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.PhylogenyMethods;
  46 import org.forester.phylogeny.data.Identifier;
  47 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  48 import org.forester.phylogeny.factories.PhylogenyFactory;
  49 import org.forester.util.ForesterUtil;
  50
  51 public class UrlTreeReader implements Runnable {
  52
  53     private final MainFrame _main_frame;
  54     private final int       _webservice_client_index;
  55
  56     UrlTreeReader( final MainFrame mf, final int webservice_client_index ) {
  57         _main_frame = mf;
  58         _webservice_client_index = webservice_client_index;
  59     }
  60
  61     synchronized void readPhylogeniesFromWebservice() {
  62         final long start_time = new Date().getTime();
  63         URL url = null;
  64         Phylogeny[] trees = null;
  65         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
  66         final PhylogeniesWebserviceClient client = webservices_manager
  67                 .getAvailablePhylogeniesWebserviceClient( _webservice_client_index );
  68         String identifier = JOptionPane.showInputDialog( _main_frame, client.getInstructions() + "\n(Reference: "
  69                 + client.getReference() + ")", client.getDescription(), JOptionPane.QUESTION_MESSAGE );
  70         if ( ( identifier != null ) && ( identifier.trim().length() > 0 ) ) {
  71             identifier = identifier.trim();
  72             if ( client.isQueryInteger() ) {
  73                 identifier = identifier.replaceAll( "^\\D+", "" );
  74                 int id = -1;
  75                 try {
  76                     id = Integer.parseInt( identifier );
  77                 }
  78                 catch ( final NumberFormatException e ) {
  79                     id = -1;
  80                 }
  81                 if ( id < 1 ) {
  82                     JOptionPane.showMessageDialog( _main_frame,
  83                                                    "Identifier is expected to be a number",
  84                                                    "Can not open URL",
  85                                                    JOptionPane.ERROR_MESSAGE );
  86                     return;
  87                 }
  88                 identifier = id + "";
  89             }
  90             try {
  91                 String url_str = client.getUrl();
  92                 url_str = url_str.replaceFirst( PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier );
  93                 url = new URL( url_str );
  94                 PhylogenyParser parser = null;
  95                 switch ( client.getReturnFormat() ) {
  96                     case TOL_XML_RESPONSE:
  97                         parser = new TolParser();
  98                         break;
  99                     case NEXUS:
 100                         parser = new NexusPhylogeniesParser();
 101                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 102                         break;
 103                     case NH:
 104                         parser = new NHXParser();
 105                         ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
 106                         ( ( NHXParser ) parser ).setReplaceUnderscores( true );
 107                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 108                         break;
 109                     case NH_EXTRACT_TAXONOMY:
 110                         parser = new NHXParser();
 111                         ( ( NHXParser ) parser )
 112                                 .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
 113                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 114                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 115                         break;
 116                     case PFAM:
 117                         parser = new NHXParser();
 118                         ( ( NHXParser ) parser )
 119                                 .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
 120                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 121                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 122                         break;
 123                     case NHX:
 124                         parser = new NHXParser();
 125                         ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
 126                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 127                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 128                         break;
 129                     case PHYLOXML:
 130                         parser = new PhyloXmlParser();
 131                         break;
 132                     default:
 133                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
 134                 }
 135                 if ( _main_frame.getMainPanel().getCurrentTreePanel() != null ) {
 136                     _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
 137                 }
 138                 else {
 139                     _main_frame.getMainPanel().setWaitCursor();
 140                 }
 141                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 142                 trees = factory.create( url.openStream(), parser );
 143             }
 144             catch ( final MalformedURLException e ) {
 145                 JOptionPane.showMessageDialog( _main_frame,
 146                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
 147                                                "Malformed URL",
 148                                                JOptionPane.ERROR_MESSAGE );
 149             }
 150             catch ( final IOException e ) {
 151                 JOptionPane.showMessageDialog( _main_frame,
 152                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 153                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 154                                                JOptionPane.ERROR_MESSAGE );
 155             }
 156             catch ( final NumberFormatException e ) {
 157                 JOptionPane.showMessageDialog( _main_frame,
 158                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 159                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 160                                                JOptionPane.ERROR_MESSAGE );
 161             }
 162             catch ( final Exception e ) {
 163                 e.printStackTrace();
 164                 JOptionPane.showMessageDialog( _main_frame,
 165                                                e.getLocalizedMessage(),
 166                                                "Unexpected Exception",
 167                                                JOptionPane.ERROR_MESSAGE );
 168             }
 169             finally {
 170                 if ( _main_frame.getCurrentTreePanel() != null ) {
 171                     _main_frame.getCurrentTreePanel().setArrowCursor();
 172                 }
 173                 else {
 174                     _main_frame.getMainPanel().setArrowCursor();
 175                 }
 176             }
 177             if ( ( trees != null ) && ( trees.length > 0 ) ) {
 178                 for( final Phylogeny phylogeny : trees ) {
 179                     if ( !phylogeny.isEmpty() ) {
 180                         if ( client.getName().equals( WebserviceUtil.TREE_FAM_NAME ) ) {
 181                             phylogeny.setRerootable( false );
 182                             phylogeny.setRooted( true );
 183                         }
 184                         if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
 185                             phylogeny.setRerootable( false );
 186                             phylogeny.setRooted( true );
 187                             PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny );
 188                         }
 189                         if ( client.getProcessingInstructions() != null ) {
 190                             WebserviceUtil.processInstructions( client, phylogeny );
 191                         }
 192                         if ( client.getNodeField() != null ) {
 193                             PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField() );
 194                         }
 195                         phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
 196                         _main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );
 197                         _main_frame.getMenuBarOfMainFrame().add( _main_frame.getHelpMenu() );
 198                         _main_frame.getMainPanel().addPhylogenyInNewTab( phylogeny,
 199                                                                          _main_frame.getConfiguration(),
 200                                                                          new File( url.getFile() ).getName(),
 201                                                                          url.toString() );
 202                         String my_name_for_file = "";
 203                         if ( !ForesterUtil.isEmpty( phylogeny.getName() ) ) {
 204                             my_name_for_file = new String( phylogeny.getName() ).replaceAll( " ", "_" );
 205                         }
 206                         else if ( phylogeny.getIdentifier() != null ) {
 207                             final StringBuffer sb = new StringBuffer();
 208                             if ( !ForesterUtil.isEmpty( phylogeny.getIdentifier().getProvider() ) ) {
 209                                 sb.append( phylogeny.getIdentifier().getProvider() );
 210                                 sb.append( "_" );
 211                             }
 212                             sb.append( phylogeny.getIdentifier().getValue() );
 213                             my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 214                         }
 215                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 216                         AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
 217                                 .getControlPanel(), _main_frame.getConfiguration() );
 218                         _main_frame.getMainPanel().getControlPanel().showWhole();
 219                     }
 220                 }
 221             }
 222             _main_frame.getContentPane().repaint();
 223             if ( ( ( trees != null ) && ( trees.length > 0 ) ) && ( ( new Date().getTime() - start_time ) > 20000 ) ) {
 224                 try {
 225                     JOptionPane.showMessageDialog( null,
 226                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length
 227                                                            + " evolutionry tree(s) from [" + url + "]", 80 ),
 228                                                    "Success",
 229                                                    JOptionPane.INFORMATION_MESSAGE );
 230                 }
 231                 catch ( final Exception e ) {
 232                     // Not important if this fails, do nothing.
 233                 }
 234                 _main_frame.getContentPane().repaint();
 235             }
 236         }
 237         _main_frame.activateSaveAllIfNeeded();
 238         System.gc();
 239     }
 240
 241     @Override
 242     public void run() {
 243         readPhylogeniesFromWebservice();
 244     }
 245 }