X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=a3328b317d8d7e31acf9940392e04848fbca6ab5;hb=1dabf099b7c77fb0a80039f72cef34669df9b2e1;hp=4f7fd9340cc4b211fb9a8d500d7e8e16246593cf;hpb=1e184475a6f6ba43584580b55351331a8b57b350;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 4f7fd93..a3328b3 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -103,6 +103,21 @@ public class AlignmentAnnotation
 
   public SequenceGroup groupRef =null ;
 
+  /**
+   * display every column label, even if there is a row of identical labels
+   */
+  public boolean showAllColLabels=false;
+  
+  /**
+   * scale the column label to fit within the alignment column.
+   */
+  public boolean scaleColLabel = false;
+
+  /**
+   * centre the column labels relative to the alignment column
+   */
+  public boolean centreColLabels = false;
+
   
   /* (non-Javadoc)
    * @see java.lang.Object#finalize()
@@ -186,10 +201,9 @@ public class AlignmentAnnotation
         firstChar != 'H'
                 && firstChar != 'E'
                 && firstChar != '-'
-                && firstChar != '-'
                 && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23)
+          if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO: parameterise to gap symbol number
           {
             nonSSLabel = true;
           }
@@ -296,6 +310,15 @@ public class AlignmentAnnotation
           min = annotations[i].value;
         }
       }
+      // ensure zero is origin for min/max ranges on only one side of zero
+      if (min>0) {
+        min = 0;
+      } else {
+        if (max<0)
+        {
+          max = 0;
+        }
+        }
     }
 
     graphMin = min;
@@ -498,8 +521,8 @@ public class AlignmentAnnotation
 
       buffer.append(", ");
     }
-
-    if (label.equals("Consensus"))
+    // TODO: remove disgusting hack for 'special' treatment of consensus line.
+    if (label.indexOf("Consensus")==0)
     {
       buffer.append("\n");