JAL-2344 FileFormats singleton for formats, FileFormatI simplified

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index aa3cad4..e36204c 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,6 +38,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
@@ -77,7 +79,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPopupMenu;
 import javax.swing.JRadioButtonMenuItem;
 
@@ -247,17 +248,15 @@ public class PopupMenu extends JPopupMenu
     colours.add(strandColour);
     colours.add(turnColour);
     colours.add(buriedColour);
-    colours.add(abovePIDColour);
     colours.add(userDefinedColour);
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormats.getInstance().getWritableFormats(true))
     {
-      JMenuItem item = new JMenuItem(
-              jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+      JMenuItem item = new JMenuItem(ff);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -535,9 +534,16 @@ public class PopupMenu extends JPopupMenu
         noColourmenuItem.setSelected(true);
       }
 
-      if (sg.cs != null && sg.cs.conservationApplied())
+      if (sg.cs != null)
       {
+        if (sg.cs.conservationApplied())
+        {
         conservationMenuItem.setSelected(true);
+        }
+        if (sg.cs.getThreshold() > 0)
+        {
+          abovePIDColour.setSelected(true);
+        }
       }
       displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
@@ -616,7 +622,7 @@ public class PopupMenu extends JPopupMenu
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-    Map<String, String[]> linkset = new LinkedHashMap<String, String[]>();
+    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
 
     for (String link : links)
     {
@@ -641,6 +647,16 @@ public class PopupMenu extends JPopupMenu
 
     addshowLinks(linkMenu, linkset.values());
 
+    // disable link menu if there are no valid entries
+    if (linkMenu.getItemCount() > 0)
+    {
+      linkMenu.setEnabled(true);
+    }
+    else
+    {
+      linkMenu.setEnabled(false);
+    }
+
     if (sequence != null)
     {
       sequenceMenu.add(linkMenu);
@@ -649,6 +665,7 @@ public class PopupMenu extends JPopupMenu
     {
       add(linkMenu);
     }
+
   }
 
 
@@ -927,12 +944,12 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
-  private void addshowLinks(JMenu linkMenu, Collection<String[]> linkset)
+  private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
   {
-    for (String[] linkstrset : linkset)
+    for (List<String> linkstrset : linkset)
     {
       // split linkstr into label and url
-      addshowLink(linkMenu, linkstrset[1], linkstrset[3]);
+      addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
     }
   }
 
@@ -1666,7 +1683,7 @@ public class PopupMenu extends JPopupMenu
   public void createSequenceDetailsReport(SequenceI[] sequences)
   {
     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
-    StringBuffer contents = new StringBuffer();
+    StringBuilder contents = new StringBuilder(128);
     for (SequenceI seq : sequences)
     {
       contents.append("<p><h2>"
@@ -1681,7 +1698,6 @@ public class PopupMenu extends JPopupMenu
                       seq,
                       true,
                       true,
-                      false,
                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
                               .getSeqPanel().seqCanvas.fr.getMinMax()
                               : null);
@@ -1969,7 +1985,7 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       // JBPNote: Conservation name shouldn't be i18n translated
-      Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+      Conservation c = new Conservation("Group", sg.getSequences(ap.av
               .getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);
 
@@ -2078,14 +2094,14 @@ public class PopupMenu extends JPopupMenu
     {
       if (dialog.getName().indexOf(" ") > -1)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         ap,
                         MessageManager
                                 .getString("label.spaces_converted_to_backslashes"),
                         MessageManager
                                 .getString("label.no_spaces_allowed_sequence_name"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
@@ -2184,10 +2200,10 @@ public class PopupMenu extends JPopupMenu
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager.getString("label.web_browser_not_found_unix"),
               MessageManager.getString("label.web_browser_not_found"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
 
       ex.printStackTrace();
     }
@@ -2263,8 +2279,9 @@ public class PopupMenu extends JPopupMenu
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
-            ap, true));
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
+    cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
   }
 
   public void sequenceFeature_actionPerformed()