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;
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.phylogeny.Phylogeny;
35 import org.forester.ws.uniprot.UniProtWsTools;
37 public class AncestralTaxonomyInferrer implements Runnable {
39 private final Phylogeny _phy;
40 private final MainFrameApplication _mf;
41 private final TreePanel _treepanel;
43 AncestralTaxonomyInferrer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
46 _treepanel = treepanel;
49 private String getBaseUrl() {
50 return UniProtWsTools.BASE_URL;
53 private void inferTaxonomies() {
54 _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
55 SortedSet<String> not_found = null;
57 not_found = AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
59 catch ( final IllegalArgumentException e ) {
60 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
61 JOptionPane.showMessageDialog( _mf,
63 "Error during ancestral taxonomy inference",
64 JOptionPane.ERROR_MESSAGE );
67 catch ( final UnknownHostException e ) {
68 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
69 JOptionPane.showMessageDialog( _mf,
70 "Could not connect to \"" + getBaseUrl() + "\"",
71 "Network error during ancestral taxonomy inference",
72 JOptionPane.ERROR_MESSAGE );
75 catch ( final Exception e ) {
76 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
78 JOptionPane.showMessageDialog( _mf,
80 "Unexpected error during ancestral taxonomy inference",
81 JOptionPane.ERROR_MESSAGE );
84 _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
85 _phy.setRerootable( false );
86 _treepanel.setTree( _phy );
88 _treepanel.setEdited( true );
89 if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
90 int max = not_found.size();
96 final StringBuffer sb = new StringBuffer();
97 sb.append( "Not all taxonomies could be resolved.\n" );
98 sb.append( "The result is incomplete, and, possibly, misleading.\n" );
99 if ( not_found.size() == 1 ) {
100 sb.append( "The following taxonomy was not found:\n" );
103 sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
106 for( final String string : not_found ) {
118 JOptionPane.showMessageDialog( _mf,
120 "Ancestral Taxonomy Inference Completed",
121 JOptionPane.WARNING_MESSAGE );
123 catch ( final Exception e ) {
124 // Not important if this fails, do nothing.
129 JOptionPane.showMessageDialog( _mf,
130 "Ancestral taxonomy inference successfully completed",
131 "Ancestral Taxonomy Inference Completed",
132 JOptionPane.INFORMATION_MESSAGE );
134 catch ( final Exception e ) {
135 // Not important if this fails, do nothing.