X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=bef5e1abe5bcb121dd442228c02a40685a327d8a;hb=c5ae36527ac4366160ba09b88e5e74568f71b836;hp=40d3dd499a51bb149c8ce4c70616cc70c16bd648;hpb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d3dd4..bef5e1a 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,7 +36,7 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-  boolean showFullId = true;
+  boolean showJVSuffix = true;
   boolean showText = true;
   boolean showColourText = false;
   boolean showBoxes = true;
@@ -57,8 +57,7 @@ public class AlignViewport
 
   int charHeight;
   int charWidth;
-  int chunkWidth;
-  int chunkHeight;
+  int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
   AlignmentI alignment;
@@ -74,6 +73,11 @@ public class AlignViewport
   boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
 
+  // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+  Hashtable featuresDisplayed = null;
+
+
   public Vector vconsensus;
   AlignmentAnnotation consensus;
   AlignmentAnnotation conservation;
@@ -99,7 +103,7 @@ public class AlignViewport
       String param = applet.getParameter("showFullId");
       if (param != null)
       {
-        showFullId = Boolean.valueOf(param).booleanValue();
+        showJVSuffix = Boolean.valueOf(param).booleanValue();
       }
 
       param = applet.getParameter("showAnnotation");
@@ -147,9 +151,17 @@ public class AlignViewport
     showSequenceFeatures = b;
   }
 
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
+
 
   public void updateConservation()
   {
+    if(alignment.isNucleotide())
+          return;
+
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
@@ -219,7 +231,7 @@ public class AlignViewport
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
-                                             1);
+                                             AlignmentAnnotation.BAR_GRAPH);
       if (showConservation)
       {
         alignment.addAnnotation(conservation);
@@ -229,7 +241,7 @@ public class AlignViewport
                                         qannotations,
                                         cons.qualityRange[0].floatValue(),
                                         cons.qualityRange[1].floatValue(),
-                                        1);
+                                        AlignmentAnnotation.BAR_GRAPH);
       if (showQuality)
       {
         alignment.addAnnotation(quality);
@@ -292,7 +304,7 @@ public class AlignViewport
     if (consensus == null)
     {
       consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, 1);
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       if (showConsensus)
       {
         alignment.addAnnotation(consensus);
@@ -440,24 +452,14 @@ public class AlignViewport
     return charHeight;
   }
 
-  public void setChunkWidth(int w)
-  {
-    this.chunkWidth = w;
-  }
-
-  public int getChunkWidth()
-  {
-    return chunkWidth;
-  }
-
-  public void setChunkHeight(int h)
+  public void setWrappedWidth(int w)
   {
-    this.chunkHeight = h;
+    this.wrappedWidth = w;
   }
 
-  public int getChunkHeight()
+  public int getwrappedWidth()
   {
-    return chunkHeight;
+    return wrappedWidth;
   }
 
   public AlignmentI getAlignment()
@@ -604,14 +606,14 @@ public class AlignViewport
     return colourAppliesToAllGroups;
   }
 
-  public boolean getShowFullId()
+  public boolean getShowJVSuffix()
   {
-    return showFullId;
+    return showJVSuffix;
   }
 
-  public void setShowFullId(boolean b)
+  public void setShowJVSuffix(boolean b)
   {
-    showFullId = b;
+    showJVSuffix = b;
   }
 
   public boolean getShowAnnotation()