X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=088d4273b8397893f8fd4fea13df5e64b43218c1;hb=b321b54427b86297419763808dda86e9b10e7a00;hp=3420993f9e753f49bb7102e185fa47fdf9dc6448;hpb=ce728f87f1f43be3041ef02f7f2cc2e39314711a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3420993..088d427 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 +86,17 @@ public class AlignViewport
 
     boolean ignoreGapsInConsensusCalculation = false;
 
+    boolean isDataset = false;
+
+    boolean antiAlias = false;
+
+
+    public AlignViewport(AlignmentI al, boolean dataset)
+    {
+      isDataset = dataset;
+      setAlignment(al);
+      init();
+    }
     /**
      * Creates a new AlignViewport object.
      *
@@ -94,20 +105,19 @@ 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;
 
-        updateFromPreferences();
-    }
+      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateFromPreferences()
-    {
-      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);
 
@@ -137,8 +147,11 @@ 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)
         {
@@ -175,6 +188,9 @@ public class AlignViewport
      */
     public void updateConservation()
     {
+      if(alignment.isNucleotide())
+          return;
+
       try{
         Conservation cons = new jalview.analysis.Conservation("All",
             jalview.schemes.ResidueProperties.propHash, 3,
@@ -252,7 +268,7 @@ public class AlignViewport
                                                  ConsPercGaps + "% gaps",
                                                  annotations, 0f, // cons.qualityRange[0].floatValue(),
                                                  11f, // cons.qualityRange[1].floatValue()
-                                                 1);
+                                                 AlignmentAnnotation.BAR_GRAPH);
 
           if (showConservation)
           {
@@ -264,7 +280,7 @@ public class AlignViewport
                                             qannotations,
                                             cons.qualityRange[0].floatValue(),
                                             cons.qualityRange[1].floatValue(),
-                                            1);
+                                            AlignmentAnnotation.BAR_GRAPH);
 
           if (showQuality)
           {
@@ -348,7 +364,7 @@ public class AlignViewport
         if (consensus == null)
         {
           consensus = new AlignmentAnnotation("Consensus", "PID",
-                                              annotations, 0f, 100f, 1);
+                                              annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
 
           if (showIdentity)
           {
@@ -910,9 +926,9 @@ public class AlignViewport
      *
      * @return DOCUMENT ME!
      */
-    public boolean getShowFullId()
+    public boolean getShowJVSuffix()
     {
-        return showFullId;
+        return showJVSuffix;
     }
 
     /**
@@ -920,11 +936,12 @@ public class AlignViewport
      *
      * @param b DOCUMENT ME!
      */
-    public void setShowFullId(boolean b)
+    public void setShowJVSuffix(boolean b)
     {
-        showFullId = b;
+        showJVSuffix = b;
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -1054,4 +1071,14 @@ public class AlignViewport
     {
      return ignoreGapsInConsensusCalculation;
     }
+
+    public void setDataset(boolean b)
+    {
+      isDataset = b;
+    }
+
+    public boolean isDataset()
+    {
+      return isDataset;
+    }
 }