X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=2881e8150261b33d066158fd6399ed0c6b270bb2;hb=8a0c21a00b4ac6925f6b6a04d1ea43cff44eea50;hp=60cee46bffe03d8c89b689a56e69c8716e36d151;hpb=3f91bb1385ab9ac8fdd15e3bc9378f5b554e1642;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 60cee46..2881e81 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -405,6 +405,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void setWrapAlignment(boolean state)
   {
     viewStyle.setWrapAlignment(state);
+    ranges.setWrappedMode(state);
   }
 
   /**
@@ -642,6 +643,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         residueShading.setConservation(hconservation);
       }
+      /*
+       * reset conservation flag in case just set to false if
+       * Conservation was null (calculation still in progress)
+       */
+      residueShading.setConservationApplied(getConservationSelected());
       residueShading.alignmentChanged(alignment, hiddenRepSequences);
     }
 
@@ -1159,7 +1165,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean hasHiddenColumns()
   {
-    return colSel != null
+    return alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns();
   }
 
@@ -1390,6 +1396,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
   // common hide/show seq stuff
   public void showAllHiddenSeqs()
   {
+    int startSeq = ranges.getStartSeq();
+    int endSeq = ranges.getEndSeq();
+
     if (alignment.getHiddenSequences().getSize() > 0)
     {
       if (selectionGroup == null)
@@ -1407,6 +1416,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
       hiddenRepSequences = null;
 
+      ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
       firePropertyChange("alignment", null, alignment.getSequences());
       // used to set hasHiddenRows/hiddenRepSequences here, after the property
       // changed event
@@ -1416,6 +1427,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void showSequence(int index)
   {
+    int startSeq = ranges.getStartSeq();
+    int endSeq = ranges.getEndSeq();
+
     List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
             index, hiddenRepSequences);
     if (tmp.size() > 0)
@@ -1431,6 +1445,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup.addSequence(seq, false);
         setSequenceAnnotationsVisible(seq, true);
       }
+
+      ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
       firePropertyChange("alignment", null, alignment.getSequences());
       sendSelection();
     }
@@ -1452,6 +1469,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   public void hideSequence(SequenceI[] seq)
   {
+    /*
+     * cache offset to first visible sequence
+     */
+    int startSeq = ranges.getStartSeq();
+
     if (seq != null)
     {
       for (int i = 0; i < seq.length; i++)
@@ -1459,6 +1481,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         alignment.getHiddenSequences().hideSequence(seq[i]);
         setSequenceAnnotationsVisible(seq[i], false);
       }
+      ranges.setStartSeq(startSeq);
       firePropertyChange("alignment", null, alignment.getSequences());
     }
   }
@@ -2870,4 +2893,45 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation
+   * row.
+   * 
+   * @return consensus sequence as a new sequence object
+   */
+  public SequenceI getConsensusSeq()
+  {
+    if (consensus == null)
+    {
+      updateConsensus(null);
+    }
+    if (consensus == null)
+    {
+      return null;
+    }
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      Annotation annotation = consensus.annotations[i];
+      if (annotation != null)
+      {
+        String description = annotation.description;
+        if (description != null && description.startsWith("["))
+        {
+          // consensus is a tie - just pick the first one
+          seqs.append(description.charAt(1));
+        }
+        else
+        {
+          seqs.append(annotation.displayCharacter);
+        }
+      }
+    }
+  
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
 }