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.MainFrame;
  35 import org.forester.archaeopteryx.MainFrameApplication;
  36 import org.forester.archaeopteryx.TreePanel;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.ws.seqdb.SequenceDbWsTools;
  39
  40 public class AncestralTaxonomyInferrer extends RunnableProcess {
  41
  42     private final Phylogeny            _phy;
  43     private final MainFrame _mf;
  44     private final TreePanel            _treepanel;
  45
  46     public AncestralTaxonomyInferrer( final MainFrame mf, final TreePanel treepanel, final Phylogeny phy ) {
  47         _phy = phy;
  48         _mf = mf;
  49         _treepanel = treepanel;
  50     }
  51
  52     public static String getBaseUrl() {
  53         return SequenceDbWsTools.BASE_UNIPROT_URL;
  54     }
  55
  56     private void inferTaxonomies() {
  57         start( _mf, "ancestral taxonomy" );
  58         try {
  59             AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
  60         }
  61         catch ( final AncestralTaxonomyInferenceException e ) {
  62             end( _mf );
  63             JOptionPane.showMessageDialog( _mf,
  64                                            e.getMessage(),
  65                                            "Error during ancestral taxonomy inference",
  66                                            JOptionPane.ERROR_MESSAGE );
  67             return;
  68         }
  69         catch ( final UnknownHostException e ) {
  70             end( _mf );
  71             JOptionPane.showMessageDialog( _mf,
  72                                            "Could not connect to \"" + getBaseUrl() + "\"",
  73                                            "Network error during ancestral taxonomy inference",
  74                                            JOptionPane.ERROR_MESSAGE );
  75             return;
  76         }
  77         catch ( final Exception e ) {
  78             end( _mf );
  79             e.printStackTrace();
  80             JOptionPane.showMessageDialog( _mf,
  81                                            e.toString(),
  82                                            "Unexpected exception during ancestral taxonomy inference",
  83                                            JOptionPane.ERROR_MESSAGE );
  84             return;
  85         }
  86         catch ( final Error e ) {
  87             end( _mf );
  88             JOptionPane.showMessageDialog( _mf,
  89                                            e.toString(),
  90                                            "Unexpected error during ancestral taxonomy inference",
  91                                            JOptionPane.ERROR_MESSAGE );
  92             return;
  93         }
  94         _phy.setRerootable( false );
  95         _treepanel.setTree( _phy );
  96         _mf.showWhole();
  97         _treepanel.setEdited( true );
  98         end( _mf );
  99         try {
 100             JOptionPane.showMessageDialog( _mf,
 101                                            "Ancestral taxonomy inference successfully completed",
 102                                            "Ancestral Taxonomy Inference Completed",
 103                                            JOptionPane.INFORMATION_MESSAGE );
 104         }
 105         catch ( final Exception e ) {
 106             // Not important if this fails, do nothing.
 107         }
 108     }
 109
 110     @Override
 111     public void run() {
 112         inferTaxonomies();
 113     }
 114 }