-// package jalview.ext.forester.io;
-//
-// import jalview.ext.archaeopteryx.AptxInit;
-// import jalview.ext.archaeopteryx.JalviewBinding;
-// import jalview.ext.archaeopteryx.LoadedTreeAssociation;
-// import jalview.ext.treeviewer.ExternalTreeParserI;
-// import jalview.gui.Desktop;
-// import jalview.gui.JvOptionPane;
-// import jalview.util.MessageManager;
-// import jalview.viewmodel.AlignmentViewport;
-//
-// import java.io.File;
-// import java.io.IOException;
-//
-// import org.forester.archaeopteryx.Archaeopteryx;
-// import org.forester.archaeopteryx.MainFrame;
-// import org.forester.util.ForesterUtil;
-//
-// public class TreeParser implements ExternalTreeParserI<MainFrame>
-// {
-// private final String filePath;
-//
-// private final File file;
-//
-// public TreeParser(final String treeFilePath)
-// {
-// final String possibleError = ForesterUtil.isReadableFile(treeFilePath);
-// if (possibleError != null)
-// {
-// JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
-// MessageManager.getString("label.problem_reading_tree_file"),
-// JvOptionPane.WARNING_MESSAGE);
-//
-// }
-// filePath = treeFilePath;
-// file = new File(filePath);
-//
-//
-// }
-//
-// public TreeParser(final File treeFile) throws IOException
-// {
-// final String possibleError = ForesterUtil.isReadableFile(treeFile);
-// if (possibleError != null)
-// {
-// JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
-// MessageManager.getString("label.problem_reading_tree_file"),
-// JvOptionPane.WARNING_MESSAGE);
-//
-// }
-// file = treeFile;
-// filePath = file.getCanonicalPath();
-// }
+package jalview.ext.forester.io;
+
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.gui.AlignViewport;
+//import jalview.ext.treeviewer.ExternalTreeParserI;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.NewickFile;
+import jalview.util.MessageManager;
+
+import java.io.File;
+import java.io.IOException;
+
+public class TreeParser // implements ExternalTreeParserI<MainFrame>
+{
+ private final String filePath;
+
+ private final File file;
+
+ public TreeParser(final String treeFilePath)
+ {
+
+ filePath = treeFilePath;
+ file = new File(filePath);
+
+ }
+
+ public TreeParser(final File treeFile) throws IOException
+ {
+ file = treeFile;
+ filePath = file.getCanonicalPath();
+ }
+
+ public void loadTree(AlignViewport viewport)
+ {
+
+ NewickFile fin = null; // old tree
+ try
+ {
+ AptxInit.createInstancesFromFile(filePath, viewport);
+
+ fin = new NewickFile(filePath, DataSourceType.FILE);
+ viewport.setCurrentTree(viewport.getAlignPanel().alignFrame
+ .showNewickTree(fin, filePath).getTree());
+
+ } catch (Exception ex)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager.getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager
+ .getString("label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }
+
+
//
// @Override
// public MainFrame loadTreeFile(AlignmentViewport viewport)
//
// }
// //
-// // void readPhylogeniesFromURL() {
-// // URL url = null;
-// // Phylogeny[] phys = null;
-// // final String message = "Please enter a complete URL, for example
-// // \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
-// // final String url_string = JOptionPane
-// // .showInputDialog( this,
-// // message,
-// // "Use URL/webservice to obtain a phylogeny",
-// // JOptionPane.QUESTION_MESSAGE );
-// // boolean nhx_or_nexus = false;
-// // if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
-// // try {
-// // url = new URL( url_string );
-// // PhylogenyParser parser = null;
-// // if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
-// // parser = new TolParser();
-// // }
-// // else {
-// // parser = ParserUtils
-// // .createParserDependingOnUrlContents( url,
-// // getConfiguration().isValidatePhyloXmlAgainstSchema() );
-// // }
-// // if ( parser instanceof NexusPhylogeniesParser ) {
-// // nhx_or_nexus = true;
-// // }
-// // else if ( parser instanceof NHXParser ) {
-// // nhx_or_nexus = true;
-// // }
-// // if ( _mainpanel.getCurrentTreePanel() != null ) {
-// // _mainpanel.getCurrentTreePanel().setWaitCursor();
-// // }
-// // else {
-// // _mainpanel.setWaitCursor();
-// // }
-// // final PhylogenyFactory factory =
+// void readPhylogeniesFromURL() {
+// URL url = null;
+// Phylogeny[] phys = null;
+// final String message = "Please enter a complete URL, for example
+// \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
+// final String url_string = JOptionPane
+// .showInputDialog( this,
+// message,
+// "Use URL/webservice to obtain a phylogeny",
+// JOptionPane.QUESTION_MESSAGE );
+// boolean nhx_or_nexus = false;
+// if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
+// try {
+// url = new URL( url_string );
+// PhylogenyParser parser = null;
+// if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
+// parser = new TolParser();
+// }
+// else {
+// parser = ParserUtils
+// .createParserDependingOnUrlContents( url,
+// getConfiguration().isValidatePhyloXmlAgainstSchema() );
+// }
+// if ( parser instanceof NexusPhylogeniesParser ) {
+// nhx_or_nexus = true;
+// }
+// else if ( parser instanceof NHXParser ) {
+// nhx_or_nexus = true;
+// }
+// if ( _mainpanel.getCurrentTreePanel() != null ) {
+// _mainpanel.getCurrentTreePanel().setWaitCursor();
+// }
+// else {
+// _mainpanel.setWaitCursor();
+// }
+// final PhylogenyFactory factory =
// ParserBasedPhylogenyFactory.getInstance();
-// // phys = factory.create( url.openStream(), parser );
-// // }
-// // catch ( final MalformedURLException e ) {
-// // JOptionPane.showMessageDialog( this,
-// // "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
-// // "Malformed URL",
-// // JOptionPane.ERROR_MESSAGE );
-// // }
-// // catch ( final IOException e ) {
-// // JOptionPane.showMessageDialog( this,
-// // "Could not read from " + url + "\n"
-// // + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
-// // "Failed to read URL",
-// // JOptionPane.ERROR_MESSAGE );
-// // }
-// // catch ( final Exception e ) {
-// // JOptionPane.showMessageDialog( this,
-// // ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
-// // "Unexpected Exception",
-// // JOptionPane.ERROR_MESSAGE );
-// // }
-// // finally {
-// // if ( _mainpanel.getCurrentTreePanel() != null ) {
-// // _mainpanel.getCurrentTreePanel().setArrowCursor();
-// // }
-// // else {
-// // _mainpanel.setArrowCursor();
-// // }
-// // }
-// // if ( ( phys != null ) && ( phys.length > 0 ) ) {
-// // if ( nhx_or_nexus &&
-// // getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
-// // for( final Phylogeny phy : phys ) {
-// // PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
-// // }
-// // }
-// // AptxUtil.addPhylogeniesToTabs( phys,
-// // new File( url.getFile() ).getName(),
-// // new File( url.getFile() ).toString(),
-// // getConfiguration(),
-// // getMainPanel() );
-// // _mainpanel.getControlPanel().showWhole();
-// // }
-// // }
-// // activateSaveAllIfNeeded();
-// // System.gc();
-// // }
+// phys = factory.create( url.openStream(), parser );
+// }
+// catch ( final MalformedURLException e ) {
+// JOptionPane.showMessageDialog( this,
+// "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
+// "Malformed URL",
+// JOptionPane.ERROR_MESSAGE );
+// }
+// catch ( final IOException e ) {
+// JOptionPane.showMessageDialog( this,
+// "Could not read from " + url + "\n"
+// + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+// "Failed to read URL",
+// JOptionPane.ERROR_MESSAGE );
+// }
+// catch ( final Exception e ) {
+// JOptionPane.showMessageDialog( this,
+// ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
+// "Unexpected Exception",
+// JOptionPane.ERROR_MESSAGE );
+// }
+// finally {
+// if ( _mainpanel.getCurrentTreePanel() != null ) {
+// _mainpanel.getCurrentTreePanel().setArrowCursor();
+// }
+// else {
+// _mainpanel.setArrowCursor();
+// }
+// }
+// if ( ( phys != null ) && ( phys.length > 0 ) ) {
+// if ( nhx_or_nexus &&
+// getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
+// for( final Phylogeny phy : phys ) {
+// PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+// }
+// }
+// AptxUtil.addPhylogeniesToTabs( phys,
+// new File( url.getFile() ).getName(),
+// new File( url.getFile() ).toString(),
+// getConfiguration(),
+// getMainPanel() );
+// _mainpanel.getControlPanel().showWhole();
+// }
+// }
+// activateSaveAllIfNeeded();
+// System.gc();
+// }
//
// }
//
git://source.jalview.org / jalview.git / blobdiff