Hide Tab settings for build

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cfbd186..65b9a08 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -34,6 +34,7 @@ import jalview.io.*;
 import jalview.jbgui.*;\r
 import jalview.schemes.*;\r
 import jalview.ws.*;\r
+import javax.swing.event.AncestorEvent;\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -94,21 +95,24 @@ public class AlignFrame
     else if(sortby.equals("Pairwise Identity"))\r
       sortPairwiseMenuItem_actionPerformed(null);\r
 \r
-    tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+   // remove(tabbedPane);\r
+    getContentPane().add(alignPanel, BorderLayout.CENTER);\r
+\r
+    setGUINucleotide(al.isNucleotide());\r
+\r
+  //  tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
 \r
     ///Dataset tab\r
     /////////////////////////\r
-\r
     if(al.getDataset()==null)\r
     {\r
       al.setDataset(null);\r
     }\r
-\r
-    AlignViewport ds = new AlignViewport(al.getDataset(), true);\r
-    AlignmentPanel dap = new AlignmentPanel(this, ds);\r
-    tabbedPane.add("Dataset", dap);\r
-    viewports.add(ds);\r
-    alignPanels.add(dap);\r
+   // AlignViewport ds = new AlignViewport(al.getDataset(), true);\r
+   // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+  //  tabbedPane.add("Dataset", dap);\r
+  //  viewports.add(ds);\r
+  //  alignPanels.add(dap);\r
     /////////////////////////\r
 \r
 \r
@@ -123,7 +127,6 @@ public class AlignFrame
      }\r
    });\r
 \r
-\r
        if(Desktop.desktop!=null)\r
     addServiceListeners();\r
   }\r
@@ -162,6 +165,26 @@ public class AlignFrame
 \r
   }\r
 \r
+  public void setGUINucleotide(boolean nucleotide)\r
+  {\r
+    showTranslation.setVisible( nucleotide );\r
+    sequenceFeatures.setVisible(!nucleotide );\r
+    featureSettings.setVisible( !nucleotide );\r
+    conservationMenuItem.setVisible( !nucleotide );\r
+    modifyConservation.setVisible(   !nucleotide );\r
+\r
+    //Deal with separators\r
+    //Remember AlignFrame always starts as protein\r
+    if(nucleotide)\r
+    {\r
+      viewMenu.remove(viewMenu.getItemCount()-2);\r
+    }\r
+    else\r
+    {\r
+      calculateMenu.remove(calculateMenu.getItemCount()-2);\r
+    }\r
+  }\r
+\r
 \r
   /*\r
    Added so Castor Mapping file can obtain Jalview Version\r
@@ -384,7 +407,9 @@ public class AlignFrame
    */\r
   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    new HTMLOutput(viewport);\r
+    new HTMLOutput(viewport,\r
+                   alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
   }\r
 \r
   public void createImageMap(File file, String image)\r
@@ -2495,29 +2520,20 @@ public class AlignFrame
 \r
 public void showTranslation_actionPerformed(ActionEvent e)\r
 {\r
-\r
-  if(!viewport.alignment.isNucleotide())\r
-    return;\r
-\r
-  viewport.showTranslation(showTranslation.isSelected());\r
-\r
-  if(!viewport.alignment.isNucleotide())\r
-    return;\r
-\r
   int s, sSize = viewport.alignment.getHeight();\r
   SequenceI [] newSeq = new SequenceI[sSize];\r
 \r
   int res, resSize;\r
   StringBuffer protein;\r
-  SequenceI seq;\r
+  String seq;\r
   for(s=0; s<sSize; s++)\r
   {\r
     protein = new StringBuffer();\r
-    seq = (SequenceI)viewport.alignment.getSequenceAt(s);\r
-    resSize = seq.getLength();\r
+    seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+    resSize = seq.length();\r
     for(res = 0; res < resSize; res+=3)\r
     {\r
-      String codon = seq.getSequence(res, res+3);\r
+      String codon = seq.substring(res, res+3);\r
       codon = codon.replace('U', 'T');\r
       String aa = ResidueProperties.codonTranslate(codon);\r
       if(aa==null)\r
@@ -2527,7 +2543,7 @@ public void showTranslation_actionPerformed(ActionEvent e)
       else\r
         protein.append( aa );\r
     }\r
-    newSeq[s] = new Sequence(seq.getName(), protein.toString());\r
+    newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
   }\r
 \r
 \r
@@ -2576,35 +2592,36 @@ public void showTranslation_actionPerformed(ActionEvent e)
   }\r
 \r
 \r
-   // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
-    //                         NEW_WINDOW_WIDTH,\r
-     //                        NEW_WINDOW_HEIGHT);\r
+    AlignFrame af = new AlignFrame(al);\r
+    Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+                             NEW_WINDOW_WIDTH,\r
+                             NEW_WINDOW_HEIGHT);\r
 \r
-    AlignViewport newViewport = new AlignViewport(al);\r
-    AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
-    tabbedPane.add("Protein", ap);\r
-    viewports.add(newViewport);\r
-    alignPanels.add(ap);\r
+\r
+   // AlignViewport newViewport = new AlignViewport(al);\r
+   // AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+   // tabbedPane.add("Protein", ap);\r
+   // viewports.add(newViewport);\r
+  //  alignPanels.add(ap);\r
 \r
     ///Dataset tab\r
   /////////////////////////\r
 \r
-    AlignViewport ds = new AlignViewport(al.getDataset());\r
-    ds.setDataset(true);\r
-    AlignmentPanel dap = new AlignmentPanel(this, ds);\r
-    tabbedPane.add("Dataset", dap);\r
-    viewports.add(ds);\r
-    alignPanels.add(dap);\r
+  //  AlignViewport ds = new AlignViewport(al.getDataset());\r
+  //  ds.setDataset(true);\r
+  //  AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+  //  tabbedPane.add("Dataset", dap);\r
+  //  viewports.add(ds);\r
+  //  alignPanels.add(dap);\r
   /////////////////////////\r
 \r
 \r
 }\r
 \r
-public void tabSelected()\r
-{\r
+/*public void tabSelected()\r
+ {\r
   int index = tabbedPane.getSelectedIndex();\r
   viewport = (AlignViewport)viewports.elementAt(index);\r
   alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
-}\r
-\r
+ }*/\r
 }\r