3 // forester -- software libraries and applications
4 // for genomics and evolutionary biology research.
6 // Copyright (C) 2010 Christian M Zmasek
7 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
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.
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.
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
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/forester
27 package org.forester.archaeopteryx.tools;
29 import java.io.IOException;
30 import java.net.UnknownHostException;
31 import java.util.SortedSet;
33 import javax.swing.JOptionPane;
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;
41 public class TaxonomyDataObtainer implements Runnable {
43 private final Phylogeny _phy;
44 private final MainFrameApplication _mf;
45 private final TreePanel _treepanel;
46 private final boolean _delete;
48 public TaxonomyDataObtainer( final MainFrameApplication mf,
49 final TreePanel treepanel,
51 final boolean delete ) {
54 _treepanel = treepanel;
58 public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
61 _treepanel = treepanel;
65 private String getBaseUrl() {
66 return UniProtWsTools.BASE_URL;
69 private void execute() {
70 _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
71 SortedSet<String> not_found = null;
73 not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy, _delete );
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 );
83 catch ( final IOException e ) {
84 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
86 JOptionPane.showMessageDialog( _mf,
88 "Failed to obtain taxonomic information",
89 JOptionPane.ERROR_MESSAGE );
93 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
95 _treepanel.setTree( _phy );
97 _treepanel.setEdited( true );
98 if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
99 int max = not_found.size();
100 boolean more = false;
105 final StringBuffer sb = new StringBuffer();
106 sb.append( "Not all taxonomies could be resolved.\n" );
107 if ( not_found.size() == 1 ) {
109 sb.append( "The following taxonomy was not found and deleted (if external):\n" );
112 sb.append( "The following taxonomy was not found:\n" );
117 sb.append( "The following taxonomies were not found and deleted (if external) (total: "
118 + not_found.size() + "):\n" );
121 sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
125 for( final String string : not_found ) {
137 JOptionPane.showMessageDialog( _mf,
139 "Taxonomy Tool Completed",
140 JOptionPane.WARNING_MESSAGE );
142 catch ( final Exception e ) {
143 // Not important if this fails, do nothing.
148 JOptionPane.showMessageDialog( _mf,
149 "Taxonomy tool successfully completed",
150 "Taxonomy Tool Completed",
151 JOptionPane.INFORMATION_MESSAGE );
153 catch ( final Exception e ) {
154 // Not important if this fails, do nothing.