new tool

diff --git a/forester/java/src/org/forester/application/subtree_feature_count.java b/forester/java/src/org/forester/application/subtree_feature_count.java
new file mode 100644 (file)
index 0000000..cde4cbb
--- /dev/null
+++ b/forester/java/src/org/forester/application/subtree_feature_count.java
@@ -0,0 +1,162 @@
+
+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 ) || ( cla.getNumberOfNames() != 3 ) ) {
+                printHelp();
+                System.exit( 0 );
+            }
+            final List<String> allowed_options = new ArrayList<String>();
+            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, new PhyloXmlParser() )[ 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 );
+        for( final PhylogenyNode ext : node.getAllExternalDescendants() ) {
+            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 : node.getAllExternalDescendants() ) {
+            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<Accession> 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;
+        double current_depth = 0.0;
+        while ( current_depth < depth ) {
+            current_depth += n.getDistanceToParent();
+            if ( n.getParent() == null ) {
+                throw new IllegalArgumentException( "Depth " + depth + " is too large" );
+            }
+            n = n.getParent();
+        }
+        return n;
+    }
+
+    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( " exmple: " );
+        System.out.println();
+        System.out
+                .println( "dom_dup \"HUMAN~[12]-2\" groups.txt RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_gsdi.phylo.xml" );
+        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 );
+        }
+    }
+}