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 extends RunnableProcess {
  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         start( _mf, "taxonomy data" );
  72         SortedSet<String> not_found = null;
  73         try {
  74             not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy, _delete );
  75         }
  76         catch ( final UnknownHostException e ) {
  77             JOptionPane.showMessageDialog( _mf,
  78                                            "Could not connect to \"" + getBaseUrl() + "\"",
  79                                            "Network error during taxonomic information gathering",
  80                                            JOptionPane.ERROR_MESSAGE );
  81             return;
  82         }
  83         catch ( final IOException e ) {
  84             e.printStackTrace();
  85             JOptionPane.showMessageDialog( _mf,
  86                                            e.toString(),
  87                                            "Failed to obtain taxonomic information",
  88                                            JOptionPane.ERROR_MESSAGE );
  89             return;
  90         }
  91         catch ( final AncestralTaxonomyInferenceException e ) {
  92             e.printStackTrace();
  93             JOptionPane.showMessageDialog( _mf,
  94                                            e.toString(),
  95                                            "Failed to obtain taxonomic information",
  96                                            JOptionPane.ERROR_MESSAGE );
  97             return;
  98         }
  99         finally {
 100             end( _mf );
 101         }
 102         if ( _phy == null || _phy.isEmpty() ) {
 103             try {
 104                 JOptionPane.showMessageDialog( _mf,
 105                                                "None of the external node taxonomies could be resolved",
 106                                                "Taxonomy Tool Failed",
 107                                                JOptionPane.WARNING_MESSAGE );
 108             }
 109             catch ( final Exception e ) {
 110                 // Not important if this fails, do nothing.
 111             }
 112             return;
 113         }
 114         _treepanel.setTree( _phy );
 115         _mf.showWhole();
 116         _treepanel.setEdited( true );
 117         if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
 118             int max = not_found.size();
 119             boolean more = false;
 120             if ( max > 20 ) {
 121                 more = true;
 122                 max = 20;
 123             }
 124             final StringBuffer sb = new StringBuffer();
 125             sb.append( "Not all taxonomies could be resolved.\n" );
 126             if ( not_found.size() == 1 ) {
 127                 if ( _delete ) {
 128                     sb.append( "The following taxonomy was not found and deleted (if external):\n" );
 129                 }
 130                 else {
 131                     sb.append( "The following taxonomy was not found:\n" );
 132                 }
 133             }
 134             else {
 135                 if ( _delete ) {
 136                     sb.append( "The following taxonomies were not found and deleted (if external) (total: "
 137                             + not_found.size() + "):\n" );
 138                 }
 139                 else {
 140                     sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
 141                 }
 142             }
 143             int i = 0;
 144             for( final String string : not_found ) {
 145                 if ( i > 19 ) {
 146                     break;
 147                 }
 148                 sb.append( string );
 149                 sb.append( "\n" );
 150                 ++i;
 151             }
 152             if ( more ) {
 153                 sb.append( "..." );
 154             }
 155             try {
 156                 JOptionPane.showMessageDialog( _mf,
 157                                                sb.toString(),
 158                                                "Taxonomy Tool Completed",
 159                                                JOptionPane.WARNING_MESSAGE );
 160             }
 161             catch ( final Exception e ) {
 162                 // Not important if this fails, do nothing.
 163             }
 164         }
 165         else {
 166             try {
 167                 JOptionPane.showMessageDialog( _mf,
 168                                                "Taxonomy tool successfully completed",
 169                                                "Taxonomy Tool Completed",
 170                                                JOptionPane.INFORMATION_MESSAGE );
 171             }
 172             catch ( final Exception e ) {
 173                 // Not important if this fails, do nothing.
 174             }
 175         }
 176     }
 177
 178     @Override
 179     public void run() {
 180         execute();
 181     }
 182 }