forester/java/src/org/forester/archaeopteryx/tools/GoAnnotation.java

   1 // $Id:
   2 // forester -- software libraries and applications
   3 // for genomics and evolutionary biology research.
   4 //
   5 // Copyright (C) 2010 Christian M Zmasek
   6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.archaeopteryx.tools;
  27
  28 import java.io.BufferedReader;
  29 import java.io.IOException;
  30 import java.io.InputStreamReader;
  31 import java.net.HttpURLConnection;
  32 import java.net.URL;
  33 import java.util.Arrays;
  34 import java.util.List;
  35
  36 import org.forester.archaeopteryx.MainFrameApplication;
  37 import org.forester.archaeopteryx.TreePanel;
  38 import org.forester.phylogeny.Phylogeny;
  39 import org.forester.phylogeny.PhylogenyNode;
  40 import org.forester.phylogeny.data.Accession;
  41 import org.forester.phylogeny.data.Annotation;
  42 import org.forester.phylogeny.data.Sequence;
  43 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  44 import org.forester.util.ForesterUtil;
  45
  46 public class GoAnnotation implements Runnable {
  47
  48     private static final String        SYMBOL   = "Symbol";
  49     private static final String        ASPECT   = "Aspect";
  50     private static final String        DB       = "DB";
  51     private static final String        EVIDENCE = "Evidence";
  52     private static final String        GO_NAME  = "GO Name";
  53     private static final String        GO_ID    = "GO ID";
  54     private final Phylogeny            _phy;
  55     private final MainFrameApplication _mf;
  56     private final TreePanel            _treepanel;
  57
  58     public GoAnnotation( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
  59         _phy = phy;
  60         _mf = mf;
  61         _treepanel = treepanel;
  62     }
  63
  64     private void annotate() {
  65         _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
  66         for( final PhylogenyNodeIterator iter = _phy.iteratorPostorder(); iter.hasNext(); ) {
  67             final PhylogenyNode node = iter.next();
  68             if ( ( node.getNodeData().getSequences() != null ) && !node.getNodeData().getSequences().isEmpty() ) {
  69                 for( final Sequence seq : node.getNodeData().getSequences() ) {
  70                     if ( ( ( seq.getAccession() != null ) && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) && ( seq
  71                             .getAnnotations() == null ) ) || seq.getAnnotations().isEmpty() ) {
  72                         final Accession acc = seq.getAccession();
  73                         try {
  74                             final URL url = new URL( "http://www.ebi.ac.uk/QuickGO/GAnnotation?protein="
  75                                     + acc.getValue() + "&format=tsv" );
  76                             final HttpURLConnection url_connection = ( HttpURLConnection ) url.openConnection();
  77                             final BufferedReader br = new BufferedReader( new InputStreamReader( url_connection.getInputStream() ) );
  78                             final List<String> columns = Arrays.asList( br.readLine().split( "\t" ) );
  79                             System.out.println( columns );
  80                             final int db_index = columns.indexOf( DB );
  81                             final int goid_index = columns.indexOf( GO_ID );
  82                             final int name_index = columns.indexOf( GO_NAME );
  83                             final int evidence_index = columns.indexOf( EVIDENCE );
  84                             final int taxon_index = columns.indexOf( "Taxon" );
  85                             final int qualifier_index = columns.indexOf( "Qualifier" );
  86                             final int reference_index = columns.indexOf( "Reference" );
  87                             final int symbol_index = columns.indexOf( SYMBOL );
  88                             final int splice_index = columns.indexOf( "Splice" );
  89                             final int with_index = columns.indexOf( "With" );
  90                             final int aspect_index = columns.indexOf( ASPECT );
  91                             final int source_index = columns.indexOf( "Source" );
  92                             String line;
  93                             while ( ( line = br.readLine() ) != null ) {
  94                                 final String[] fields = line.split( "\t" );
  95                                 final Annotation a = new Annotation( fields[ goid_index ] );
  96                                 a.setDesc( name_index >= 0 ? fields[ name_index ] : "" );
  97                                 a.setSource( db_index >= 0 ? fields[ db_index ] : "" );
  98                                 a.setEvidence( evidence_index >= 0 ? fields[ evidence_index ] : "" );
  99                                 a.setType( aspect_index >= 0 ? fields[ aspect_index ] : "" );
 100                                 seq.addAnnotation( a );
 101                                 if ( ForesterUtil.isEmpty( seq.getSymbol() ) && ( symbol_index >= 0 )
 102                                         && !ForesterUtil.isEmpty( fields[ symbol_index ] ) ) {
 103                                     seq.setSymbol( fields[ symbol_index ] );
 104                                 }
 105                                 System.out.println( DB + ": " + fields[ db_index ] );
 106                                 System.out.println( GO_ID + ": " + fields[ goid_index ] );
 107                                 System.out.println( GO_NAME + ": " + fields[ name_index ] );
 108                                 System.out.println( EVIDENCE + ": " + fields[ evidence_index ] );
 109                                 System.out.println( " taxon" + ": " + fields[ taxon_index ] );
 110                                 System.out.println( " qualifier" + ": " + fields[ qualifier_index ] );
 111                                 System.out.println( " reference" + ": " + fields[ reference_index ] );
 112                                 System.out.println( SYMBOL + ": " + fields[ symbol_index ] );
 113                                 System.out.println( " splice" + ": " + fields[ splice_index ] );
 114                                 System.out.println( " with" + ": " + fields[ with_index ] );
 115                                 System.out.println( ASPECT + ": " + fields[ aspect_index ] );
 116                                 System.out.println( " source" + ": " + fields[ source_index ] );
 117                             }
 118                             br.close();
 119                         }
 120                         catch ( final IOException e ) {
 121                             // TODO Auto-generated catch block
 122                             e.printStackTrace();
 123                         }
 124                     }
 125                 }
 126             }
 127         }
 128         _treepanel.repaint();
 129         _treepanel.setEdited( true );
 130     }
 131
 132     @Override
 133     public void run() {
 134         annotate();
 135     }
 136 }