X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7f8675375da91f3acaba5922e27fde0170325f5e;hb=3cc7418f801593f64e73d7ccdbed3d557398aa45;hp=2922f0910e5b23904b95946ab7f6d96cd4601067;hpb=92f934a3ed429a46227cf829f985d72cb7e86fb7;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2922f09..7f86753 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -43,7 +43,7 @@ public class AlignViewport
     int endRes;
     int startSeq;
     int endSeq;
-    boolean showFullId = false;
+    boolean showJVSuffix = true;
     boolean showText = true;
     boolean showColourText = false;
     boolean showBoxes = true;
@@ -86,6 +86,15 @@ public class AlignViewport
 
     boolean ignoreGapsInConsensusCalculation = false;
 
+    boolean isDataset = false;
+
+
+    public AlignViewport(AlignmentI al, boolean dataset)
+    {
+      isDataset = dataset;
+      setAlignment(al);
+      init();
+    }
     /**
      * Creates a new AlignViewport object.
      *
@@ -94,20 +103,17 @@ public class AlignViewport
     public AlignViewport(AlignmentI al)
     {
         setAlignment(al);
-        this.startRes = 0;
-        this.endRes = al.getWidth() - 1;
-        this.startSeq = 0;
-        this.endSeq = al.getHeight() - 1;
-
-        updateFromPreferences();
+        init();
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateFromPreferences()
+    void init()
     {
-      showFullId = Cache.getDefault("SHOW_FULL_ID", true);
+        this.startRes = 0;
+        this.endRes = alignment.getWidth() - 1;
+        this.startSeq = 0;
+        this.endSeq = alignment.getHeight() - 1;
+
+      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
 
@@ -137,9 +143,11 @@ public class AlignViewport
 
         // We must set conservation and consensus before setting colour,
         // as Blosum and Clustal require this to be done
-        updateConservation();
-
-        updateConsensus();
+        if(vconsensus==null && !isDataset)
+        {
+          updateConservation();
+          updateConsensus();
+        }
 
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
         {
@@ -914,9 +922,9 @@ public class AlignViewport
      *
      * @return DOCUMENT ME!
      */
-    public boolean getShowFullId()
+    public boolean getShowJVSuffix()
     {
-        return showFullId;
+        return showJVSuffix;
     }
 
     /**
@@ -924,11 +932,12 @@ public class AlignViewport
      *
      * @param b DOCUMENT ME!
      */
-    public void setShowFullId(boolean b)
+    public void setShowJVSuffix(boolean b)
     {
-        showFullId = b;
+        showJVSuffix = b;
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -1058,4 +1067,14 @@ public class AlignViewport
     {
      return ignoreGapsInConsensusCalculation;
     }
+
+    public void setDataset(boolean b)
+    {
+      isDataset = b;
+    }
+
+    public boolean isDataset()
+    {
+      return isDataset;
+    }
 }