JAL-2388 Initial removal of hidden cols/seqs out of overview

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index d30f10d..dc622f5 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -284,6 +284,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     if (viewport.getAlignment().isNucleotide())
     {
+      conservationMenuItem.setEnabled(false);
+      clustalColour.setEnabled(false);
+      BLOSUM62Colour.setEnabled(false);
+      zappoColour.setEnabled(false);
+      taylorColour.setEnabled(false);
+      hydrophobicityColour.setEnabled(false);
+      helixColour.setEnabled(false);
+      strandColour.setEnabled(false);
+      turnColour.setEnabled(false);
+      buriedColour.setEnabled(false);
       viewport.updateStrucConsensus(alignPanel);
       if (viewport.getAlignment().hasRNAStructure())
       {
@@ -561,8 +571,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               new String[] { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+        alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
+        alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
       }
       break;
 
@@ -588,8 +598,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                - viewport.endSeq + viewport.startSeq);
+        alignPanel.setScrollValues(viewport.getStartRes(),
+                2 * viewport.getStartSeq() - viewport.getEndSeq());
       }
       break;
 
@@ -600,8 +610,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                + viewport.endSeq - viewport.startSeq);
+        alignPanel.setScrollValues(viewport.getStartRes(),
+                viewport.getEndSeq());
       }
       break;
 
@@ -2378,7 +2388,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(viewport.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
@@ -2410,7 +2420,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(viewport.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
@@ -2642,7 +2652,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getViewportColourScheme(), alignPanel.getViewName());
+              viewport.getResidueShading(), alignPanel.getViewName());
       SliderPanel.showPIDSlider();
     }
   }
@@ -2653,7 +2663,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.getViewportColourScheme(), alignPanel.getViewName());
+              viewport.getResidueShading(), alignPanel.getViewName());
       SliderPanel.showConservationSlider();
     }
   }