X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8f615aa55480e4eda1d6155f2e371d13e0b0dcd7;hb=8c2e72fec911f86333cbc82aaed4d29fadac542c;hp=c168b7b8d527fd2cbb312bbba417b3e9ef70e85c;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index c168b7b..8f615aa 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -133,9 +133,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
    */
   Hashtable featuresDisplayed = null;
 
-
-  boolean isDataset = false;
-
   boolean antiAlias = false;
 
   Rectangle explodedPosition;
@@ -331,68 +328,23 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     {
       if (!alignment.isNucleotide())
       {
-        conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than " + getConsPercGaps()
-                        + "% gaps", new Annotation[1], 0f, 11f,
-                AlignmentAnnotation.BAR_GRAPH);
-        conservation.hasText = true;
-        conservation.autoCalculated = true;
-
-        if (Cache.getDefault("SHOW_CONSERVATION", true))
-        {
-          alignment.addAnnotation(conservation);
-        }
-
-        if (Cache.getDefault("SHOW_QUALITY", true))
-        {
-          quality = new AlignmentAnnotation("Quality",
-                  "Alignment Quality based on Blosum62 scores",
-                  new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
-          quality.hasText = true;
-          quality.autoCalculated = true;
-
-          alignment.addAnnotation(quality);
-        }
+        showConservation=Cache.getDefault("SHOW_CONSERVATION", true);
+        showQuality=Cache.getDefault("SHOW_QUALITY", true);
         showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
                 false);
-
-        {
-
-        }
-      }
+      } 
       showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
               true);
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
-      // TODO: add menu option action that nulls or creates consensus object
-      // depending on if the user wants to see the annotation or not in a
-      // specific alignment
+      showConsensus=Cache.getDefault("SHOW_IDENTITY", true);
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       consensus.hasText = true;
       consensus.autoCalculated = true;
-
-      if (alignment.isNucleotide() && alignment.hasRNAStructure())
-      {
-        strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-                new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-        strucConsensus.hasText = true;
-        strucConsensus.autoCalculated = true;
-      }
-      
-      if (Cache.getDefault("SHOW_IDENTITY", true))
-      {
-        alignment.addAnnotation(consensus);
-        // TODO: Make own if for structure
-        if (alignment.isNucleotide() && alignment.hasRNAStructure())
-        {
-          alignment.addAnnotation(strucConsensus);
-        }
-      }
-
     }
-
+    initAutoAnnotation();
     if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
     {
       globalColourScheme = ColourSchemeProperty.getColour(alignment,