// $Id: UrlTreeReader.java,v 1.10 2010/06/23 22:20:31 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.archaeopteryx;
import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Date;
import javax.swing.JOptionPane;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebserviceUtil;
import org.forester.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.data.Identifier;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.util.ForesterUtil;
public class UrlTreeReader implements Runnable {
private final MainFrame _main_frame;
private final int _webservice_client_index;
UrlTreeReader( final MainFrame mf, final int webservice_client_index ) {
_main_frame = mf;
_webservice_client_index = webservice_client_index;
}
synchronized void readPhylogeniesFromWebservice() {
final long start_time = new Date().getTime();
URL url = null;
Phylogeny[] trees = null;
final WebservicesManager webservices_manager = WebservicesManager.getInstance();
final PhylogeniesWebserviceClient client = webservices_manager
.getAvailablePhylogeniesWebserviceClient( _webservice_client_index );
String identifier = JOptionPane.showInputDialog( _main_frame, client.getInstructions() + "\n(Reference: "
+ client.getReference() + ")", client.getDescription(), JOptionPane.QUESTION_MESSAGE );
if ( ( identifier != null ) && ( identifier.trim().length() > 0 ) ) {
identifier = identifier.trim();
if ( client.isQueryInteger() ) {
identifier = identifier.replaceAll( "^\\D+", "" );
int id = -1;
try {
id = Integer.parseInt( identifier );
}
catch ( final NumberFormatException e ) {
id = -1;
}
if ( id < 1 ) {
JOptionPane.showMessageDialog( _main_frame,
"Identifier is expected to be a number",
"Can not open URL",
JOptionPane.ERROR_MESSAGE );
return;
}
identifier = id + "";
}
try {
String url_str = client.getUrl();
url_str = url_str.replaceFirst( PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier );
url = new URL( url_str );
PhylogenyParser parser = null;
switch ( client.getReturnFormat() ) {
case TOL_XML_RESPONSE:
parser = new TolParser();
break;
case NEXUS:
parser = new NexusPhylogeniesParser();
( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( true );
break;
case NH:
parser = new NHXParser();
( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( true );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
( ( NHXParser ) parser )
.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser )
.setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NHX:
parser = new NHXParser();
( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PHYLOXML:
parser = new PhyloXmlParser();
break;
default:
throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
}
if ( _main_frame.getMainPanel().getCurrentTreePanel() != null ) {
_main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
}
else {
_main_frame.getMainPanel().setWaitCursor();
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
trees = factory.create( url.openStream(), parser );
}
catch ( final MalformedURLException e ) {
JOptionPane.showMessageDialog( _main_frame,
"Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
"Malformed URL",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IOException e ) {
JOptionPane.showMessageDialog( _main_frame, "Could not read from " + url + "\n"
+ e.getLocalizedMessage(), "Failed to read tree from " + client.getName() + " for "
+ identifier, JOptionPane.ERROR_MESSAGE );
}
catch ( final NumberFormatException e ) {
JOptionPane.showMessageDialog( _main_frame, "Could not read from " + url + "\n"
+ e.getLocalizedMessage(), "Failed to read tree from " + client.getName() + " for "
+ identifier, JOptionPane.ERROR_MESSAGE );
}
catch ( final Exception e ) {
e.printStackTrace();
JOptionPane.showMessageDialog( _main_frame,
e.getLocalizedMessage(),
"Unexpected Exception",
JOptionPane.ERROR_MESSAGE );
}
finally {
if ( _main_frame.getCurrentTreePanel() != null ) {
_main_frame.getCurrentTreePanel().setArrowCursor();
}
else {
_main_frame.getMainPanel().setArrowCursor();
}
}
if ( ( trees != null ) && ( trees.length > 0 ) ) {
for( final Phylogeny phylogeny : trees ) {
if ( !phylogeny.isEmpty() ) {
if ( client.getName().equals( WebserviceUtil.TREE_FAM_NAME ) ) {
phylogeny.setRerootable( false );
phylogeny.setRooted( true );
}
if ( client.getName().equals( WebserviceUtil.PFAM_NAME ) ) {
phylogeny.setRerootable( false );
phylogeny.setRooted( true );
ForesterUtil.transferInternalNodeNamesToConfidence( phylogeny );
}
if ( client.getProcessingInstructions() != null ) {
WebserviceUtil.processInstructions( client, phylogeny );
}
if ( client.getNodeField() != null ) {
ForesterUtil.transferNodeNameToField( phylogeny, client.getNodeField() );
}
phylogeny.setIdentifier( new Identifier( identifier, client.getName() ) );
_main_frame.getJMenuBar().remove( _main_frame.getHelpMenu() );
_main_frame.getMenuBarOfMainFrame().add( _main_frame.getHelpMenu() );
_main_frame.getMainPanel().addPhylogenyInNewTab( phylogeny,
_main_frame.getConfiguration(),
new File( url.getFile() ).getName(),
url.toString() );
String my_name_for_file = "";
if ( !ForesterUtil.isEmpty( phylogeny.getName() ) ) {
my_name_for_file = new String( phylogeny.getName() ).replaceAll( " ", "_" );
}
else if ( phylogeny.getIdentifier() != null ) {
final StringBuffer sb = new StringBuffer();
if ( !ForesterUtil.isEmpty( phylogeny.getIdentifier().getProvider() ) ) {
sb.append( phylogeny.getIdentifier().getProvider() );
sb.append( "_" );
}
sb.append( phylogeny.getIdentifier().getValue() );
my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
}
_main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
Util.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
.getControlPanel(), _main_frame.getConfiguration() );
_main_frame.getMainPanel().getControlPanel().showWhole();
}
}
}
_main_frame.getContentPane().repaint();
if ( ( ( trees != null ) && ( trees.length > 0 ) ) && ( ( new Date().getTime() - start_time ) > 20000 ) ) {
try {
JOptionPane.showMessageDialog( null,
ForesterUtil.wordWrap( "Successfully read in " + trees.length
+ " evolutionry tree(s) from [" + url + "]", 80 ),
"Success",
JOptionPane.INFORMATION_MESSAGE );
}
catch ( final Exception e ) {
// Not important if this fails, do nothing.
}
_main_frame.getContentPane().repaint();
}
}
_main_frame.activateSaveAllIfNeeded();
System.gc();
}
@Override
public void run() {
readPhylogeniesFromWebservice();
}
}