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 static int           DEFAULT_LINES_TO_RETURN = 4000;
  42     private final Phylogeny            _phy;
  43     private final MainFrameApplication _mf;
  44     private final TreePanel            _treepanel;
  45     public final static boolean        DEBUG                   = false;
  46
  47     public SequenceDataRetriver( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
  48         _phy = phy;
  49         _mf = mf;
  50         _treepanel = treepanel;
  51     }
  52
  53     @Override
  54     public void run() {
  55         execute();
  56     }
  57
  58     private void execute() {
  59         start( _mf, "sequence data" );
  60         SortedSet<String> not_found = null;
  61         try {
  62             not_found = SequenceDbWsTools.obtainSeqInformation( _phy, false, true, DEFAULT_LINES_TO_RETURN );
  63         }
  64         catch ( final UnknownHostException e ) {
  65             JOptionPane.showMessageDialog( _mf,
  66                                            e.getLocalizedMessage(),
  67                                            "Network error during sequence data gathering",
  68                                            JOptionPane.ERROR_MESSAGE );
  69             return;
  70         }
  71         catch ( final IOException e ) {
  72             e.printStackTrace();
  73             JOptionPane.showMessageDialog( _mf,
  74                                            e.toString(),
  75                                            "Failed to obtain sequence data",
  76                                            JOptionPane.ERROR_MESSAGE );
  77             return;
  78         }
  79         finally {
  80             end( _mf );
  81         }
  82         _treepanel.setTree( _phy );
  83         _mf.showWhole();
  84         _treepanel.setEdited( true );
  85         if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
  86             int max = not_found.size();
  87             boolean more = false;
  88             if ( max > 20 ) {
  89                 more = true;
  90                 max = 20;
  91             }
  92             final StringBuffer sb = new StringBuffer();
  93             if ( not_found.size() == 1 ) {
  94                 sb.append( "For the following node no data was found:\n" );
  95             }
  96             else {
  97                 sb.append( "For the following nodes no data was found: (total: " + not_found.size() + "):\n" );
  98             }
  99             int i = 0;
 100             for( final String string : not_found ) {
 101                 if ( i > 19 ) {
 102                     break;
 103                 }
 104                 sb.append( string );
 105                 sb.append( "\n" );
 106                 ++i;
 107             }
 108             if ( more ) {
 109                 sb.append( "..." );
 110             }
 111             try {
 112                 JOptionPane.showMessageDialog( _mf,
 113                                                sb.toString(),
 114                                                "Sequence Tool Completed",
 115                                                JOptionPane.WARNING_MESSAGE );
 116             }
 117             catch ( final Exception e ) {
 118                 // Not important if this fails, do nothing.
 119             }
 120         }
 121         else {
 122             try {
 123                 JOptionPane.showMessageDialog( _mf,
 124                                                "Sequence tool successfully completed",
 125                                                "Sequence Tool Completed",
 126                                                JOptionPane.INFORMATION_MESSAGE );
 127             }
 128             catch ( final Exception e ) {
 129                 // Not important if this fails, do nothing.
 130             }
 131         }
 132     }
 133 }