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.analysis.AncestralTaxonomyInferenceException;
  34 import org.forester.archaeopteryx.Constants;
  35 import org.forester.archaeopteryx.MainFrameApplication;
  36 import org.forester.archaeopteryx.TreePanel;
  37 import org.forester.phylogeny.Phylogeny;
  38 import org.forester.util.ForesterUtil;
  39 import org.forester.ws.uniprot.UniProtWsTools;
  40
  41 public class AncestralTaxonomyInferrer implements Runnable {
  42
  43     private final Phylogeny            _phy;
  44     private final MainFrameApplication _mf;
  45     private final TreePanel            _treepanel;
  46     private long                       _process_id;
  47
  48     private long getProcessId() {
  49         return _process_id;
  50     }
  51
  52     private void setProcessId( final long process_id ) {
  53         _process_id = process_id;
  54     }
  55
  56     public AncestralTaxonomyInferrer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
  57         _phy = phy;
  58         _mf = mf;
  59         _treepanel = treepanel;
  60     }
  61
  62     private String getBaseUrl() {
  63         return UniProtWsTools.BASE_URL;
  64     }
  65
  66     private void start() {
  67         _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
  68         setProcessId( _mf.getProcessPool().addProcess( "ancestral taxonomy" ) );
  69     }
  70
  71     private void end() {
  72         final boolean removed = _mf.getProcessPool().removeProcess( getProcessId() );
  73         if ( !removed ) {
  74             ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not remove process " + getProcessId()
  75                     + " from process pool" );
  76         }
  77         _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
  78     }
  79
  80     private void inferTaxonomies() {
  81         start();
  82         try {
  83             AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
  84         }
  85         catch ( final AncestralTaxonomyInferenceException e ) {
  86             end();
  87             JOptionPane.showMessageDialog( _mf,
  88                                            e.getMessage(),
  89                                            "Error during ancestral taxonomy inference",
  90                                            JOptionPane.ERROR_MESSAGE );
  91             return;
  92         }
  93         catch ( final UnknownHostException e ) {
  94             end();
  95             JOptionPane.showMessageDialog( _mf,
  96                                            "Could not connect to \"" + getBaseUrl() + "\"",
  97                                            "Network error during ancestral taxonomy inference",
  98                                            JOptionPane.ERROR_MESSAGE );
  99             return;
 100         }
 101         catch ( final Exception e ) {
 102             end();
 103             e.printStackTrace();
 104             JOptionPane.showMessageDialog( _mf,
 105                                            e.toString(),
 106                                            "Unexpected exception during ancestral taxonomy inference",
 107                                            JOptionPane.ERROR_MESSAGE );
 108             return;
 109         }
 110         catch ( final Error e ) {
 111             end();
 112             e.printStackTrace();
 113             JOptionPane.showMessageDialog( _mf,
 114                                            e.toString(),
 115                                            "Unexpected error during ancestral taxonomy inference",
 116                                            JOptionPane.ERROR_MESSAGE );
 117             return;
 118         }
 119         _phy.setRerootable( false );
 120         _treepanel.setTree( _phy );
 121         _mf.showWhole();
 122         _treepanel.setEdited( true );
 123         end();
 124         try {
 125             JOptionPane.showMessageDialog( _mf,
 126                                            "Ancestral taxonomy inference successfully completed",
 127                                            "Ancestral Taxonomy Inference Completed",
 128                                            JOptionPane.INFORMATION_MESSAGE );
 129         }
 130         catch ( final Exception e ) {
 131             // Not important if this fails, do nothing.
 132         }
 133     }
 134
 135     @Override
 136     public void run() {
 137         inferTaxonomies();
 138     }
 139 }