forester/java/src/org/forester/application/subtree_feature_count.java

   1
   2 package org.forester.application;
   3
   4 import java.io.File;
   5 import java.util.ArrayList;
   6 import java.util.List;
   7 import java.util.SortedSet;
   8
   9 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  10 import org.forester.phylogeny.Phylogeny;
  11 import org.forester.phylogeny.PhylogenyNode;
  12 import org.forester.phylogeny.data.Accession;
  13 import org.forester.phylogeny.data.Sequence;
  14 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  15 import org.forester.phylogeny.factories.PhylogenyFactory;
  16 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  17 import org.forester.util.CommandLineArguments;
  18 import org.forester.util.ForesterUtil;
  19
  20 public class subtree_feature_count {
  21
  22     final static private String DEPTH_OPTION  = "d";
  23     final static private String E_MAIL        = "phylosoft@gmail.com";
  24     final static private String HELP_OPTION_1 = "help";
  25     final static private String HELP_OPTION_2 = "h";
  26     final static private String PRG_DATE      = "131120";
  27     final static private String PRG_DESC      = "";
  28     final static private String PRG_NAME      = "subtree_feature_count";
  29     final static private String PRG_VERSION   = "0.90";
  30     final static private String WWW           = "sites.google.com/site/cmzmasek/home/software/forester";
  31
  32     public static void main( final String args[] ) {
  33         try {
  34             final CommandLineArguments cla = new CommandLineArguments( args );
  35             if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( cla.getNumberOfNames() != 3 ) ) {
  36                 printHelp();
  37                 System.exit( 0 );
  38             }
  39             final List<String> allowed_options = new ArrayList<String>();
  40             allowed_options.add( DEPTH_OPTION );
  41             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
  42             if ( dissallowed_options.length() > 0 ) {
  43                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
  44             }
  45             final double depth = cla.getOptionValueAsDouble( DEPTH_OPTION );
  46             final File intree_file = cla.getFile( 0 );
  47             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  48             final Phylogeny phy = factory.create( intree_file, new PhyloXmlParser() )[ 0 ];
  49             execute( phy, depth );
  50         }
  51         catch ( final Exception e ) {
  52             e.printStackTrace();
  53             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  54         }
  55     }
  56
  57     private static StringBuilder analyzeSubtree( final PhylogenyNode n, final double depth ) {
  58         final PhylogenyNode node = moveUp( n, depth );
  59         for( final PhylogenyNode ext : node.getAllExternalDescendants() ) {
  60             ext.setIndicator( ( byte ) 1 );
  61         }
  62         int xray = 0;
  63         int nmr = 0;
  64         int model = 0;
  65         boolean is_first = true;
  66         PhylogenyNode first_node = null;
  67         PhylogenyNode last_node = null;
  68         int c = 0;
  69         for( final PhylogenyNode ext : node.getAllExternalDescendants() ) {
  70             if ( is_first ) {
  71                 first_node = ext;
  72                 is_first = false;
  73             }
  74             last_node = ext;
  75             ++c;
  76             if ( ext.getNodeData().isHasSequence() ) {
  77                 final Sequence seq = ext.getNodeData().getSequence();
  78                 final SortedSet<Accession> xrefs = seq.getCrossReferences();
  79                 if ( !ForesterUtil.isEmpty( xrefs ) ) {
  80                     for( final Accession xref : xrefs ) {
  81                         if ( xref.getSource().equalsIgnoreCase( "pdb" ) ) {
  82                             if ( xref.getComment().equalsIgnoreCase( "x-ray" )
  83                                     || xref.getComment().equalsIgnoreCase( "xray" ) ) {
  84                                 ++xray;
  85                             }
  86                             if ( xref.getComment().equalsIgnoreCase( "nmr" ) ) {
  87                                 ++nmr;
  88                             }
  89                             if ( xref.getComment().equalsIgnoreCase( "model" ) ) {
  90                                 ++model;
  91                             }
  92                         }
  93                     }
  94                 }
  95             }
  96         }
  97         final StringBuilder sb = new StringBuilder();
  98         sb.append( String.valueOf( c ) );
  99         sb.append( "\t" );
 100         sb.append( first_node.getName() );
 101         sb.append( "\t" );
 102         sb.append( last_node.getName() );
 103         sb.append( "\t" );
 104         sb.append( String.valueOf( xray ) );
 105         sb.append( "\t" );
 106         sb.append( String.valueOf( nmr ) );
 107         sb.append( "\t" );
 108         sb.append( String.valueOf( model ) );
 109         return sb;
 110     }
 111
 112     private static void execute( final Phylogeny phy, final double depth ) {
 113         setAllIndicatorsToZero( phy );
 114         for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
 115             final PhylogenyNode n = it.next();
 116             if ( n.getIndicator() != 0 ) {
 117                 continue;
 118             }
 119             final StringBuilder s = analyzeSubtree( n, depth );
 120             System.out.println( s.toString() );
 121         }
 122     }
 123
 124     private static PhylogenyNode moveUp( final PhylogenyNode node, final double depth ) {
 125         PhylogenyNode n = node;
 126         double current_depth = 0.0;
 127         while ( current_depth < depth ) {
 128             current_depth += n.getDistanceToParent();
 129             if ( n.getParent() == null ) {
 130                 throw new IllegalArgumentException( "Depth " + depth + " is too large" );
 131             }
 132             n = n.getParent();
 133         }
 134         return n;
 135     }
 136
 137     private static void printHelp() {
 138         ForesterUtil.printProgramInformation( PRG_NAME,
 139                                               PRG_DESC,
 140                                               PRG_VERSION,
 141                                               PRG_DATE,
 142                                               E_MAIL,
 143                                               WWW,
 144                                               ForesterUtil.getForesterLibraryInformation() );
 145         System.out.println( "Usage:" );
 146         System.out.println();
 147         System.out.println( PRG_NAME + "" );
 148         System.out.println();
 149         System.out.println( " exmple: " );
 150         System.out.println();
 151         System.out
 152                 .println( "dom_dup \"HUMAN~[12]-2\" groups.txt RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_gsdi.phylo.xml" );
 153         System.out.println();
 154         System.out.println();
 155     }
 156
 157     private static void setAllIndicatorsToZero( final Phylogeny phy ) {
 158         for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
 159             it.next().setIndicator( ( byte ) 0 );
 160         }
 161     }
 162 }