forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java

   1 // Exp $
   2 // forester -- software libraries and applications
   3 // for genomics and evolutionary biology research.
   4 //
   5 // Copyright (C) 2010 Christian M Zmasek
   6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
   7 // All rights reserved
   8 //
   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.
  13 //
  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.
  18 //
  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
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.archaeopteryx.tools;
  27
  28 import java.io.IOException;
  29 import java.net.UnknownHostException;
  30 import java.util.SortedSet;
  31
  32 import javax.swing.JOptionPane;
  33
  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;
  38
  39 public final class SequenceDataRetriver extends RunnableProcess {
  40
  41     private final Phylogeny            _phy;
  42     private final MainFrameApplication _mf;
  43     private final TreePanel            _treepanel;
  44     public final static boolean        DEBUG = false;
  45
  46     public SequenceDataRetriver( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
  47         _phy = phy;
  48         _mf = mf;
  49         _treepanel = treepanel;
  50     }
  51
  52     @Override
  53     public void run() {
  54         execute();
  55     }
  56
  57     private void execute() {
  58         start( _mf, "sequence data" );
  59         SortedSet<String> not_found = null;
  60         try {
  61             not_found = SequenceDbWsTools.obtainSeqInformation( _phy,
  62                                                                 false,
  63                                                                 true,
  64                                                                 SequenceDbWsTools.DEFAULT_LINES_TO_RETURN );
  65         }
  66         catch ( final UnknownHostException e ) {
  67             JOptionPane.showMessageDialog( _mf,
  68                                            e.getLocalizedMessage(),
  69                                            "Network error during sequence data gathering",
  70                                            JOptionPane.ERROR_MESSAGE );
  71             return;
  72         }
  73         catch ( final IOException e ) {
  74             e.printStackTrace();
  75             JOptionPane.showMessageDialog( _mf,
  76                                            e.toString(),
  77                                            "Failed to obtain sequence data",
  78                                            JOptionPane.ERROR_MESSAGE );
  79             return;
  80         }
  81         finally {
  82             end( _mf );
  83         }
  84         _treepanel.setTree( _phy );
  85         _mf.showWhole();
  86         _treepanel.setEdited( true );
  87         if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
  88             int max = not_found.size();
  89             boolean more = false;
  90             if ( max > 20 ) {
  91                 more = true;
  92                 max = 20;
  93             }
  94             final StringBuffer sb = new StringBuffer();
  95             if ( not_found.size() == 1 ) {
  96                 sb.append( "For the following node no data was found:\n" );
  97             }
  98             else {
  99                 sb.append( "For the following nodes no data was found (total: " + not_found.size() + "):\n" );
 100             }
 101             int i = 0;
 102             for( final String string : not_found ) {
 103                 if ( i > 19 ) {
 104                     break;
 105                 }
 106                 sb.append( string );
 107                 sb.append( "\n" );
 108                 ++i;
 109             }
 110             if ( more ) {
 111                 sb.append( "..." );
 112             }
 113             try {
 114                 JOptionPane.showMessageDialog( _mf,
 115                                                sb.toString(),
 116                                                "Sequence Tool Completed",
 117                                                JOptionPane.WARNING_MESSAGE );
 118             }
 119             catch ( final Exception e ) {
 120                 // Not important if this fails, do nothing.
 121             }
 122         }
 123         else {
 124             try {
 125                 JOptionPane.showMessageDialog( _mf,
 126                                                "Sequence tool successfully completed",
 127                                                "Sequence Tool Completed",
 128                                                JOptionPane.INFORMATION_MESSAGE );
 129             }
 130             catch ( final Exception e ) {
 131                 // Not important if this fails, do nothing.
 132             }
 133         }
 134     }
 135 }