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

   1 // Exp $
   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: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.archaeopteryx.tools;
  27
  28 import java.net.UnknownHostException;
  29
  30 import javax.swing.JOptionPane;
  31
  32 import org.forester.analysis.AncestralTaxonomyInference;
  33 import org.forester.analysis.AncestralTaxonomyInferenceException;
  34 import org.forester.archaeopteryx.MainFrameApplication;
  35 import org.forester.archaeopteryx.TreePanel;
  36 import org.forester.phylogeny.Phylogeny;
  37 import org.forester.ws.seqdb.SequenceDbWsTools;
  38
  39 public class AncestralTaxonomyInferrer extends RunnableProcess {
  40
  41     private final Phylogeny            _phy;
  42     private final MainFrameApplication _mf;
  43     private final TreePanel            _treepanel;
  44
  45     public AncestralTaxonomyInferrer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
  46         _phy = phy;
  47         _mf = mf;
  48         _treepanel = treepanel;
  49     }
  50
  51     public static String getBaseUrl() {
  52         return SequenceDbWsTools.BASE_UNIPROT_URL;
  53     }
  54
  55     private void inferTaxonomies() {
  56         start( _mf, "ancestral taxonomy" );
  57         try {
  58             AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
  59         }
  60         catch ( final AncestralTaxonomyInferenceException e ) {
  61             end( _mf );
  62             JOptionPane.showMessageDialog( _mf,
  63                                            e.getMessage(),
  64                                            "Error during ancestral taxonomy inference",
  65                                            JOptionPane.ERROR_MESSAGE );
  66             return;
  67         }
  68         catch ( final UnknownHostException e ) {
  69             end( _mf );
  70             JOptionPane.showMessageDialog( _mf,
  71                                            "Could not connect to \"" + getBaseUrl() + "\"",
  72                                            "Network error during ancestral taxonomy inference",
  73                                            JOptionPane.ERROR_MESSAGE );
  74             return;
  75         }
  76         catch ( final Exception e ) {
  77             end( _mf );
  78             e.printStackTrace();
  79             JOptionPane.showMessageDialog( _mf,
  80                                            e.toString(),
  81                                            "Unexpected exception during ancestral taxonomy inference",
  82                                            JOptionPane.ERROR_MESSAGE );
  83             return;
  84         }
  85         catch ( final Error e ) {
  86             end( _mf );
  87             JOptionPane.showMessageDialog( _mf,
  88                                            e.toString(),
  89                                            "Unexpected error during ancestral taxonomy inference",
  90                                            JOptionPane.ERROR_MESSAGE );
  91             return;
  92         }
  93         _phy.setRerootable( false );
  94         _treepanel.setTree( _phy );
  95         _mf.showWhole();
  96         _treepanel.setEdited( true );
  97         end( _mf );
  98         try {
  99             JOptionPane.showMessageDialog( _mf,
 100                                            "Ancestral taxonomy inference successfully completed",
 101                                            "Ancestral Taxonomy Inference Completed",
 102                                            JOptionPane.INFORMATION_MESSAGE );
 103         }
 104         catch ( final Exception e ) {
 105             // Not important if this fails, do nothing.
 106         }
 107     }
 108
 109     @Override
 110     public void run() {
 111         inferTaxonomies();
 112     }
 113 }