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