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: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx.tools;
28 import java.net.UnknownHostException;
30 import javax.swing.JOptionPane;
32 import org.forester.analysis.AncestralTaxonomyInference;
33 import org.forester.analysis.AncestralTaxonomyInferenceException;
34 import org.forester.archaeopteryx.MainFrameApplication;
35 import org.forester.archaeopteryx.TreePanel;
36 import org.forester.phylogeny.Phylogeny;
37 import org.forester.ws.seqdb.SequenceDbWsTools;
39 public class AncestralTaxonomyInferrer extends RunnableProcess {
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 public static String getBaseUrl() {
52 return SequenceDbWsTools.BASE_UNIPROT_URL;
55 private void inferTaxonomies() {
56 start( _mf, "ancestral taxonomy" );
58 AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
60 catch ( final AncestralTaxonomyInferenceException e ) {
62 JOptionPane.showMessageDialog( _mf,
64 "Error during ancestral taxonomy inference",
65 JOptionPane.ERROR_MESSAGE );
68 catch ( final UnknownHostException e ) {
70 JOptionPane.showMessageDialog( _mf,
71 "Could not connect to \"" + getBaseUrl() + "\"",
72 "Network error during ancestral taxonomy inference",
73 JOptionPane.ERROR_MESSAGE );
76 catch ( final Exception e ) {
79 JOptionPane.showMessageDialog( _mf,
81 "Unexpected exception during ancestral taxonomy inference",
82 JOptionPane.ERROR_MESSAGE );
85 catch ( final Error e ) {
87 JOptionPane.showMessageDialog( _mf,
89 "Unexpected error during ancestral taxonomy inference",
90 JOptionPane.ERROR_MESSAGE );
93 _phy.setRerootable( false );
94 _treepanel.setTree( _phy );
96 _treepanel.setEdited( true );
99 JOptionPane.showMessageDialog( _mf,
100 "Ancestral taxonomy inference successfully completed",
101 "Ancestral Taxonomy Inference Completed",
102 JOptionPane.INFORMATION_MESSAGE );
104 catch ( final Exception e ) {
105 // Not important if this fails, do nothing.