From: cmzmasek@gmail.com Date: Wed, 12 Oct 2011 19:57:29 +0000 (+0000) Subject: moved classes into different project X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e4dd63c7d7ee80a0e3092a49b804381bbed3b708;p=jalview.git moved classes into different project --- diff --git a/forester/java/src/org/forester/application/get_subtree_specific_chars.java b/forester/java/src/org/forester/application/get_subtree_specific_chars.java deleted file mode 100644 index e0d754f..0000000 --- a/forester/java/src/org/forester/application/get_subtree_specific_chars.java +++ /dev/null @@ -1,148 +0,0 @@ -// $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 " ); - 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 all_external_ids = getAllExternalDescendantsNodeIds( phy.getRoot() ); - final SortedSet 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 external_ids = getAllExternalDescendantsNodeIds( node ); - final SortedSet not_external_ids = copy( all_external_ids ); - not_external_ids.removeAll( external_ids ); - final SortedSet not_node_chars = new TreeSet(); - for( final Integer id : not_external_ids ) { - not_node_chars.addAll( getAllExternalPresentAndGainedCharacters( phy.getNode( id ) ) ); - } - final SortedSet node_chars = getAllExternalPresentAndGainedCharacters( node ); - final SortedSet unique_chars = new TreeSet(); - 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 copy( final SortedSet set ) { - final SortedSet copy = new TreeSet(); - for( final Integer i : set ) { - copy.add( i ); - } - return copy; - } - - private static SortedSet getAllExternalDescendantsNodeIds( final PhylogenyNode node ) { - final SortedSet ids = new TreeSet(); - final List descs = node.getAllExternalDescendants(); - for( final PhylogenyNode desc : descs ) { - ids.add( desc.getId() ); - } - return ids; - } - - private static SortedSet getAllExternalPresentAndGainedCharacters( final PhylogenyNode node ) { - final SortedSet chars = new TreeSet(); - final List descs = node.getAllExternalDescendants(); - for( final PhylogenyNode desc : descs ) { - chars.addAll( desc.getNodeData().getBinaryCharacters().getGainedCharacters() ); - chars.addAll( desc.getNodeData().getBinaryCharacters().getPresentCharacters() ); - } - return chars; - } -} diff --git a/forester/java/src/org/forester/application/map_lengths.java b/forester/java/src/org/forester/application/map_lengths.java deleted file mode 100644 index 70bde38..0000000 --- a/forester/java/src/org/forester/application/map_lengths.java +++ /dev/null @@ -1,88 +0,0 @@ -// $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 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(); - } - } -} diff --git a/forester/java/src/org/forester/application/simple_node_processor.java b/forester/java/src/org/forester/application/simple_node_processor.java deleted file mode 100644 index a190edf..0000000 --- a/forester/java/src/org/forester/application/simple_node_processor.java +++ /dev/null @@ -1,90 +0,0 @@ -// $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 ); - } - } -}