// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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.io.parsers.util.PhylogenyParserException;
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.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
public final class ForesterUtil {
}
}
- 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;
- }
-
/**
* 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,
return true;
}
+ 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 isEmpty( final String s ) {
return ( ( s == null ) || ( s.length() < 1 ) );
}
System.out.println( "[" + prg_name + "] > " + message );
}
+ public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] trees = factory.create( file, parser );
+ if ( ( trees == null ) || ( trees.length == 0 ) ) {
+ throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+ }
+ return trees;
+ }
+
final public static String removeSuffix( final String file_name ) {
final int i = file_name.lastIndexOf( '.' );
if ( 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 "";
return str.split( regex );
}
- final public static String stringArrayToString( final String[] a ) {
- final StringBuffer sb = new StringBuffer();
+ 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 ] + ", " );
+ sb.append( a[ i ] + separator );
}
sb.append( a[ a.length - 1 ] );
}
return sb.toString();
}
+ 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 public static String stringArrayToString( final String[] a ) {
+ return stringArrayToString( a, ", " );
+ }
+
+ 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 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 transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
}
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( 0, i );
+ }
+ 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( i + 1, name.length() );
+ }
+ else {
+ n.setName( "" );
+ }
+ n.getNodeData().getTaxonomy()
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+ break;
+ }
}
}
}
}
public static enum PhylogenyNodeField {
- CLADE_NAME, TAXONOMY_CODE, TAXONOMY_SCIENTIFIC_NAME, TAXONOMY_COMMON_NAME, SEQUENCE_SYMBOL, SEQUENCE_NAME;
+ 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 {
git://source.jalview.org / jalview.git / blobdiff