From 60a5ed3360e059bf15e6b2e008d491e86474893b Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 19 Dec 2017 14:16:49 +0000
Subject: [PATCH] JAL-281 cleared out useless tree parser class

---
 src/jalview/ext/forester/io/TreeParser.java |  174 +--------------------------
 src/jalview/gui/AlignFrame.java             |   19 ++-
 2 files changed, 18 insertions(+), 175 deletions(-)

diff --git a/src/jalview/ext/forester/io/TreeParser.java b/src/jalview/ext/forester/io/TreeParser.java
index cbdc3e8..29131c5 100644
--- a/src/jalview/ext/forester/io/TreeParser.java
+++ b/src/jalview/ext/forester/io/TreeParser.java
@@ -1,180 +1,10 @@
 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.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)
+  public TreeParser()
   {
 
-    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)
-// {
-// 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();
-// }
-//
-// }
-//
-//
-//
-//
-//
-//
+}
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index dbcddf9..cb5c14f 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,7 +63,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.AptxInit;
 import jalview.ext.forester.io.SupportedTreeFileFilter;
-import jalview.ext.forester.io.TreeParser;
 import jalview.ext.treeviewer.TreeFrameI;
 import jalview.ext.treeviewer.TreeViewerBindingI;
 import jalview.ext.treeviewer.TreeViewerUtils;
@@ -4024,8 +4023,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       Cache.setProperty("LAST_DIRECTORY", filePath);
       
       
-      TreeParser treeParser = new TreeParser(filePath);
-      treeParser.loadTree(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(this, ex.getMessage(),
+                MessageManager.getString("label.problem_reading_tree_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
 
     }
   }
-- 
1.7.10.2