2 // forester -- software libraries and applications
3 // for genomics and evolutionary biology research.
5 // Copyright (C) 2010 Christian M Zmasek
6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.archaeopteryx.tools;
28 import java.net.UnknownHostException;
29 import java.util.SortedSet;
31 import javax.swing.JOptionPane;
33 import org.forester.analysis.AncestralTaxonomyInference;
34 import org.forester.archaeopteryx.MainFrameApplication;
35 import org.forester.archaeopteryx.TreePanel;
36 import org.forester.phylogeny.Phylogeny;
37 import org.forester.ws.uniprot.UniProtWsTools;
39 public class AncestralTaxonomyInferrer implements Runnable {
41 private final Phylogeny _phy;
42 private final MainFrameApplication _mf;
43 private final TreePanel _treepanel;
45 public AncestralTaxonomyInferrer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
48 _treepanel = treepanel;
51 private String getBaseUrl() {
52 return UniProtWsTools.BASE_URL;
55 private void inferTaxonomies() {
56 _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
57 SortedSet<String> not_found = null;
59 not_found = AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
61 catch ( final IllegalArgumentException e ) {
62 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
63 JOptionPane.showMessageDialog( _mf,
65 "Error during ancestral taxonomy inference",
66 JOptionPane.ERROR_MESSAGE );
69 catch ( final UnknownHostException e ) {
70 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
71 JOptionPane.showMessageDialog( _mf,
72 "Could not connect to \"" + getBaseUrl() + "\"",
73 "Network error during ancestral taxonomy inference",
74 JOptionPane.ERROR_MESSAGE );
77 catch ( final Exception e ) {
78 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
80 JOptionPane.showMessageDialog( _mf,
82 "Unexpected error during ancestral taxonomy inference",
83 JOptionPane.ERROR_MESSAGE );
86 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
87 _phy.setRerootable( false );
88 _treepanel.setTree( _phy );
90 _treepanel.setEdited( true );
91 if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
92 int max = not_found.size();
98 final StringBuffer sb = new StringBuffer();
99 sb.append( "Not all taxonomies could be resolved.\n" );
100 sb.append( "The result is incomplete, and, possibly, misleading.\n" );
101 if ( not_found.size() == 1 ) {
102 sb.append( "The following taxonomy was not found:\n" );
105 sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
108 for( final String string : not_found ) {
120 JOptionPane.showMessageDialog( _mf,
122 "Ancestral Taxonomy Inference Completed",
123 JOptionPane.WARNING_MESSAGE );
125 catch ( final Exception e ) {
126 // Not important if this fails, do nothing.
131 JOptionPane.showMessageDialog( _mf,
132 "Ancestral taxonomy inference successfully completed",
133 "Ancestral Taxonomy Inference Completed",
134 JOptionPane.INFORMATION_MESSAGE );
136 catch ( final Exception e ) {
137 // Not important if this fails, do nothing.