X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=652d8d1bd5ad5209f8b81ac5568f52594c31be96;hb=bcfc087d75da78963a3bba83ee2a206035297ee7;hp=cbb19fb99f2a23ecbd585b9613130f6cc878892a;hpb=fd618c7346eab858aa0039376872820aca37783a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index cbb19fb..652d8d1 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -29,6 +29,7 @@ import jalview.bin.*;
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
 
 /**
  * DOCUMENT ME!
@@ -166,7 +167,7 @@ public class AlignViewport
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
       rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
+      centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
       autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
       padGaps = Cache.getDefault("PAD_GAPS", true);
@@ -455,9 +456,14 @@ public class AlignViewport
     boolean updatingConsensus = false;
 
     boolean updatingConservation = false;
+    /**
+     * centre columnar annotation labels in displayed alignment annotation
+     * TODO: add to jalviewXML and annotation display settings
+     */
+    boolean centreColumnLabels=false;
 
     /**
-     * DOCUMENT ME!
+     * trigger update of conservation annotation
      */
     public void updateConservation(final AlignmentPanel ap)
     {
@@ -471,7 +477,7 @@ public class AlignViewport
     }
 
     /**
-     * DOCUMENT ME!
+     * trigger update of consensus annotation
      */
     public void updateConsensus(final AlignmentPanel ap)
     {
@@ -512,7 +518,7 @@ public class AlignViewport
 
         try
         {
-          int aWidth = alignment.getWidth();
+          int aWidth = (alignment!=null) ? alignment.getWidth() : 0; // null pointer possibility here.
           if(aWidth<0)
         {
             return;
@@ -916,7 +922,15 @@ public class AlignViewport
      */
     public void setAlignment(AlignmentI align)
     {
+      if (alignment!=null && alignment.getCodonFrames()!=null)
+      {
+        StructureSelectionManager.getStructureSelectionManager().removeMappings(alignment.getCodonFrames());
+      }
         this.alignment = align;
+        if (alignment.getCodonFrames()!=null)
+        {
+          StructureSelectionManager.getStructureSelectionManager().addMappings(alignment.getCodonFrames());
+        }
     }
 
     /**
@@ -1444,20 +1458,7 @@ public class AlignViewport
 
     public void invertColumnSelection()
     {
-      for(int i=0; i<alignment.getWidth(); i++)
-      {
-        if(colSel.contains(i))
-      {
-          colSel.removeElement(i);
-      }
-        else
-        {
-          if (!hasHiddenColumns || colSel.isVisible(i))
-          {
-            colSel.addElement(i);
-          }
-        }
-      }
+      colSel.invertColumnSelection(0,alignment.getWidth());
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1470,7 +1471,7 @@ public class AlignViewport
      * derived from the whole alignment or just the current
      * selection with start and end points adjusted
      * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
-     * @return String[]
+     * @return selection as new sequenceI objects
      */
     public SequenceI[] getSelectionAsNewSequence()
     {
@@ -1492,6 +1493,7 @@ public class AlignViewport
 
       return sequences;
     }
+    
     /**
      * get the currently selected sequence objects or all the sequences in the alignment.
      * @return array of references to sequence objects
@@ -1862,6 +1864,47 @@ public class AlignViewport
       viscontigs = colSel.getVisibleContigs(start, end);
       return viscontigs;
     }
-
-
+    /**
+     * get hash of undo and redo list for the alignment
+     * @return long[] { historyList.hashCode, redoList.hashCode };
+     */
+    public long[] getUndoRedoHash()
+    {
+      if (historyList==null || redoList==null)
+        return new long[] { -1, -1};
+      return new long[] { historyList.hashCode(), this.redoList.hashCode() };
+    }
+    /**
+     * test if a particular set of hashcodes are different to the hashcodes for the undo and redo list.
+     * @param undoredo the stored set of hashcodes as returned by getUndoRedoHash
+     * @return true if the hashcodes differ (ie the alignment has been edited) or the stored hashcode array differs in size
+     */
+    public boolean isUndoRedoHashModified(long[] undoredo)
+    {
+      if (undoredo==null)
+      {
+        return true;
+      }
+      long[] cstate = getUndoRedoHash();
+      if (cstate.length!=undoredo.length)
+      {  return true; }
+      
+      for (int i=0; i<cstate.length; i++)
+      {
+        if (cstate[i]!=undoredo[i])
+        {
+          return true;
+        }
+      }
+      return false;
+    }
+    
+    public boolean getCentreColumnLabels()
+    {
+      return centreColumnLabels;
+    }
+    public void setCentreColumnLabels(boolean centrecolumnlabels)
+    {
+      centreColumnLabels =  centrecolumnlabels;
+    }
 }