ) && ai.equals( element ) ) {
return true;
}
}
return map;
}
+ final public static void map2file( final File file,
+ final Map<?, ?> data,
+ final String entry_separator,
+ final String data_separator ) throws IOException {
+ final Writer writer = new BufferedWriter( new FileWriter( file ) );
+ map2writer( writer, data, entry_separator, data_separator );
+ writer.close();
+ }
+
+ final public static void map2writer( final Writer writer,
+ final Map<?, ?> data,
+ final String entry_separator,
+ final String data_separator ) throws IOException {
+ boolean first = true;
+ for( final Entry<?, ?> entry : data.entrySet() ) {
+ if ( !first ) {
+ writer.write( data_separator );
+ }
+ else {
+ first = false;
+ }
+ writer.write( entry.getKey().toString() );
+ writer.write( entry_separator );
+ writer.write( entry.getValue().toString() );
+ }
+ }
+
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(); ) {
return Integer.parseInt( str );
}
- final public static void postOrderRelabelInternalNodes( final Phylogeny phylogeny, final int starting_number ) {
- int i = starting_number;
- for( final PhylogenyNodeIterator it = phylogeny.iteratorPostorder(); it.hasNext(); ) {
- final PhylogenyNode node = it.next();
- if ( !node.isExternal() ) {
- node.setName( String.valueOf( i++ ) );
- }
- }
- }
-
final public static void printArray( final Object[] a ) {
for( int i = 0; i < a.length; ++i ) {
System.out.println( "[" + i + "]=" + a[ i ] );
}
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 ) {
}
final public static void printProgramInformation( final String prg_name,
+ final String desc,
final String prg_version,
final String date,
final String email,
- final String www ) {
- final int l = prg_name.length() + prg_version.length() + date.length() + 4;
+ final String www,
+ final String based_on ) {
+ String my_prg_name = new String( prg_name );
+ if ( !ForesterUtil.isEmpty( desc ) ) {
+ my_prg_name += ( " - " + desc );
+ }
+ final int l = my_prg_name.length() + prg_version.length() + date.length() + 4;
System.out.println();
- System.out.println( prg_name + " " + prg_version + " (" + date + ")" );
+ System.out.println( my_prg_name + " " + prg_version + " (" + date + ")" );
for( int i = 0; i < l; ++i ) {
System.out.print( "_" );
}
System.out.println();
System.out.println();
- System.out.println( "WWW : " + www );
- System.out.println( "Contact: " + email );
+ System.out.println( "WWW : " + www );
+ System.out.println( "Contact : " + email );
+ if ( !ForesterUtil.isEmpty( based_on ) ) {
+ System.out.println( "Based on: " + based_on );
+ }
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();
}
+ 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 public static String removeWhiteSpace( String s ) {
int i;
- for( i = 0; i <= s.length() - 1; i++ ) {
+ for( i = 0; i <= ( s.length() - 1 ); i++ ) {
if ( ( s.charAt( i ) == ' ' ) || ( s.charAt( i ) == '\t' ) || ( s.charAt( i ) == '\n' )
|| ( s.charAt( i ) == '\r' ) ) {
s = s.substring( 0, i ) + s.substring( i + 1 );
return s;
}
- final public static boolean isContainsParanthesesableNhCharacter( final String nh ) {
- return PARANTHESESABLE_NH_CHARS_PATTERN.matcher( nh ).find();
- }
-
final public static String replaceIllegalNhCharacters( final String nh ) {
if ( nh == null ) {
return "";
return ( int ) ( f + 0.5f );
}
+ final public static short roundToShort( final double d ) {
+ return ( short ) ( d + 0.5 );
+ }
+
final public static String sanitizeString( final String s ) {
if ( s == null ) {
return "";
}
final public static String stringArrayToString( final String[] a ) {
- final StringBuffer sb = new StringBuffer();
+ return stringArrayToString( a, ", " );
+ }
+
+ final public static String stringArrayToString( final String[] a, final String separator ) {
+ final StringBuilder sb = new StringBuilder();
if ( ( a != null ) && ( a.length > 0 ) ) {
- for( int i = 0; i < a.length - 1; ++i ) {
- sb.append( a[ i ] + ", " );
+ for( int i = 0; i < ( a.length - 1 ); ++i ) {
+ sb.append( a[ i ] + separator );
}
sb.append( a[ a.length - 1 ] );
}
return sb.toString();
}
- final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
- double value = -1;
- try {
- value = Double.parseDouble( n.getName() );
- }
- catch ( final NumberFormatException e ) {
- throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
- + e.getLocalizedMessage() );
- }
- if ( value >= 0.0 ) {
- n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
- n.setName( "" );
- }
+ final public static String[] stringListToArray( final List<String> list ) {
+ if ( list != null ) {
+ final String[] str = new String[ list.size() ];
+ int i = 0;
+ for( final String l : list ) {
+ str[ i++ ] = l;
}
+ return str;
}
+ return null;
}
- final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isRoot() && !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- double d = -1.0;
- try {
- d = Double.parseDouble( n.getName() );
- }
- catch ( final Exception e ) {
- d = -1.0;
- }
- if ( d >= 0.0 ) {
- n.getBranchData().addConfidence( new Confidence( d, "" ) );
- n.setName( "" );
- }
- }
+ final public static String stringListToString( final List<String> l, final String separator ) {
+ final StringBuilder sb = new StringBuilder();
+ if ( ( l != null ) && ( l.size() > 0 ) ) {
+ for( int i = 0; i < ( l.size() - 1 ); ++i ) {
+ sb.append( l.get( i ) + separator );
}
+ sb.append( l.get( l.size() - 1 ) );
}
+ return sb.toString();
}
- final static public void transferNodeNameToField( final Phylogeny phy, final PhylogenyNodeField field ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- final String name = n.getName().trim();
- if ( !ForesterUtil.isEmpty( name ) ) {
- switch ( field ) {
- case TAXONOMY_CODE:
- //temp hack
- // if ( name.length() > 5 ) {
- // n.setName( "" );
- // if ( !n.getNodeData().isHasTaxonomy() ) {
- // n.getNodeData().setTaxonomy( new Taxonomy() );
- // }
- // n.getNodeData().getTaxonomy().setScientificName( name );
- // break;
- // }
- //
- n.setName( "" );
- PhylogenyMethods.setTaxonomyCode( n, name );
- break;
- case TAXONOMY_SCIENTIFIC_NAME:
- n.setName( "" );
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- n.getNodeData().getTaxonomy().setScientificName( name );
- break;
- case TAXONOMY_COMMON_NAME:
- n.setName( "" );
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- n.getNodeData().getTaxonomy().setCommonName( name );
- break;
- case SEQUENCE_SYMBOL:
- n.setName( "" );
- if ( !n.getNodeData().isHasSequence() ) {
- n.getNodeData().setSequence( new Sequence() );
- }
- n.getNodeData().getSequence().setSymbol( name );
- break;
- case SEQUENCE_NAME:
- n.setName( "" );
- if ( !n.getNodeData().isHasSequence() ) {
- n.getNodeData().setSequence( new Sequence() );
- }
- n.getNodeData().getSequence().setName( name );
- break;
- case TAXONOMY_ID_UNIPROT_1: {
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- String id = name;
- final int i = name.indexOf( '_' );
- if ( i > 0 ) {
- id = name.substring( i, name.length() );
- }
- else {
- n.setName( "" );
- }
- n.getNodeData().getTaxonomy()
- .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
- break;
- }
- case TAXONOMY_ID_UNIPROT_2: {
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- String id = name;
- final int i = name.indexOf( '_' );
- if ( i > 0 ) {
- id = name.substring( 0, i );
- }
- else {
- n.setName( "" );
- }
- n.getNodeData().getTaxonomy()
- .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
- break;
- }
- }
- }
+ final public static String[] stringSetToArray( final Set<String> strings ) {
+ final String[] str_array = new String[ strings.size() ];
+ int i = 0;
+ for( final String e : strings ) {
+ str_array[ i++ ] = e;
}
+ return str_array;
}
final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
ls = -1;
start = i + 1;
}
- if ( i > start + width - 1 ) {
+ if ( i > ( ( start + width ) - 1 ) ) {
if ( ls != -1 ) {
sb.setCharAt( ls, '\n' );
start = ls + 1;
}
return sb.toString();
}
-
- public static enum PhylogenyNodeField {
- CLADE_NAME,
- TAXONOMY_CODE,
- TAXONOMY_SCIENTIFIC_NAME,
- TAXONOMY_COMMON_NAME,
- SEQUENCE_SYMBOL,
- SEQUENCE_NAME,
- TAXONOMY_ID_UNIPROT_1,
- TAXONOMY_ID_UNIPROT_2;
- }
-
- public static enum TAXONOMY_EXTRACTION {
- NO, YES, PFAM_STYLE_ONLY;
- }
}
git://source.jalview.org / jalview.git / blobdiff