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.MainFrame;
35 import org.forester.archaeopteryx.MainFrameApplication;
36 import org.forester.archaeopteryx.TreePanel;
37 import org.forester.phylogeny.Phylogeny;
38 import org.forester.ws.seqdb.SequenceDbWsTools;
40 public class AncestralTaxonomyInferrer extends RunnableProcess {
42 private final Phylogeny _phy;
43 private final MainFrame _mf;
44 private final TreePanel _treepanel;
46 public AncestralTaxonomyInferrer( final MainFrame mf, final TreePanel treepanel, final Phylogeny phy ) {
49 _treepanel = treepanel;
52 public static String getBaseUrl() {
53 return SequenceDbWsTools.BASE_UNIPROT_URL;
56 private void inferTaxonomies() {
57 start( _mf, "ancestral taxonomy" );
59 AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
61 catch ( final AncestralTaxonomyInferenceException e ) {
63 JOptionPane.showMessageDialog( _mf,
65 "Error during ancestral taxonomy inference",
66 JOptionPane.ERROR_MESSAGE );
69 catch ( final UnknownHostException e ) {
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 ) {
80 JOptionPane.showMessageDialog( _mf,
82 "Unexpected exception during ancestral taxonomy inference",
83 JOptionPane.ERROR_MESSAGE );
86 catch ( final Error e ) {
88 JOptionPane.showMessageDialog( _mf,
90 "Unexpected error during ancestral taxonomy inference",
91 JOptionPane.ERROR_MESSAGE );
94 _phy.setRerootable( false );
95 _treepanel.setTree( _phy );
97 _treepanel.setEdited( true );
100 JOptionPane.showMessageDialog( _mf,
101 "Ancestral taxonomy inference successfully completed",
102 "Ancestral Taxonomy Inference Completed",
103 JOptionPane.INFORMATION_MESSAGE );
105 catch ( final Exception e ) {
106 // Not important if this fails, do nothing.