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.PhyloXmlDataFormatException;
  43 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  44 import org.forester.io.parsers.tol.TolParser;
  45 import org.forester.phylogeny.Phylogeny;
  46 import org.forester.phylogeny.PhylogenyMethods;
  47 import org.forester.phylogeny.data.Identifier;
  48 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  49 import org.forester.phylogeny.factories.PhylogenyFactory;
  50 import org.forester.util.ForesterUtil;
  51
  52 public class UrlTreeReader implements Runnable {
  53
  54     private final MainFrame _main_frame;
  55     private final int       _webservice_client_index;
  56
  57     UrlTreeReader( final MainFrame mf, final int webservice_client_index ) {
  58         _main_frame = mf;
  59         _webservice_client_index = webservice_client_index;
  60     }
  61
  62     synchronized void readPhylogeniesFromWebservice() {
  63         final long start_time = new Date().getTime();
  64         URL url = null;
  65         Phylogeny[] trees = null;
  66         final WebservicesManager webservices_manager = WebservicesManager.getInstance();
  67         final PhylogeniesWebserviceClient client = webservices_manager
  68                 .getAvailablePhylogeniesWebserviceClient( _webservice_client_index );
  69         String identifier = JOptionPane.showInputDialog( _main_frame, client.getInstructions() + "\n(Reference: "
  70                 + client.getReference() + ")", client.getDescription(), JOptionPane.QUESTION_MESSAGE );
  71         if ( ( identifier != null ) && ( identifier.trim().length() > 0 ) ) {
  72             identifier = identifier.trim();
  73             if ( client.isQueryInteger() ) {
  74                 identifier = identifier.replaceAll( "^\\D+", "" );
  75                 int id = -1;
  76                 try {
  77                     id = Integer.parseInt( identifier );
  78                 }
  79                 catch ( final NumberFormatException e ) {
  80                     id = -1;
  81                 }
  82                 if ( id < 1 ) {
  83                     JOptionPane.showMessageDialog( _main_frame,
  84                                                    "Identifier is expected to be a number",
  85                                                    "Can not open URL",
  86                                                    JOptionPane.ERROR_MESSAGE );
  87                     return;
  88                 }
  89                 identifier = id + "";
  90             }
  91             try {
  92                 String url_str = client.getUrl();
  93                 url_str = url_str.replaceFirst( PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier );
  94                 url = new URL( url_str );
  95                 PhylogenyParser parser = null;
  96                 switch ( client.getReturnFormat() ) {
  97                     case TOL_XML_RESPONSE:
  98                         parser = new TolParser();
  99                         break;
 100                     case NEXUS:
 101                         parser = new NexusPhylogeniesParser();
 102                         ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
 103                         break;
 104                     case NH:
 105                         parser = new NHXParser();
 106                         ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
 107                         ( ( NHXParser ) parser ).setReplaceUnderscores( true );
 108                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 109                         break;
 110                     case NH_EXTRACT_TAXONOMY:
 111                         parser = new NHXParser();
 112                         ( ( NHXParser ) parser )
 113                                 .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
 114                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 115                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 116                         break;
 117                     case PFAM:
 118                         parser = new NHXParser();
 119                         ( ( NHXParser ) parser )
 120                                 .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
 121                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 122                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 123                         break;
 124                     case NHX:
 125                         parser = new NHXParser();
 126                         ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
 127                         ( ( NHXParser ) parser ).setReplaceUnderscores( false );
 128                         ( ( NHXParser ) parser ).setGuessRootedness( true );
 129                         break;
 130                     case PHYLOXML:
 131                         parser = new PhyloXmlParser();
 132                         break;
 133                     default:
 134                         throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
 135                 }
 136                 if ( _main_frame.getMainPanel().getCurrentTreePanel() != null ) {
 137                     _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
 138                 }
 139                 else {
 140                     _main_frame.getMainPanel().setWaitCursor();
 141                 }
 142                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 143                 trees = factory.create( url.openStream(), parser );
 144             }
 145             catch ( final MalformedURLException e ) {
 146                 JOptionPane.showMessageDialog( _main_frame,
 147                                                "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
 148                                                "Malformed URL",
 149                                                JOptionPane.ERROR_MESSAGE );
 150             }
 151             catch ( final IOException e ) {
 152                 JOptionPane.showMessageDialog( _main_frame,
 153                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 154                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 155                                                JOptionPane.ERROR_MESSAGE );
 156             }
 157             catch ( final NumberFormatException e ) {
 158                 JOptionPane.showMessageDialog( _main_frame,
 159                                                "Could not read from " + url + "\n" + e.getLocalizedMessage(),
 160                                                "Failed to read tree from " + client.getName() + " for " + identifier,
 161                                                JOptionPane.ERROR_MESSAGE );
 162             }
 163             catch ( final Exception e ) {
 164                 e.printStackTrace();
 165                 JOptionPane.showMessageDialog( _main_frame,
 166                                                e.getLocalizedMessage(),
 167                                                "Unexpected Exception",
 168                                                JOptionPane.ERROR_MESSAGE );
 169             }
 170             finally {
 171                 if ( _main_frame.getCurrentTreePanel() != null ) {
 172                     _main_frame.getCurrentTreePanel().setArrowCursor();
 173                 }
 174                 else {
 175                     _main_frame.getMainPanel().setArrowCursor();
 176                 }
 177             }
 178             if ( ( trees != null ) && ( trees.length > 0 ) ) {
 179                 for( final Phylogeny phylogeny : trees ) {
 180                     if ( !phylogeny.isEmpty() ) {
 181                         if ( client.getName().equals( WebserviceUtil.TREE_FAM_NAME ) ) {
 182                             phylogeny.setRerootable( false );
 183                             phylogeny.setRooted( true );
 184                         }
 185                         if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
 186                             phylogeny.setRerootable( false );
 187                             phylogeny.setRooted( true );
 188                             PhylogenyMethods.transferInternalNodeNamesToConfidence( phylogeny );
 189                         }
 190                         if ( client.getProcessingInstructions() != null ) {
 191                             try {
 192                                 WebserviceUtil.processInstructions( client, phylogeny );
 193                             }
 194                             catch ( final PhyloXmlDataFormatException e ) {
 195                                 JOptionPane.showMessageDialog( _main_frame,
 196                                                                "Error:\n" + e.getLocalizedMessage(),
 197                                                                "Error",
 198                                                                JOptionPane.ERROR_MESSAGE );
 199                             }
 200                         }
 201                         if ( client.getNodeField() != null ) {
 202                             try {
 203                                 PhylogenyMethods.transferNodeNameToField( phylogeny, client.getNodeField(), false );
 204                             }
 205                             catch ( final PhyloXmlDataFormatException e ) {
 206                                 JOptionPane.showMessageDialog( _main_frame,
 207                                                                "Error:\n" + e.getLocalizedMessage(),
 208                                                                "Error",
 209                                                                JOptionPane.ERROR_MESSAGE );
 210                             }
 211                         }
 212                         phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
 213                         _main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );
 214                         _main_frame.getMenuBarOfMainFrame().add( _main_frame.getHelpMenu() );
 215                         _main_frame.getMainPanel().addPhylogenyInNewTab( phylogeny,
 216                                                                          _main_frame.getConfiguration(),
 217                                                                          new File( url.getFile() ).getName(),
 218                                                                          url.toString() );
 219                         String my_name_for_file = "";
 220                         if ( !ForesterUtil.isEmpty( phylogeny.getName() ) ) {
 221                             my_name_for_file = new String( phylogeny.getName() ).replaceAll( " ", "_" );
 222                         }
 223                         else if ( phylogeny.getIdentifier() != null ) {
 224                             final StringBuffer sb = new StringBuffer();
 225                             if ( !ForesterUtil.isEmpty( phylogeny.getIdentifier().getProvider() ) ) {
 226                                 sb.append( phylogeny.getIdentifier().getProvider() );
 227                                 sb.append( "_" );
 228                             }
 229                             sb.append( phylogeny.getIdentifier().getValue() );
 230                             my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 231                         }
 232                         _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 233                         AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
 234                                 .getControlPanel(), _main_frame.getConfiguration() );
 235                         _main_frame.getMainPanel().getControlPanel().showWhole();
 236                     }
 237                 }
 238             }
 239             _main_frame.getContentPane().repaint();
 240             if ( ( ( trees != null ) && ( trees.length > 0 ) ) && ( ( new Date().getTime() - start_time ) > 20000 ) ) {
 241                 try {
 242                     JOptionPane.showMessageDialog( null,
 243                                                    ForesterUtil.wordWrap( "Successfully read in " + trees.length
 244                                                            + " evolutionry tree(s) from [" + url + "]", 80 ),
 245                                                    "Success",
 246                                                    JOptionPane.INFORMATION_MESSAGE );
 247                 }
 248                 catch ( final Exception e ) {
 249                     // Not important if this fails, do nothing.
 250                 }
 251                 _main_frame.getContentPane().repaint();
 252             }
 253         }
 254         _main_frame.activateSaveAllIfNeeded();
 255         System.gc();
 256     }
 257
 258     @Override
 259     public void run() {
 260         readPhylogeniesFromWebservice();
 261     }
 262 }