From: cmzmasek@gmail.com Date: Thu, 21 Nov 2013 03:09:13 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1d144f35479f96cb36c5247d9711e22ed234651a;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/application/subtree_feature_count.java b/forester/java/src/org/forester/application/subtree_feature_count.java deleted file mode 100644 index da23024..0000000 --- a/forester/java/src/org/forester/application/subtree_feature_count.java +++ /dev/null @@ -1,161 +0,0 @@ - -package org.forester.application; - -import java.io.File; -import java.util.ArrayList; -import java.util.List; -import java.util.SortedSet; - -import org.forester.io.parsers.phyloxml.PhyloXmlParser; -import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.data.Accession; -import org.forester.phylogeny.data.Sequence; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.phylogeny.iterators.PhylogenyNodeIterator; -import org.forester.util.CommandLineArguments; -import org.forester.util.ForesterUtil; - -public class subtree_feature_count { - - final static private String DEPTH_OPTION = "d"; - final static private String E_MAIL = "phylosoft@gmail.com"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String PRG_DATE = "131120"; - final static private String PRG_DESC = ""; - final static private String PRG_NAME = "subtree_feature_count"; - final static private String PRG_VERSION = "0.90"; - final static private String WWW = "sites.google.com/site/cmzmasek/home/software/forester"; - - public static void main( final String args[] ) { - try { - final CommandLineArguments cla = new CommandLineArguments( args ); - if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length < 2 ) ) { - printHelp(); - System.exit( 0 ); - } - final List allowed_options = new ArrayList(); - allowed_options.add( DEPTH_OPTION ); - final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); - if ( dissallowed_options.length() > 0 ) { - ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); - } - final double depth = cla.getOptionValueAsDouble( DEPTH_OPTION ); - final File intree_file = cla.getFile( 0 ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny phy = factory.create( intree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ]; - execute( phy, depth ); - } - catch ( final Exception e ) { - e.printStackTrace(); - ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); - } - } - - private static StringBuilder analyzeSubtree( final PhylogenyNode n, final double depth ) { - final PhylogenyNode node = moveUp( n, depth ); - final List ext_descs = node.getAllExternalDescendants(); - for( final PhylogenyNode ext : ext_descs ) { - if ( ext.getIndicator() != 0 ) { - throw new RuntimeException( "this should not have happened" ); - } - ext.setIndicator( ( byte ) 1 ); - } - int xray = 0; - int nmr = 0; - int model = 0; - boolean is_first = true; - PhylogenyNode first_node = null; - PhylogenyNode last_node = null; - int c = 0; - for( final PhylogenyNode ext : ext_descs ) { - if ( is_first ) { - first_node = ext; - is_first = false; - } - last_node = ext; - ++c; - if ( ext.getNodeData().isHasSequence() ) { - final Sequence seq = ext.getNodeData().getSequence(); - final SortedSet xrefs = seq.getCrossReferences(); - if ( !ForesterUtil.isEmpty( xrefs ) ) { - for( final Accession xref : xrefs ) { - if ( xref.getSource().equalsIgnoreCase( "pdb" ) ) { - if ( xref.getComment().equalsIgnoreCase( "x-ray" ) - || xref.getComment().equalsIgnoreCase( "xray" ) ) { - ++xray; - } - if ( xref.getComment().equalsIgnoreCase( "nmr" ) ) { - ++nmr; - } - if ( xref.getComment().equalsIgnoreCase( "model" ) ) { - ++model; - } - } - } - } - } - } - final StringBuilder sb = new StringBuilder(); - sb.append( String.valueOf( c ) ); - sb.append( "\t" ); - sb.append( first_node.getName() ); - sb.append( "\t" ); - sb.append( last_node.getName() ); - sb.append( "\t" ); - sb.append( String.valueOf( xray ) ); - sb.append( "\t" ); - sb.append( String.valueOf( nmr ) ); - sb.append( "\t" ); - sb.append( String.valueOf( model ) ); - return sb; - } - - private static void execute( final Phylogeny phy, final double depth ) { - setAllIndicatorsToZero( phy ); - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( n.getIndicator() != 0 ) { - continue; - } - final StringBuilder s = analyzeSubtree( n, depth ); - System.out.println( s.toString() ); - } - } - - private static PhylogenyNode moveUp( final PhylogenyNode node, final double depth ) { - PhylogenyNode n = node; - PhylogenyNode prev = node; - while ( depth < n.calculateDistanceToRoot() ) { - prev = n; - n = n.getParent(); - } - return prev; - } - - private static void printHelp() { - ForesterUtil.printProgramInformation( PRG_NAME, - PRG_DESC, - PRG_VERSION, - PRG_DATE, - E_MAIL, - WWW, - ForesterUtil.getForesterLibraryInformation() ); - System.out.println( "Usage:" ); - System.out.println(); - System.out.println( PRG_NAME + "" ); - System.out.println(); - System.out.println( " example: " ); - System.out.println(); - System.out.println(); - System.out.println(); - } - - private static void setAllIndicatorsToZero( final Phylogeny phy ) { - for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) { - it.next().setIndicator( ( byte ) 0 ); - } - } -} diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index b644e9e..6086534 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -410,6 +410,26 @@ public class PhylogenyMethods { phy.externalNodesHaveChanged(); } + public final static List> divideIntoSubTrees( final Phylogeny phy, + final double min_distance_to_root ) { + if ( min_distance_to_root <= 0 ) { + throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root ); + } + final List> l = new ArrayList>(); + setAllIndicatorsToZero( phy ); + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( n.getIndicator() != 0 ) { + continue; + } + l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) ); + if ( l.isEmpty() ) { + throw new RuntimeException( "this should not have happened" ); + } + } + return l; + } + public static List getAllDescendants( final PhylogenyNode node ) { final List descs = new ArrayList(); final Set encountered = new HashSet(); @@ -1141,6 +1161,12 @@ public class PhylogenyMethods { return nodes; } + public static void setAllIndicatorsToZero( final Phylogeny phy ) { + for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) { + it.next().setIndicator( ( byte ) 0 ); + } + } + /** * Convenience method. * Sets value for the first confidence value (created if not present, values overwritten otherwise). @@ -1632,6 +1658,20 @@ public class PhylogenyMethods { } } + private final static List divideIntoSubTreesHelper( final PhylogenyNode node, + final double min_distance_to_root ) { + final List l = new ArrayList(); + final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root ); + for( final PhylogenyNode ext : r.getAllExternalDescendants() ) { + if ( ext.getIndicator() != 0 ) { + throw new RuntimeException( "this should not have happened" ); + } + ext.setIndicator( ( byte ) 1 ); + l.add( ext ); + } + return l; + } + /** * Calculates the distance between PhylogenyNodes n1 and n2. * PRECONDITION: n1 is a descendant of n2. @@ -1673,19 +1713,29 @@ public class PhylogenyMethods { } } + private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) { + PhylogenyNode n = node; + PhylogenyNode prev = node; + while ( min_distance_to_root < n.calculateDistanceToRoot() ) { + prev = n; + n = n.getParent(); + } + return prev; + } + public static enum DESCENDANT_SORT_PRIORITY { - TAXONOMY, SEQUENCE, NODE_NAME; + NODE_NAME, SEQUENCE, TAXONOMY; } public static enum PhylogenyNodeField { CLADE_NAME, + SEQUENCE_NAME, + SEQUENCE_SYMBOL, TAXONOMY_CODE, - TAXONOMY_SCIENTIFIC_NAME, TAXONOMY_COMMON_NAME, - SEQUENCE_SYMBOL, - SEQUENCE_NAME, + TAXONOMY_ID, TAXONOMY_ID_UNIPROT_1, TAXONOMY_ID_UNIPROT_2, - TAXONOMY_ID; + TAXONOMY_SCIENTIFIC_NAME; } }