Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

[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
new file mode 100644 (file)
index 0000000..43fd1fa
--- /dev/null
+++ b/src/jalview/ext/forester/io/TreeParser.java
@@ -0,0 +1,198 @@
+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();
+// }
+//
+// }
+//
+//
+//
+//
+//
+//