X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=99084ba1c7c519c50e50b2ae231feaa4aec89174;hb=244f5b89912c1e8eb42fe8befee08dfa3643ae16;hp=c5adccbf39ca08be6c60887ab44ade8245b10f31;hpb=c564d188c1a8106d866651eba5c4cf60fbc0c232;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index c5adccb..99084ba 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -286,13 +286,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     // do we need to scroll the panel?
     if (results != null && results.getSize() > 0)
     {
-      int seqIndex = av.alignment.findIndex(results);
+      AlignmentI alignment=av.getAlignment();
+      int seqIndex = alignment.findIndex(results);
       if (seqIndex == -1)
       {
         return false;
       }
-      SequenceI seq = av.alignment.getSequenceAt(seqIndex);
-      int[] r = results.getResults(seq, 0,av.alignment.getWidth());
+      SequenceI seq = alignment.getSequenceAt(seqIndex);
+      int[] r = results.getResults(seq, 0,alignment.getWidth());
       if (r == null)
       {
         if (av.applet.debug) {// DEBUG
@@ -327,13 +328,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 	    int startv, endv, starts, ends, width;
 
 	  int start=-1;
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       start = av.getColumnSelection().findColumnPosition(ostart);
       end = av.getColumnSelection().findColumnPosition(end);
       if (start == end)
       {
-        if (!scrollToNearest && !av.colSel.isVisible(ostart))
+        if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
         {
           // don't scroll - position isn't visible
           return false;
@@ -373,18 +374,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
                 || (av.getEndRes() < start)
                 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
         {
-          if (start > av.alignment.getWidth() - hextent)
+          if (start > av.getAlignment().getWidth() - hextent)
           {
-            start = av.alignment.getWidth() - hextent;
+            start = av.getAlignment().getWidth() - hextent;
             if (start < 0)
             {
               start = 0;
             }
 
           }
-          if (seqIndex > av.alignment.getHeight() - vextent)
+          if (seqIndex > av.getAlignment().getHeight() - vextent)
           {
-            seqIndex = av.alignment.getHeight() - vextent;
+            seqIndex = av.getAlignment().getHeight() - vextent;
             if (seqIndex < 0)
             {
               seqIndex = 0;
@@ -588,10 +589,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
   public void setScrollValues(int x, int y)
   {
-    int width = av.alignment.getWidth();
-    int height = av.alignment.getHeight();
+    int width = av.getAlignment().getWidth();
+    int height = av.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       width = av.getColumnSelection().findColumnPosition(width);
     }
@@ -636,9 +637,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     av.setStartSeq(y);
 
     int endSeq = y + vextent;
-    if (endSeq > av.alignment.getHeight())
+    if (endSeq > av.getAlignment().getHeight())
     {
-      endSeq = av.alignment.getHeight();
+      endSeq = av.getAlignment().getHeight();
     }
 
     av.setEndSeq(endSeq);
@@ -768,9 +769,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     
     if (av.getWrapAlignment())
     {
-      int maxwidth = av.alignment.getWidth();
+      int maxwidth = av.getAlignment().getWidth();
 
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
@@ -918,10 +919,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
     // remove old automatic annotation
     // add any new annotation
 
-    Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+    Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.alignment.getSequencesArray());
     // intersect alignment annotation with alignment groups
 
-    AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
     Hashtable oldrfs = new Hashtable();
     if (aan != null)
     {
@@ -930,7 +931,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
         if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
           oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-          av.alignment.deleteAnnotation(aan[an]);
+          av.getAlignment().deleteAnnotation(aan[an]);
           aan[an] = null;
         }
       }
@@ -951,12 +952,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
         if (conv)
         {
           updateCalcs = true;
-          av.alignment.addAnnotation(sg.getConservationRow(), 0);
+          av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
         }
         if (cons)
         {
           updateCalcs = true;
-          av.alignment.addAnnotation(sg.getConsensus(), 0);
+          av.getAlignment().addAnnotation(sg.getConsensus(), 0);
         }
         // refresh the annotation rows
         if (updateCalcs)
@@ -972,7 +973,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
   @Override
   public AlignmentI getAlignment()
   {
-    return av.alignment;
+    return av.getAlignment();
   }
   @Override
   public StructureSelectionManager getStructureSelectionManager()