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