JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / ext / forester / io / TreeParser.java

diff --git a/src/jalview/ext/forester/io/TreeParser.java b/src/jalview/ext/forester/io/TreeParser.java
deleted file mode 100644 (file)
index 43fd1fa..0000000
--- a/src/jalview/ext/forester/io/TreeParser.java
+++ /dev/null
@@ -1,198 +0,0 @@
-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;
-
-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();
-  }
-
-  public void loadTree(AlignViewport viewport)
-  {
-
-    NewickFile fin = null; // old tree
-      try
-      {
-        AptxInit.createInstanceFromFile(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)
-// {
-// String[] AptxArgs = new String[] { "-c",
-// "_aptx_jalview_configuration_file", filePath };
-// MainFrame aptx = Archaeopteryx.main(AptxArgs);
-//
-// LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
-// viewport.getAlignment().getSequencesArray(),
-// aptx.getMainPanel().getCurrentTreePanel().getPhylogeny());
-//
-// bindAptxNodes.associateLeavesToSequences();
-//
-// new JalviewBinding(aptx, viewport, bindAptxNodes.getAlignmentWithNodes(),
-// bindAptxNodes.getNodesWithAlignment());
-//
-// AptxInit.bindFrameToJalview(aptx);
-//
-// return aptx;
-//
-//
-// }
-// //
-// 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();
-// }
-//
-// }
-//
-//
-//
-//
-//
-//