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.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;
42 public class TaxonomyDataObtainer implements Runnable {
44 private final Phylogeny _phy;
45 private final MainFrameApplication _mf;
46 private final TreePanel _treepanel;
47 private final boolean _delete;
49 public TaxonomyDataObtainer( final MainFrameApplication mf,
50 final TreePanel treepanel,
52 final boolean delete ) {
55 _treepanel = treepanel;
59 public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
62 _treepanel = treepanel;
66 private String getBaseUrl() {
67 return UniProtWsTools.BASE_URL;
70 private void execute() {
71 _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
72 SortedSet<String> not_found = null;
74 not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy, _delete );
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 );
84 catch ( final IOException e ) {
85 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
87 JOptionPane.showMessageDialog( _mf,
89 "Failed to obtain taxonomic information",
90 JOptionPane.ERROR_MESSAGE );
93 catch ( final AncestralTaxonomyInferenceException e ) {
94 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
96 JOptionPane.showMessageDialog( _mf,
98 "Failed to obtain taxonomic information",
99 JOptionPane.ERROR_MESSAGE );
103 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
105 _treepanel.setTree( _phy );
107 _treepanel.setEdited( true );
108 if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
109 int max = not_found.size();
110 boolean more = false;
115 final StringBuffer sb = new StringBuffer();
116 sb.append( "Not all taxonomies could be resolved.\n" );
117 if ( not_found.size() == 1 ) {
119 sb.append( "The following taxonomy was not found and deleted (if external):\n" );
122 sb.append( "The following taxonomy was not found:\n" );
127 sb.append( "The following taxonomies were not found and deleted (if external) (total: "
128 + not_found.size() + "):\n" );
131 sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
135 for( final String string : not_found ) {
147 JOptionPane.showMessageDialog( _mf,
149 "Taxonomy Tool Completed",
150 JOptionPane.WARNING_MESSAGE );
152 catch ( final Exception e ) {
153 // Not important if this fails, do nothing.
158 JOptionPane.showMessageDialog( _mf,
159 "Taxonomy tool successfully completed",
160 "Taxonomy Tool Completed",
161 JOptionPane.INFORMATION_MESSAGE );
163 catch ( final Exception e ) {
164 // Not important if this fails, do nothing.