X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7f8675375da91f3acaba5922e27fde0170325f5e;hb=3cc7418f801593f64e73d7ccdbed3d557398aa45;hp=f57e9938d12fea49aac9523a4f7f8eaf25195e5b;hpb=783520af519c958e10a2af29f1d4242e1ab890a3;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f57e993..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;
@@ -86,10 +86,15 @@ public class AlignViewport
 
     boolean ignoreGapsInConsensusCalculation = false;
 
-    boolean showTranslation = false;
-
     boolean isDataset = false;
 
+
+    public AlignViewport(AlignmentI al, boolean dataset)
+    {
+      isDataset = dataset;
+      setAlignment(al);
+      init();
+    }
     /**
      * Creates a new AlignViewport object.
      *
@@ -98,13 +103,17 @@ public class AlignViewport
     public AlignViewport(AlignmentI al)
     {
         setAlignment(al);
+        init();
+    }
+
+    void init()
+    {
         this.startRes = 0;
-        this.endRes = al.getWidth() - 1;
+        this.endRes = alignment.getWidth() - 1;
         this.startSeq = 0;
-        this.endSeq = al.getHeight() - 1;
-
+        this.endSeq = alignment.getHeight() - 1;
 
-      showFullId = Cache.getDefault("SHOW_FULL_ID", true);
+      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
 
@@ -134,7 +143,7 @@ public class AlignViewport
 
         // We must set conservation and consensus before setting colour,
         // as Blosum and Clustal require this to be done
-        if(vconsensus==null)
+        if(vconsensus==null && !isDataset)
         {
           updateConservation();
           updateConsensus();
@@ -913,9 +922,9 @@ public class AlignViewport
      *
      * @return DOCUMENT ME!
      */
-    public boolean getShowFullId()
+    public boolean getShowJVSuffix()
     {
-        return showFullId;
+        return showJVSuffix;
     }
 
     /**
@@ -923,11 +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!
      *
@@ -1058,16 +1068,6 @@ public class AlignViewport
      return ignoreGapsInConsensusCalculation;
     }
 
-    public void showTranslation(boolean b)
-    {
-      this.showTranslation = b;
-    }
-
-    public boolean getShowTranslation()
-    {
-      return showTranslation;
-    }
-
     public void setDataset(boolean b)
     {
       isDataset = b;