X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f79867132ec7daec4a2c974233f51af6f5cab18c;hb=3d1147ffae5fbc5bdb7c80caa9655df656b8e67b;hp=41341d068c9d02e6208d5ea8924ddbc530077805;hpb=c52b6c076aca667347250b5ee896f36bb60a3d60;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 41341d0..f798671 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -167,7 +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);
@@ -456,9 +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)
     {
@@ -472,7 +477,7 @@ public class AlignViewport
     }
 
     /**
-     * DOCUMENT ME!
+     * trigger update of consensus annotation
      */
     public void updateConsensus(final AlignmentPanel ap)
     {
@@ -513,7 +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;
@@ -1453,20 +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)
@@ -1479,7 +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()
     {
@@ -1501,6 +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
@@ -1905,4 +1898,33 @@ public class AlignViewport
       }
       return false;
     }
+    
+    public boolean getCentreColumnLabels()
+    {
+      return centreColumnLabels;
+    }
+    public void setCentreColumnLabels(boolean centrecolumnlabels)
+    {
+      centreColumnLabels =  centrecolumnlabels;
+    }
+    public void updateSequenceIdColours()
+    {
+      Vector groups = alignment.getGroups();
+      if (sequenceColours==null)
+      {
+        sequenceColours = new Hashtable();
+      }
+      for (int ig=0,igSize=groups.size(); ig<igSize; ig++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+        if (sg.idColour!=null)
+        {
+          Vector sqs = sg.getSequences(hiddenRepSequences);
+          for (int s=0,sSize=sqs.size();s<sSize;s++)
+          {
+            sequenceColours.put(sqs.elementAt(s), sg.idColour);
+          } 
+        }
+      }
+    }
 }