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