X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3644b28691d0fddff130add1c80773c72656cf4c;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=7dff2ac8ed213b75add7590222efb53700d28c03;hpb=d7361eaa08dc9af7d996851f39b7a2007d1b8832;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7dff2ac..3644b28 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,14 +63,19 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
+import jalview.io.StructureFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.Blosum62ColourScheme;
@@ -175,7 +180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Last format used to load or save alignments in this window
    */
-  String currentFileFormat = null;
+  FileFormatI currentFileFormat = null;
 
   /**
    * Current filename for this alignment
@@ -484,7 +489,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param format
    *          format of file
    */
-  public void setFileName(String file, String format)
+  public void setFileName(String file, FileFormatI format)
   {
     fileName = file;
     setFileFormat(format);
@@ -669,6 +674,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           toggleHiddenRegions(toggleSeqs, toggleCols);
           break;
         }
+        case KeyEvent.VK_B:
+        {
+          boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
+          boolean modifyExisting = true; // always modify, don't clear
+                                         // evt.isShiftDown();
+          boolean invertHighlighted = evt.isAltDown();
+          avc.markHighlightedColumns(invertHighlighted, modifyExisting,
+                  toggleSel);
+          break;
+        }
         case KeyEvent.VK_PAGE_UP:
           if (viewport.getWrapAlignment())
           {
@@ -1003,7 +1018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // originating file's format
       // TODO: work out how to recover feature settings for correct view(s) when
       // file is reloaded.
-      if (currentFileFormat.equals("Jalview"))
+      if (FileFormat.Jalview.equals(currentFileFormat))
       {
         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
         for (int i = 0; i < frames.length; i++)
@@ -1025,7 +1040,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+                : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
@@ -1033,7 +1049,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Rectangle bounds = this.getBounds();
 
         FileLoader loader = new FileLoader();
-        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+                : DataSourceType.FILE;
         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
                 protocol, currentFileFormat);
 
@@ -1077,9 +1094,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void save_actionPerformed(ActionEvent e)
   {
-    if (fileName == null
-            || (currentFileFormat == null || !jalview.io.FormatAdapter
-                    .isValidIOFormat(currentFileFormat, true))
+    if (fileName == null || (currentFileFormat == null)
             || fileName.startsWith("http"))
     {
       saveAs_actionPerformed(null);
@@ -1099,11 +1114,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
-            currentFileFormat, false);
+    JalviewFileChooser chooser = JalviewFileChooser.forWrite(
+            Cache.getProperty("LAST_DIRECTORY"),
+            // AppletFormatAdapter.WRITABLE_EXTENSIONS,
+            // AppletFormatAdapter.WRITABLE_FNAMES,
+            currentFileFormat.toString(), false);
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
@@ -1117,14 +1132,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       currentFileFormat = chooser.getSelectedFormat();
       while (currentFileFormat == null)
       {
-        JOptionPane
+        JvOptionPane
                 .showInternalMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.select_file_format_before_saving"),
                         MessageManager
                                 .getString("label.file_format_not_specified"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         currentFileFormat = chooser.getSelectedFormat();
         value = chooser.showSaveDialog(this);
         if (value != JalviewFileChooser.APPROVE_OPTION)
@@ -1135,24 +1150,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       fileName = chooser.getSelectedFile().getPath();
 
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
-              currentFileFormat);
+      Cache.setProperty("DEFAULT_FILE_FORMAT",
+              currentFileFormat.toString());
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-      if (currentFileFormat.indexOf(" ") > -1)
-      {
-        currentFileFormat = currentFileFormat.substring(0,
-                currentFileFormat.indexOf(" "));
-      }
+      Cache.setProperty("LAST_DIRECTORY", fileName);
       saveAlignment(fileName, currentFileFormat);
     }
   }
 
-  public boolean saveAlignment(String file, String format)
+  public boolean saveAlignment(String file, FileFormatI format)
   {
     boolean success = true;
 
-    if (format.equalsIgnoreCase("Jalview"))
+    if (FileFormat.Jalview.equals(format))
     {
       String shortName = title;
 
@@ -1171,16 +1181,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
-      {
-        warningMessage("Cannot save file " + fileName + " using format "
-                + format, "Alignment output format not supported");
-        if (!Jalview.isHeadlessMode())
-        {
-          saveAs_actionPerformed(null);
-        }
-        return false;
-      }
+      // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
+      // {
+      // warningMessage("Cannot save file " + fileName + " using format "
+      // + format, "Alignment output format not supported");
+      // if (!Jalview.isHeadlessMode())
+      // {
+      // saveAs_actionPerformed(null);
+      // }
+      // return false;
+      // }
 
       AlignmentExportData exportData = getAlignmentForExport(format,
               viewport, null);
@@ -1225,11 +1235,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!success)
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager
+      JvOptionPane.showInternalMessageDialog(this, MessageManager
               .formatMessage("label.couldnt_save_file",
                       new Object[] { fileName }), MessageManager
               .getString("label.error_saving_file"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
     }
 
     return success;
@@ -1244,8 +1254,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      JOptionPane.showInternalMessageDialog(this, warning, title,
-              JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showInternalMessageDialog(this, warning, title,
+              JvOptionPane.WARNING_MESSAGE);
     }
     return;
   }
@@ -1260,8 +1270,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void outputText_actionPerformed(ActionEvent e)
   {
 
-    AlignmentExportData exportData = getAlignmentForExport(
-            e.getActionCommand(), viewport, null);
+    FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+    AlignmentExportData exportData = getAlignmentForExport(fileFormat,
+            viewport, null);
     if (exportData.getSettings().isCancelled())
     {
       return;
@@ -1270,8 +1281,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     cap.setForInput(null);
     try
     {
+      FileFormatI format = fileFormat;
       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
-              .formatSequences(e.getActionCommand(),
+              .formatSequences(format,
                       exportData.getAlignment(),
                       exportData.getOmitHidden(),
                       exportData.getStartEndPostions(),
@@ -1288,7 +1300,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   public static AlignmentExportData getAlignmentForExport(
-          String exportFormat, AlignViewportI viewport,
+          FileFormatI format, AlignViewportI viewport,
           AlignExportSettingI exportSettings)
   {
     AlignmentI alignmentToExport = null;
@@ -1304,7 +1316,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (settings == null)
     {
       settings = new AlignExportSettings(hasHiddenSeqs,
-              viewport.hasHiddenColumns(), exportFormat);
+              viewport.hasHiddenColumns(), format);
     }
     // settings.isExportAnnotations();
 
@@ -1340,14 +1352,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HtmlSvgOutput(null, alignPanel);
+    HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
+    htmlSVG.exportHTML(null);
   }
 
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
-    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
-    bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+    bjs.exportHTML(null);
   }
 
   public void createImageMap(File file, String image)
@@ -1861,7 +1874,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       omitHidden = viewport.getViewAsString(true);
     }
 
-    String output = new FormatAdapter().formatSequences("Fasta", seqs,
+    String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+            seqs,
             omitHidden, null);
 
     StringSelection ss = new StringSelection(output);
@@ -1948,7 +1962,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return;
       }
 
-      String str, format;
+      String str;
+      FileFormatI format;
       try
       {
         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
@@ -1957,7 +1972,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           return;
         }
 
-        format = new IdentifyFile().identify(str, "Paste");
+        format = new IdentifyFile().identify(str, DataSourceType.PASTE);
 
       } catch (OutOfMemoryError er)
       {
@@ -1987,7 +2002,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // parse the clipboard as an alignment.
-        alignment = new FormatAdapter().readFile(str, "Paste", format);
+        alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
+                format);
         sequences = alignment.getSequencesArray();
       }
 
@@ -2356,13 +2372,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .getAlignment().getWidth()) ? true : false;
       if (isEntireAlignWidth)
       {
-        int confirm = JOptionPane.showConfirmDialog(this,
+        int confirm = JvOptionPane.showConfirmDialog(this,
                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
-                JOptionPane.OK_CANCEL_OPTION);
+                JvOptionPane.OK_CANCEL_OPTION);
 
-        if (confirm == JOptionPane.CANCEL_OPTION
-                || confirm == JOptionPane.CLOSED_OPTION)
+        if (confirm == JvOptionPane.CANCEL_OPTION
+                || confirm == JvOptionPane.CLOSED_OPTION)
         {
           return;
         }
@@ -3639,13 +3655,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-            int option = JOptionPane.showInternalConfirmDialog(
+            int option = JvOptionPane.showInternalConfirmDialog(
                     jalview.gui.Desktop.desktop, MessageManager
                             .getString("label.remove_from_default_list"),
                     MessageManager
                             .getString("label.remove_user_defined_colour"),
-                    JOptionPane.YES_NO_OPTION);
-            if (option == JOptionPane.YES_OPTION)
+                    JvOptionPane.YES_NO_OPTION);
+            if (option == JvOptionPane.YES_OPTION)
             {
               jalview.gui.UserDefinedColours
                       .removeColourFromDefaults(radioItem.getText());
@@ -3793,10 +3809,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if ((viewport.getSelectionGroup() == null)
             || (viewport.getSelectionGroup().getSize() < 2))
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager
+      JvOptionPane.showInternalMessageDialog(this, MessageManager
               .getString("label.you_must_select_least_two_sequences"),
               MessageManager.getString("label.invalid_selection"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -3822,14 +3838,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getSelectionGroup().getSize() > 0))
             || (viewport.getAlignment().getHeight() < 4))
     {
-      JOptionPane
+      JvOptionPane
               .showInternalMessageDialog(
                       this,
                       MessageManager
                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
                       MessageManager
                               .getString("label.sequence_selection_insufficient"),
-                      JOptionPane.WARNING_MESSAGE);
+                      JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -3927,14 +3943,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
                         MessageManager
                                 .getString("label.not_enough_sequences"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         return;
       }
 
@@ -3945,14 +3961,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (_s.getLength() < sg.getEndRes())
         {
-          JOptionPane
+          JvOptionPane
                   .showMessageDialog(
                           Desktop.desktop,
                           MessageManager
                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
                           MessageManager
                                   .getString("label.sequences_selection_not_aligned"),
-                          JOptionPane.WARNING_MESSAGE);
+                          JvOptionPane.WARNING_MESSAGE);
 
           return;
         }
@@ -3966,14 +3982,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // are the visible sequences aligned?
       if (!viewport.getAlignment().isAligned(false))
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
                         MessageManager
                                 .getString("label.sequences_not_aligned"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
 
         return;
       }
@@ -4238,11 +4254,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() == 1)
     {
-      int option = JOptionPane.showConfirmDialog(this,
+      int option = JvOptionPane.showConfirmDialog(this,
               MessageManager.getString("warn.oneseq_msainput_selection"),
               MessageManager.getString("label.invalid_selection"),
-              JOptionPane.OK_CANCEL_OPTION);
-      if (option == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION);
+      if (option == JvOptionPane.OK_OPTION)
       {
         msa = viewport.getAlignmentView(false);
       }
@@ -4314,25 +4330,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       jalview.io.NewickFile fin = null;
       try
       {
-        fin = new jalview.io.NewickFile(choice, "File");
+        fin = new NewickFile(choice, DataSourceType.FILE);
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       } catch (Exception ex)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         ex.getMessage(),
                         MessageManager
                                 .getString("label.problem_reading_tree_file"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
       if (fin != null && fin.hasWarningMessage())
       {
-        JOptionPane.showMessageDialog(Desktop.desktop, fin
+        JvOptionPane.showMessageDialog(Desktop.desktop, fin
                 .getWarningMessage(), MessageManager
                 .getString("label.possible_problem_with_tree_file"),
-                JOptionPane.WARNING_MESSAGE);
+                JvOptionPane.WARNING_MESSAGE);
       }
     }
   }
@@ -4717,8 +4733,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("label.translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
-              JOptionPane.ERROR_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+              JvOptionPane.ERROR_MESSAGE);
       return;
     }
     if (al == null || al.getHeight() == 0)
@@ -4727,8 +4743,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
       final String errorTitle = MessageManager
               .getString("label.translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
-              JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+              JvOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -4754,11 +4770,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Set the file format
    * 
-   * @param fileFormat
+   * @param format
    */
-  public void setFileFormat(String fileFormat)
+  public void setFileFormat(FileFormatI format)
   {
-    this.currentFileFormat = fileFormat;
+    this.currentFileFormat = format;
   }
 
   /**
@@ -4766,14 +4782,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param file
    *          contents or path to retrieve file
-   * @param type
+   * @param sourceType
    *          access mode of file (see jalview.io.AlignFile)
    * @return true if features file was parsed correctly.
    */
-  public boolean parseFeaturesFile(String file, String type)
+  public boolean parseFeaturesFile(String file, DataSourceType sourceType)
   {
-    return avc.parseFeaturesFile(file, type,
-            jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+    return avc.parseFeaturesFile(file, sourceType,
+            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
 
   }
 
@@ -4818,7 +4834,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // Java's Transferable for native dnd
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
+    List<String> files = new ArrayList<String>();
+    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
 
     try
     {
@@ -4844,13 +4861,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           String file = files.get(i).toString();
           String pdbfn = "";
-          String protocol = FormatAdapter.checkProtocol(file);
-          if (protocol == jalview.io.FormatAdapter.FILE)
+          DataSourceType protocol = FormatAdapter.checkProtocol(file);
+          if (protocol == DataSourceType.FILE)
           {
             File fl = new File(file);
             pdbfn = fl.getName();
           }
-          else if (protocol == jalview.io.FormatAdapter.URL)
+          else if (protocol == DataSourceType.URL)
           {
             URL url = new URL(file);
             pdbfn = url.getFile();
@@ -4874,7 +4891,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             }
             if (mtch != null)
             {
-              String type = null;
+              FileFormatI type = null;
               try
               {
                 type = new IdentifyFile().identify(file, protocol);
@@ -4884,7 +4901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (type != null)
               {
-                if (type.equalsIgnoreCase("PDB"))
+                if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type))
                 {
                   filesmatched.add(new Object[] { file, protocol, mtch });
                   continue;
@@ -4899,20 +4916,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (filesmatched.size() > 0)
         {
           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                  || JOptionPane
+                  || JvOptionPane
                           .showConfirmDialog(
                                   this,
                                   MessageManager
                                           .formatMessage(
-                                                  "label.automatically_associate_pdb_files_with_sequences_same_name",
+                                                  "label.automatically_associate_structure_files_with_sequences_same_name",
                                                   new Object[] { Integer
                                                           .valueOf(
                                                                   filesmatched
                                                                           .size())
                                                           .toString() }),
                                   MessageManager
-                                          .getString("label.automatically_associate_pdb_files_by_name"),
-                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+                                          .getString("label.automatically_associate_structure_files_by_name"),
+                                  JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
 
           {
             for (Object[] fm : filesmatched)
@@ -4924,7 +4941,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 PDBEntry pe = new AssociatePdbFileWithSeq()
                         .associatePdbWithSeq((String) fm[0],
-                                (String) fm[1], toassoc, false,
+                                (DataSourceType) fm[1], toassoc, false,
                                 Desktop.instance);
                 if (pe != null)
                 {
@@ -4942,7 +4959,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           if (assocfiles > 0
                   && (Cache.getDefault(
-                          "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+                          "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
                           .showConfirmDialog(
                                   this,
                                   "<html>"
@@ -4957,7 +4974,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                           + "</html>",
                                   MessageManager
                                           .getString("label.ignore_unmatched_dropped_files"),
-                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+                                  JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
           {
             return;
           }
@@ -4983,21 +5000,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param file
    *          either a filename or a URL string.
    */
-  public void loadJalviewDataFile(String file, String protocol,
-          String format, SequenceI assocSeq)
+  public void loadJalviewDataFile(String file, DataSourceType sourceType,
+          FileFormatI format, SequenceI assocSeq)
   {
     try
     {
-      if (protocol == null)
+      if (sourceType == null)
       {
-        protocol = FormatAdapter.checkProtocol(file);
+        sourceType = FormatAdapter.checkProtocol(file);
       }
       // if the file isn't identified, or not positively identified as some
       // other filetype (PFAM is default unidentified alignment file type) then
       // try to parse as annotation.
-      boolean isAnnotation = (format == null || format
-              .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
-              .annotateAlignmentView(viewport, file, protocol) : false;
+      boolean isAnnotation = (format == null || FileFormat.Pfam
+              .equals(format)) ? new AnnotationFile()
+              .annotateAlignmentView(viewport, file, sourceType) : false;
 
       if (!isAnnotation)
       {
@@ -5005,7 +5022,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         TCoffeeScoreFile tcf = null;
         try
         {
-          tcf = new TCoffeeScoreFile(file, protocol);
+          tcf = new TCoffeeScoreFile(file, sourceType);
           if (tcf.isValid())
           {
             if (tcf.annotateAlignment(viewport.getAlignment(), true))
@@ -5022,7 +5039,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               // some problem - if no warning its probable that the ID matching
               // process didn't work
-              JOptionPane
+              JvOptionPane
                       .showMessageDialog(
                               Desktop.desktop,
                               tcf.getWarningMessage() == null ? MessageManager
@@ -5030,7 +5047,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                       : tcf.getWarningMessage(),
                               MessageManager
                                       .getString("label.problem_reading_tcoffee_score_file"),
-                              JOptionPane.WARNING_MESSAGE);
+                              JvOptionPane.WARNING_MESSAGE);
             }
           }
           else
@@ -5051,12 +5068,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // try to parse it as a features file
           if (format == null)
           {
-            format = new IdentifyFile().identify(file, protocol);
+            format = new IdentifyFile().identify(file, sourceType);
           }
-          if (format.equalsIgnoreCase("JnetFile"))
+          if (FileFormat.Jnet.equals(format))
           {
-            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                    file, protocol);
+            JPredFile predictions = new JPredFile(
+                    file, sourceType);
             new JnetAnnotationMaker();
             JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
@@ -5067,16 +5084,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             viewport.setColumnSelection(cs);
             isAnnotation = true;
           }
-          else if (IdentifyFile.FeaturesFile.equals(format))
+          // else if (IdentifyFile.FeaturesFile.equals(format))
+          else if (FileFormat.Features.equals(format))
           {
-            if (parseFeaturesFile(file, protocol))
+            if (parseFeaturesFile(file, sourceType))
             {
               alignPanel.paintAlignment(true);
             }
           }
           else
           {
-            new FileLoader().LoadFile(viewport, file, protocol, format);
+            new FileLoader().LoadFile(viewport, file, sourceType, format);
           }
         }
       }
@@ -5101,8 +5119,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       new OOMWarning(
               "loading data "
-                      + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
-                              : "using " + protocol + " from " + file)
+                      + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
+                              : "using " + sourceType + " from " + file)
                               : ".")
                       + (format != null ? "(parsing as '" + format
                               + "' file)" : ""), oom, Desktop.desktop);
@@ -5151,8 +5169,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (e.isPopupTrigger())
     {
       String msg = MessageManager.getString("label.enter_view_name");
-      String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
-              JOptionPane.QUESTION_MESSAGE);
+      String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
+              JvOptionPane.QUESTION_MESSAGE);
 
       if (reply != null)
       {
@@ -5891,12 +5909,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       } catch (Exception ex)
       {
         System.err.println((ex.toString()));
-        JOptionPane
+        JvOptionPane
                 .showInternalMessageDialog(Desktop.desktop, MessageManager
                         .getString("label.couldnt_run_groovy_script"),
                         MessageManager
                                 .getString("label.groovy_support_failed"),
-                        JOptionPane.ERROR_MESSAGE);
+                        JvOptionPane.ERROR_MESSAGE);
       }
     }
     else
@@ -5929,6 +5947,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return false;
   }
+
+  @Override
+  protected void selectHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // include key modifier check in case user selects from menu
+    avc.markHighlightedColumns(
+            (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
+            true,
+            (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
+  }
 }
 
 class PrintThread extends Thread