From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 17 Nov 2005 15:19:20 +0000 (+0000)
Subject: Hide Tab settings for build
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a94894810c6142a94239ca239ec8e800235c3b35;p=jalview.git

Hide Tab settings for build
---

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