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.analysis.AncestralTaxonomyInferenceException;
  37 import org.forester.archaeopteryx.MainFrameApplication;
  38 import org.forester.archaeopteryx.TreePanel;
  39 import org.forester.phylogeny.Phylogeny;
  40 import org.forester.ws.uniprot.UniProtWsTools;
  41
  42 public class TaxonomyDataObtainer implements Runnable {
  43
  44     private final Phylogeny            _phy;
  45     private final MainFrameApplication _mf;
  46     private final TreePanel            _treepanel;
  47     private final boolean              _delete;
  48
  49     public TaxonomyDataObtainer( final MainFrameApplication mf,
  50                                  final TreePanel treepanel,
  51                                  final Phylogeny phy,
  52                                  final boolean delete ) {
  53         _phy = phy;
  54         _mf = mf;
  55         _treepanel = treepanel;
  56         _delete = delete;
  57     }
  58
  59     public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
  60         _phy = phy;
  61         _mf = mf;
  62         _treepanel = treepanel;
  63         _delete = false;
  64     }
  65
  66     private String getBaseUrl() {
  67         return UniProtWsTools.BASE_URL;
  68     }
  69
  70     private void execute() {
  71         _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
  72         SortedSet<String> not_found = null;
  73         try {
  74             not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy, _delete );
  75         }
  76         catch ( final UnknownHostException e ) {
  77             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
  78             JOptionPane.showMessageDialog( _mf,
  79                                            "Could not connect to \"" + getBaseUrl() + "\"",
  80                                            "Network error during taxonomic information gathering",
  81                                            JOptionPane.ERROR_MESSAGE );
  82             return;
  83         }
  84         catch ( final IOException e ) {
  85             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
  86             e.printStackTrace();
  87             JOptionPane.showMessageDialog( _mf,
  88                                            e.toString(),
  89                                            "Failed to obtain taxonomic information",
  90                                            JOptionPane.ERROR_MESSAGE );
  91             return;
  92         }
  93         catch ( final AncestralTaxonomyInferenceException e ) {
  94             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
  95             e.printStackTrace();
  96             JOptionPane.showMessageDialog( _mf,
  97                                            e.toString(),
  98                                            "Failed to obtain taxonomic information",
  99                                            JOptionPane.ERROR_MESSAGE );
 100             return;
 101         }
 102         finally {
 103             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
 104         }
 105         _treepanel.setTree( _phy );
 106         _mf.showWhole();
 107         _treepanel.setEdited( true );
 108         if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
 109             int max = not_found.size();
 110             boolean more = false;
 111             if ( max > 20 ) {
 112                 more = true;
 113                 max = 20;
 114             }
 115             final StringBuffer sb = new StringBuffer();
 116             sb.append( "Not all taxonomies could be resolved.\n" );
 117             if ( not_found.size() == 1 ) {
 118                 if ( _delete ) {
 119                     sb.append( "The following taxonomy was not found and deleted (if external):\n" );
 120                 }
 121                 else {
 122                     sb.append( "The following taxonomy was not found:\n" );
 123                 }
 124             }
 125             else {
 126                 if ( _delete ) {
 127                     sb.append( "The following taxonomies were not found and deleted (if external) (total: "
 128                             + not_found.size() + "):\n" );
 129                 }
 130                 else {
 131                     sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
 132                 }
 133             }
 134             int i = 0;
 135             for( final String string : not_found ) {
 136                 if ( i > 19 ) {
 137                     break;
 138                 }
 139                 sb.append( string );
 140                 sb.append( "\n" );
 141                 ++i;
 142             }
 143             if ( more ) {
 144                 sb.append( "..." );
 145             }
 146             try {
 147                 JOptionPane.showMessageDialog( _mf,
 148                                                sb.toString(),
 149                                                "Taxonomy Tool Completed",
 150                                                JOptionPane.WARNING_MESSAGE );
 151             }
 152             catch ( final Exception e ) {
 153                 // Not important if this fails, do nothing.
 154             }
 155         }
 156         else {
 157             try {
 158                 JOptionPane.showMessageDialog( _mf,
 159                                                "Taxonomy tool successfully completed",
 160                                                "Taxonomy Tool Completed",
 161                                                JOptionPane.INFORMATION_MESSAGE );
 162             }
 163             catch ( final Exception e ) {
 164                 // Not important if this fails, do nothing.
 165             }
 166         }
 167     }
 168
 169     @Override
 170     public void run() {
 171         execute();
 172     }
 173 }