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

   1 // $Id:
   2 //
   3 // forester -- software libraries and applications
   4 // for genomics and evolutionary biology research.
   5 //
   6 // Copyright (C) 2010 Christian M Zmasek
   7 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: www.phylosoft.org/forester
  26
  27 package org.forester.archaeopteryx.tools;
  28
  29 import java.io.IOException;
  30 import java.net.UnknownHostException;
  31 import java.util.SortedSet;
  32
  33 import javax.swing.JOptionPane;
  34
  35 import org.forester.analysis.AncestralTaxonomyInference;
  36 import org.forester.archaeopteryx.MainFrameApplication;
  37 import org.forester.archaeopteryx.TreePanel;
  38 import org.forester.phylogeny.Phylogeny;
  39 import org.forester.ws.uniprot.UniProtWsTools;
  40
  41 public class TaxonomyDataObtainer implements Runnable {
  42
  43     private final Phylogeny            _phy;
  44     private final MainFrameApplication _mf;
  45     private final TreePanel            _treepanel;
  46
  47     public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
  48         _phy = phy;
  49         _mf = mf;
  50         _treepanel = treepanel;
  51     }
  52
  53     private String getBaseUrl() {
  54         return UniProtWsTools.BASE_URL;
  55     }
  56
  57     private void execute() {
  58         _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
  59         SortedSet<String> not_found = null;
  60         try {
  61             not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy );
  62         }
  63         catch ( final UnknownHostException e ) {
  64             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
  65             JOptionPane.showMessageDialog( _mf,
  66                                            "Could not connect to \"" + getBaseUrl() + "\"",
  67                                            "Network error during taxonomic information gathering",
  68                                            JOptionPane.ERROR_MESSAGE );
  69             return;
  70         }
  71         catch ( final IOException e ) {
  72             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
  73             e.printStackTrace();
  74             JOptionPane.showMessageDialog( _mf,
  75                                            e.toString(),
  76                                            "Failed to obtain taxonomic information",
  77                                            JOptionPane.ERROR_MESSAGE );
  78             return;
  79         }
  80         finally {
  81             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
  82         }
  83         _treepanel.setTree( _phy );
  84         _mf.showWhole();
  85         _treepanel.setEdited( true );
  86         if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
  87             int max = not_found.size();
  88             boolean more = false;
  89             if ( max > 20 ) {
  90                 more = true;
  91                 max = 20;
  92             }
  93             final StringBuffer sb = new StringBuffer();
  94             sb.append( "Not all taxonomies could be resolved.\n" );
  95             if ( not_found.size() == 1 ) {
  96                 sb.append( "The following taxonomy was not found:\n" );
  97             }
  98             else {
  99                 sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
 100             }
 101             int i = 0;
 102             for( final String string : not_found ) {
 103                 if ( i > 19 ) {
 104                     break;
 105                 }
 106                 sb.append( string );
 107                 sb.append( "\n" );
 108                 ++i;
 109             }
 110             if ( more ) {
 111                 sb.append( "..." );
 112             }
 113             try {
 114                 JOptionPane.showMessageDialog( _mf,
 115                                                sb.toString(),
 116                                                "Taxonomy Tool Completed",
 117                                                JOptionPane.WARNING_MESSAGE );
 118             }
 119             catch ( final Exception e ) {
 120                 // Not important if this fails, do nothing.
 121             }
 122         }
 123         else {
 124             try {
 125                 JOptionPane.showMessageDialog( _mf,
 126                                                "Taxonomy tool successfully completed",
 127                                                "Taxonomy Tool Completed",
 128                                                JOptionPane.INFORMATION_MESSAGE );
 129             }
 130             catch ( final Exception e ) {
 131                 // Not important if this fails, do nothing.
 132             }
 133         }
 134     }
 135
 136     @Override
 137     public void run() {
 138         execute();
 139     }
 140 }