JAL-2805 code refactor (actionPerformed cleaned up) & moved tree loading

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index 2363e4c..817fef3 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -93,6 +93,97 @@ public final class AptxInit
     return bindFrameToJalview(aptxApp);
   }
 
+  public static MainFrame createInstanceFromUrl()
+  {
+
+    return null;
+    // 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();
+    // }
+
+  }
+
 
 
   public static MainFrame createAptxFrame(

diff --git a/src/jalview/ext/forester/io/SupportedTreeFileFilter.java b/src/jalview/ext/forester/io/SupportedTreeFileFilter.java
index b13c92a..b077485 100644 (file)
--- a/src/jalview/ext/forester/io/SupportedTreeFileFilter.java
+++ b/src/jalview/ext/forester/io/SupportedTreeFileFilter.java
@@ -10,7 +10,8 @@ public enum SupportedTreeFileFilter
 {
   NHFILTER(MainFrame.nhfilter), NHXFILTER(MainFrame.nhxfilter),
   XMLFILTER(MainFrame.xmlfilter), TOLFILTER(MainFrame.tolfilter),
-  NEXUSFILTER(MainFrame.nexusfilter);
+  NEXUSFILTER(MainFrame.nexusfilter),
+  DEFAULTFILTER(MainFrame.defaultfilter);
 
   private final FileFilter treeFilter;
 

diff --git a/src/jalview/ext/forester/io/TreeParser.java b/src/jalview/ext/forester/io/TreeParser.java
index b2f36b8..96b5770 100644 (file)
--- a/src/jalview/ext/forester/io/TreeParser.java
+++ b/src/jalview/ext/forester/io/TreeParser.java
@@ -1,56 +1,84 @@
-// 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;
+
+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;
+      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)
@@ -75,90 +103,90 @@
 //
 // }
 // //
-// // 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();
+// }
 //
 // }
 //

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b9bf23e..4bd20fc 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -62,6 +62,7 @@ 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.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -3870,6 +3871,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return seqs;
   }
+public void chooseTreeFile() {
+  // Pick the tree file
+  JalviewFileChooser chooser = new JalviewFileChooser(
+          jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+  chooser.setFileView(new JalviewFileView());
+  chooser.setDialogTitle(
+          MessageManager.getString("label.select_newick_like_tree_file")); // modify
+  chooser.setToolTipText(
+          MessageManager.getString("label.load_tree_file"));
+  for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
+          .values())
+  {
+    chooser.setFileFilter(treeFormat.getTreeFilter());
+  }
+
+  int value = chooser.showOpenDialog(null);
+
+  if (value == JalviewFileChooser.APPROVE_OPTION)
+  {
+    String filePath = chooser.getSelectedFile().getPath();
+    Cache.setProperty("LAST_DIRECTORY", filePath);
+
+      TreeParser treeParser = new TreeParser(filePath);
+      treeParser.loadTree(viewport);
+
+    }
+  }
 
   /**
    * DOCUMENT ME!
@@ -3880,56 +3908,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
-    // Pick the tree file
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(
-            MessageManager.getString("label.select_newick_like_tree_file")); // modify
-    chooser.setToolTipText(
-            MessageManager.getString("label.load_tree_file"));
-    for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter.values())
-    {
-      chooser.setFileFilter(treeFormat.getTreeFilter());
-    }
-
-    int value = chooser.showOpenDialog(null);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      String filePath = chooser.getSelectedFile().getPath();
-      Cache.setProperty("LAST_DIRECTORY", filePath);
-
-      NewickFile fin = null;
-      try
-      {
-        AptxInit.createInstanceFromFile(filePath, getViewport());
-
-
-
-        fin = new NewickFile(filePath, DataSourceType.FILE);
-        viewport.setCurrentTree(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);
-      }
-    }
+    chooseTreeFile();
   }
 
   @Override
   protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
   {
+    AptxInit.createInstanceFromUrl();
 
   }