+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2011 Christian M. Zmasek
-// Copyright (C) 2008-2011 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.application;
-
-import java.io.File;
-import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.ForesterUtil;
-
-public class get_subtree_specific_chars {
-
- final static boolean SIMPLE = false;
-
- public static void main( final String args[] ) {
- if ( args.length != 1 ) {
- System.err.println();
- System.err.println( "get_subtree_specific_chars: wrong number of arguments" );
- System.err.println( "Usage: \"get_subtree_specific_chars <intree>" );
- System.err.println();
- System.exit( -1 );
- }
- final File infile = new File( args[ 0 ] );
- Phylogeny phy = null;
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- phy = factory.create( infile, ForesterUtil.createParserDependingOnFileType( infile, true ) )[ 0 ];
- }
- catch ( final Exception e ) {
- System.err.println( e + "\nCould not read " + infile + "\n" );
- System.exit( -1 );
- }
- final SortedSet<Integer> all_external_ids = getAllExternalDescendantsNodeIds( phy.getRoot() );
- final SortedSet<String> all_chars = getAllExternalPresentAndGainedCharacters( phy.getRoot() );
- System.out.println( "Sum of all external characters:\t" + all_chars.size() );
- System.out.println();
- for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( !SIMPLE && node.isExternal() ) {
- continue;
- }
- if ( !node.isRoot() ) {
- System.out.println();
- if ( node.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
- System.out.print( node.getName() + " " + node.getNodeData().getTaxonomy().getScientificName() );
- }
- else {
- System.out.print( node.getName() );
- }
- System.out.println( ":" );
- final SortedSet<Integer> external_ids = getAllExternalDescendantsNodeIds( node );
- final SortedSet<Integer> not_external_ids = copy( all_external_ids );
- not_external_ids.removeAll( external_ids );
- final SortedSet<String> not_node_chars = new TreeSet<String>();
- for( final Integer id : not_external_ids ) {
- not_node_chars.addAll( getAllExternalPresentAndGainedCharacters( phy.getNode( id ) ) );
- }
- final SortedSet<String> node_chars = getAllExternalPresentAndGainedCharacters( node );
- final SortedSet<String> unique_chars = new TreeSet<String>();
- for( final String node_char : node_chars ) {
- if ( !not_node_chars.contains( node_char ) ) {
- if ( SIMPLE ) {
- unique_chars.add( node_char );
- }
- else {
- boolean found = true;
- for( final int external_id : external_ids ) {
- if ( !phy.getNode( external_id ).getNodeData().getBinaryCharacters()
- .getGainedCharacters().contains( node_char )
- && !phy.getNode( external_id ).getNodeData().getBinaryCharacters()
- .getPresentCharacters().contains( node_char ) ) {
- found = false;
- break;
- }
- }
- if ( found ) {
- unique_chars.add( node_char );
- }
- }
- }
- }
- System.out.println( "\tSUM:\t" + unique_chars.size() );
- int counter = 1;
- for( final String unique_char : unique_chars ) {
- System.out.println( "\t" + counter + ":\t" + unique_char );
- ++counter;
- }
- }
- }
- }
-
- private static SortedSet<Integer> copy( final SortedSet<Integer> set ) {
- final SortedSet<Integer> copy = new TreeSet<Integer>();
- for( final Integer i : set ) {
- copy.add( i );
- }
- return copy;
- }
-
- private static SortedSet<Integer> getAllExternalDescendantsNodeIds( final PhylogenyNode node ) {
- final SortedSet<Integer> ids = new TreeSet<Integer>();
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- for( final PhylogenyNode desc : descs ) {
- ids.add( desc.getId() );
- }
- return ids;
- }
-
- private static SortedSet<String> getAllExternalPresentAndGainedCharacters( final PhylogenyNode node ) {
- final SortedSet<String> chars = new TreeSet<String>();
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- for( final PhylogenyNode desc : descs ) {
- chars.addAll( desc.getNodeData().getBinaryCharacters().getGainedCharacters() );
- chars.addAll( desc.getNodeData().getBinaryCharacters().getPresentCharacters() );
- }
- return chars;
- }
-}
+++ /dev/null
-// $Id:
-//
-// forester -- software libraries and applications
-// for genomics and evolutionary biology research.
-//
-// Copyright (C) 2011 Christian M Zmasek
-// Copyright (C) 2011 Sanford-Burnham Medical Research Institute
-// 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.application;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-
-import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.io.parsers.FastaParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.PropertiesMap;
-import org.forester.phylogeny.data.Property;
-import org.forester.phylogeny.data.Property.AppliesTo;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.sequence.Sequence;
-import org.forester.util.CommandLineArguments;
-import org.forester.util.ForesterUtil;
-
-public class map_lengths {
-
- final static private String PRG_NAME = "map_lengths";
-
- public static void main( final String[] args ) {
- CommandLineArguments cla = null;
- try {
- cla = new CommandLineArguments( args );
- }
- catch ( final Exception e ) {
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
- }
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhyloXmlParser xml_parser = new PhyloXmlParser();
- final Phylogeny[] phylogenies_0 = factory.create( cla.getFile( 0 ), xml_parser );
- final Phylogeny phy = phylogenies_0[ 0 ];
- for( int i = 1; i < cla.getNumberOfNames(); i++ ) {
- final String fasta_name = cla.getName( i );
- final List<Sequence> seqs = FastaParser.parse( new File( fasta_name ) );
- for( int s = 0; s < seqs.size(); s++ ) {
- final Sequence seq = seqs.get( s );
- final int actual_length = seq.getLength() - seq.getNumberOfGapResidues();
- String node_name = "" + seq.getIdentifier();
- node_name = node_name.substring( 0, node_name.indexOf( "/" ) );
- final PhylogenyNode n = phy.getNode( node_name );
- if ( n.getNodeData().getProperties() == null ) {
- n.getNodeData().setProperties( new PropertiesMap() );
- }
- final PropertiesMap properties = n.getNodeData().getProperties();
- final Property p = new Property( "r:" + i, "" + actual_length, "", "xsd:integer", AppliesTo.NODE );
- properties.addProperty( p );
- }
- }
- Archaeopteryx.createApplication( phy );
- }
- catch ( final IOException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-}
+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org
-
-package org.forester.application;
-
-import java.io.File;
-
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.CommandLineArguments;
-
-public class simple_node_processor {
-
- private final static String BASE = "b_";
-
- public static void main( final String args[] ) {
- File in = null;
- final File out = null;
- try {
- CommandLineArguments cla = null;
- cla = new CommandLineArguments( args );
- in = cla.getFile( 0 );
- // out = cla.getFile( 1 );
- // if ( out.exists() ) {
- // System.out.println( out + " already exists" );
- // System.exit( -1 );
- // }
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhyloXmlParser xml_parser = new PhyloXmlParser();
- final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
- final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
- final PhylogenyNodeIterator it = phylogeny_0.iteratorPostorder();
- int i = 0;
- while ( it.hasNext() ) {
- final PhylogenyNode node = it.next();
- processNode( node, i );
- i++;
- }
- // final PhylogenyWriter writer = new PhylogenyWriter();
- // writer.toPhyloXML( out, phylogeny_0, 0 );
- }
- catch ( final Exception e ) {
- System.out.println( e.getLocalizedMessage() );
- e.printStackTrace();
- System.exit( -1 );
- }
- }
-
- // private static void processNode( final PhylogenyNode node, final int i ) {
- // node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
- // if ( !node.isExternal() ) {
- // if ( ( node.getName() == null ) || node.getName().isEmpty() ) {
- // node.setName( BASE + i );
- // }
- // }
- // }
- private static void processNode( final PhylogenyNode node, final int i ) {
- if ( node.isExternal() ) {
- final String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
- final String s = node.getNodeData().getTaxonomy().getScientificName();
- System.out.println( s + "\t" + c );
- }
- }
-}
git://source.jalview.org / jalview.git / commitdiff