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