indicate the database id source associated with the sequences being submitted.

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 81e9afe..a3328b3 100755 (executable)
--- 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;