JAL-1078 - removed 'Load Score File' menu item and extended annotation file loader...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8b71a54..bfcab9e 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3926,89 +3926,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     }
   }
-  
-  @Override
-  public void loadScores_actionPerformed(ActionEvent e)
-  {
-           // Pick the tree file
-           JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-           chooser.setFileView(new JalviewFileView());
-           chooser.setDialogTitle("Select a T-Coffee scores ascii file");
-           chooser.setToolTipText("Load a score file");
-
-           int value = chooser.showOpenDialog(null);
-
-           if (value == JalviewFileChooser.APPROVE_OPTION)
-           {
-             String sFilePath = chooser.getSelectedFile().getPath();
-             jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath);
-           
-             
-             try 
-             {
-                 TCoffeeScoreFile result = new TCoffeeScoreFile(sFilePath, FormatAdapter.FILE);
-                 if (!result.isValid()) { 
-                   JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),
-                            "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
-                   return;
-                   }
-
-                 /*
-                  * check that the score matrix matches the alignment dimensions
-                  */
-                 AlignmentI aln; 
-                 if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
-                     // TODO: raise a dialog box here rather than bomb out.
-               JOptionPane.showMessageDialog(Desktop.desktop, "The scores matrix does not match the alignment dimensions",
-                        "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
-                 }
-                 if (result.annotateAlignment(alignPanel.getAlignment(), true))
-                 {
-                         tcoffeeColour.setEnabled(true);
-                         tcoffeeColour.setSelected(true);
-                         // switch to this color
-                         changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
-                 } else {
-                   tcoffeeColour.setEnabled(false);
-                   tcoffeeColour.setSelected(false);
-                 }
-                 if (result.getWarningMessage()!=null)
-                 {
-                   JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),"Problem reading T-COFEEE score file", JOptionPane.WARNING_MESSAGE);
-                 }
-             } 
-             catch (Exception ex) {
-               JOptionPane.showMessageDialog(
-                                       Desktop.desktop, 
-                                       ex.getMessage(), 
-                                       "unexpected problem reading T-COFFEE score file", 
-                                       JOptionPane.WARNING_MESSAGE);
-
-               ex.printStackTrace();
-             }
-           }
-
-  } 
 
-  
   @Override
-  protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
-         changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
+  protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+  {
+    changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
   }
-  
-//  /**
-//   * Load the (T-Coffee) score file from the specified url 
-//   * 
-//   * @param url The absolute path from where download and read the score file
-//   * @throws IOException 
-//   */
-//  public void loadScoreFile(URL url ) throws IOException {
-//       
-//       TCoffeeScoreFile result = new TCoffeeScoreFile();
-//       result.parse( new InputStreamReader( url.openStream() ) );
-//       tcoffeeScoreFile = result;
-//  }  
-  
+
   public TreePanel ShowNewickTree(NewickFile nf, String title)
   {
     return ShowNewickTree(nf, title, 600, 500, 4, 5);
@@ -4825,54 +4749,92 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (!isAnnotation)
       {
-        // try to see if its a JNet 'concise' style annotation file *before* we
-        // try to parse it as a features file
-        if (format == null)
+        // first see if its a T-COFFEE score file
+        TCoffeeScoreFile tcf = null;
+        try
         {
-          format = new IdentifyFile().Identify(file, protocol);
-        }
-        if (format.equalsIgnoreCase("JnetFile"))
+          tcf = new TCoffeeScoreFile(file, protocol);
+          if (tcf.isValid())
+          {
+            if (tcf.annotateAlignment(viewport.getAlignment(), true))
+            {
+              tcoffeeColour.setEnabled(true);
+              tcoffeeColour.setSelected(true);
+              changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+              isAnnotation = true;
+              statusBar
+                      .setText("Successfully pasted T-Coffee scores to alignment.");
+            }
+            else
+            {
+              // some problem - if no warning its probable that the ID matching process didn't work
+              JOptionPane.showMessageDialog(Desktop.desktop,
+                      tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
+                      "Problem reading T-COFFEE score file",
+                      JOptionPane.WARNING_MESSAGE);
+            }
+          }
+          else
+          {
+            tcf = null;
+          }
+        } catch (Exception x)
         {
-          jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
-                  protocol);
-          new JnetAnnotationMaker().add_annotation(predictions,
-                  viewport.getAlignment(), 0, false);
-          isAnnotation = true;
+          Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+          tcf = null;
         }
-        else
+        if (tcf == null)
         {
-          /*
-           * if (format.equalsIgnoreCase("PDB")) {
-           * 
-           * String pdbfn = ""; // try to match up filename with sequence id try
-           * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
-           * File(file); pdbfn = fl.getName(); } else if (protocol ==
-           * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
-           * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
-           * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
-           * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
-           * attempt to find a match in the alignment SequenceI mtch =
-           * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
-           * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
-           * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
-           * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
-           * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
-           * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
-           * System.err.println("Associated file : " + file + " with " +
-           * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
-           * TODO: maybe need to load as normal otherwise return; } }
-           */
+          // try to see if its a JNet 'concise' style annotation file *before*
+          // we
           // try to parse it as a features file
-          boolean isGroupsFile = parseFeaturesFile(file, protocol);
-          // if it wasn't a features file then we just treat it as a general
-          // alignment file to load into the current view.
-          if (!isGroupsFile)
+          if (format == null)
+          {
+            format = new IdentifyFile().Identify(file, protocol);
+          }
+          if (format.equalsIgnoreCase("JnetFile"))
           {
-            new FileLoader().LoadFile(viewport, file, protocol, format);
+            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                    file, protocol);
+            new JnetAnnotationMaker().add_annotation(predictions,
+                    viewport.getAlignment(), 0, false);
+            isAnnotation = true;
           }
           else
           {
-            alignPanel.paintAlignment(true);
+            /*
+             * if (format.equalsIgnoreCase("PDB")) {
+             * 
+             * String pdbfn = ""; // try to match up filename with sequence id
+             * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+             * new File(file); pdbfn = fl.getName(); } else if (protocol ==
+             * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+             * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+             * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+             * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+             * // attempt to find a match in the alignment SequenceI mtch =
+             * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+             * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+             * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+             * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+             * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+             * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+             * { System.err.println("Associated file : " + file + " with " +
+             * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+             * TODO: maybe need to load as normal otherwise return; } }
+             */
+            // try to parse it as a features file
+            boolean isGroupsFile = parseFeaturesFile(file, protocol);
+            // if it wasn't a features file then we just treat it as a general
+            // alignment file to load into the current view.
+            if (!isGroupsFile)
+            {
+              new FileLoader().LoadFile(viewport, file, protocol, format);
+            }
+            else
+            {
+              alignPanel.paintAlignment(true);
+            }
           }
         }
       }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6e8b420..6c1c8c6 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -207,8 +207,6 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem LoadtreeMenuItem = new JMenuItem();
   
-  JMenuItem loadScoresMenuItem = new JMenuItem();
-
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
@@ -1311,16 +1309,6 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     
-    loadScoresMenuItem.setActionCommand("Load T-Coffee scores");
-    loadScoresMenuItem.setText("Load T-Coffee scores");
-    loadScoresMenuItem.addActionListener(new ActionListener() {
-               
-               @Override
-               public void actionPerformed(ActionEvent e) {
-                       loadScores_actionPerformed(e);
-               }
-       });
-    
     scaleAbove.setVisible(false);
     scaleAbove.setText("Scale Above");
     scaleAbove.addActionListener(new java.awt.event.ActionListener()
@@ -1817,7 +1805,6 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
     fileMenu.add(associatedData);
-    fileMenu.add(loadScoresMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);