forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   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: www.phylosoft.org/forester
  25
  26 package org.forester.archaeopteryx;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.net.MalformedURLException;
  31 import java.net.URL;
  32 import java.util.Date;
  33
  34 import javax.swing.JOptionPane;
  35
  36 import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
  37 import org.forester.archaeopteryx.webservices.WebserviceUtil;
  38 import org.forester.archaeopteryx.webservices.WebservicesManager;
  39 import org.forester.io.parsers.PhylogenyParser;
  40 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  41 import org.forester.io.parsers.nhx.NHXParser;
  42 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  43 import org.forester.io.parsers.tol.TolParser;
  44 import org.forester.phylogeny.Phylogeny;
  45 import org.forester.phylogeny.data.Identifier;
  46 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  47 import org.forester.phylogeny.factories.PhylogenyFactory;
  48 import org.forester.util.ForesterUtil;
  49
  50 public class UrlTreeReader implements Runnable {
  51
  52     private final MainFrame _main_frame;
  53     private final int       _webservice_client_index;
  54
  55     UrlTreeReader( final MainFrame mf, final int webservice_client_index ) {
  56         _main_frame = mf;
  57         _webservice_client_index = webservice_client_index;
  58     }
  59
  60     synchronized void readPhylogeniesFromWebservice() {
  61         final long start_time = new Date().getTime();
  62         URL url = null;
  63         Phylogeny[] trees = null;
  64         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
  65         final PhylogeniesWebserviceClient client = webservices_manager
  66                 .getAvailablePhylogeniesWebserviceClient( _webservice_client_index );
  67         String identifier = JOptionPane.showInputDialog( _main_frame, client.getInstructions() + "\n(Reference: "
  68                 + client.getReference() + ")", client.getDescription(), JOptionPane.QUESTION_MESSAGE );
  69         if ( ( identifier != null ) && ( identifier.trim().length() > 0 ) ) {
  70             identifier = identifier.trim();
  71             if ( client.isQueryInteger() ) {
  72                 identifier = identifier.replaceAll( "^\\D+", "" );
  73                 int id = -1;
  74                 try {
  75                     id = Integer.parseInt( identifier );
  76                 }
  77                 catch ( final NumberFormatException e ) {
  78                     id = -1;
  79                 }
  80                 if ( id < 1 ) {
  81                     JOptionPane.showMessageDialog( _main_frame,
  82                                                    "Identifier is expected to be a number",
  83                                                    "Can not open URL",
  84                                                    JOptionPane.ERROR_MESSAGE );
  85                     return;
  86                 }
  87                 identifier = id + "";
  88             }
  89             try {
  90                 String url_str = client.getUrl();
  91                 url_str = url_str.replaceFirst( PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier );
  92                 url = new URL( url_str );
  93                 PhylogenyParser parser = null;
  94                 switch ( client.getReturnFormat() ) {
  95                     case TOL_XML_RESPONSE:
  96                         parser = new TolParser();
  97                         break;
  98                     case NEXUS:
  99                         parser = new NexusPhylogeniesParser();
 100                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 101                         break;
 102                     case NH:
 103                         parser = new NHXParser();
 104                         ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
 105                         ( ( NHXParser ) parser ).setReplaceUnderscores( true );
 106                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 107                         break;
 108                     case NH_EXTRACT_TAXONOMY:
 109                         parser = new NHXParser();
 110                         ( ( NHXParser ) parser )
 111                                 .setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
 112                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 113                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 114                         break;
 115                     case PFAM:
 116                         parser = new NHXParser();
 117                         ( ( NHXParser ) parser )
 118                                 .setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
 119                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 120                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 121                         break;
 122                     case NHX:
 123                         parser = new NHXParser();
 124                         ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
 125                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 126                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 127                         break;
 128                     case PHYLOXML:
 129                         parser = new PhyloXmlParser();
 130                         break;
 131                     default:
 132                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
 133                 }
 134                 if ( _main_frame.getMainPanel().getCurrentTreePanel() != null ) {
 135                     _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
 136                 }
 137                 else {
 138                     _main_frame.getMainPanel().setWaitCursor();
 139                 }
 140                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 141                 trees = factory.create( url.openStream(), parser );
 142             }
 143             catch ( final MalformedURLException e ) {
 144                 JOptionPane.showMessageDialog( _main_frame,
 145                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
 146                                                "Malformed URL",
 147                                                JOptionPane.ERROR_MESSAGE );
 148             }
 149             catch ( final IOException e ) {
 150                 JOptionPane.showMessageDialog( _main_frame,
 151                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 152                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 153                                                JOptionPane.ERROR_MESSAGE );
 154             }
 155             catch ( final NumberFormatException e ) {
 156                 JOptionPane.showMessageDialog( _main_frame,
 157                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 158                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 159                                                JOptionPane.ERROR_MESSAGE );
 160             }
 161             catch ( final Exception e ) {
 162                 e.printStackTrace();
 163                 JOptionPane.showMessageDialog( _main_frame,
 164                                                e.getLocalizedMessage(),
 165                                                "Unexpected Exception",
 166                                                JOptionPane.ERROR_MESSAGE );
 167             }
 168             finally {
 169                 if ( _main_frame.getCurrentTreePanel() != null ) {
 170                     _main_frame.getCurrentTreePanel().setArrowCursor();
 171                 }
 172                 else {
 173                     _main_frame.getMainPanel().setArrowCursor();
 174                 }
 175             }
 176             if ( ( trees != null ) && ( trees.length > 0 ) ) {
 177                 for( final Phylogeny phylogeny : trees ) {
 178                     if ( !phylogeny.isEmpty() ) {
 179                         if ( client.getName().equals( WebserviceUtil.TREE_FAM_NAME ) ) {
 180                             phylogeny.setRerootable( false );
 181                             phylogeny.setRooted( true );
 182                         }
 183                         if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
 184                             phylogeny.setRerootable( false );
 185                             phylogeny.setRooted( true );
 186                             ForesterUtil.transferInternalNodeNamesToConfidence( phylogeny );
 187                         }
 188                         if ( client.getProcessingInstructions() != null ) {
 189                             WebserviceUtil.processInstructions( client, phylogeny );
 190                         }
 191                         if ( client.getNodeField() != null ) {
 192                             ForesterUtil.transferNodeNameToField( phylogeny, client.getNodeField() );
 193                         }
 194                         phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
 195                         _main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );
 196                         _main_frame.getMenuBarOfMainFrame().add( _main_frame.getHelpMenu() );
 197                         _main_frame.getMainPanel().addPhylogenyInNewTab( phylogeny,
 198                                                                          _main_frame.getConfiguration(),
 199                                                                          new File( url.getFile() ).getName(),
 200                                                                          url.toString() );
 201                         String my_name_for_file = "";
 202                         if ( !ForesterUtil.isEmpty( phylogeny.getName() ) ) {
 203                             my_name_for_file = new String( phylogeny.getName() ).replaceAll( " ", "_" );
 204                         }
 205                         else if ( phylogeny.getIdentifier() != null ) {
 206                             final StringBuffer sb = new StringBuffer();
 207                             if ( !ForesterUtil.isEmpty( phylogeny.getIdentifier().getProvider() ) ) {
 208                                 sb.append( phylogeny.getIdentifier().getProvider() );
 209                                 sb.append( "_" );
 210                             }
 211                             sb.append( phylogeny.getIdentifier().getValue() );
 212                             my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 213                         }
 214                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 215                         Util.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
 216                                 .getControlPanel(), _main_frame.getConfiguration() );
 217                         _main_frame.getMainPanel().getControlPanel().showWhole();
 218                     }
 219                 }
 220             }
 221             _main_frame.getContentPane().repaint();
 222             if ( ( ( trees != null ) && ( trees.length > 0 ) ) && ( ( new Date().getTime() - start_time ) > 20000 ) ) {
 223                 try {
 224                     JOptionPane.showMessageDialog( null,
 225                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length
 226                                                            + " evolutionry tree(s) from [" + url + "]", 80 ),
 227                                                    "Success",
 228                                                    JOptionPane.INFORMATION_MESSAGE );
 229                 }
 230                 catch ( final Exception e ) {
 231                     // Not important if this fails, do nothing.
 232                 }
 233                 _main_frame.getContentPane().repaint();
 234             }
 235         }
 236         _main_frame.activateSaveAllIfNeeded();
 237         System.gc();
 238     }
 239
 240     @Override
 241     public void run() {
 242         readPhylogeniesFromWebservice();
 243     }
 244 }