JAL-98 minor fixes to / tests for annotation derivation

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 569b036..61e11c4 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -47,18 +47,8 @@ import java.util.List;
  */
 public class AAFrequency
 {
-  public static final String MAXCOUNT = "C";
-
-  public static final String MAXRESIDUE = "R";
-
-  public static final String PID_GAPS = "G";
-
-  public static final String PID_NOGAPS = "N";
-
   public static final String PROFILE = "P";
 
-  public static final String ENCODED_CHARS = "E";
-
   /*
    * Quick look-up of String value of char 'A' to 'Z'
    */
@@ -275,7 +265,16 @@ public class AAFrequency
       String description = getTooltip(profile, value, showSequenceLogo,
               ignoreGaps, dp);
 
-      consensus.annotations[i] = new Annotation(profile.getModalResidue(),
+      String modalResidue = profile.getModalResidue();
+      if ("".equals(modalResidue))
+      {
+        modalResidue = "-";
+      }
+      else if (modalResidue.length() > 1)
+      {
+        modalResidue = "+";
+      }
+      consensus.annotations[i] = new Annotation(modalResidue,
               description, ' ', value);
     }
     // long elapsed = System.currentTimeMillis() - now;
@@ -318,15 +317,18 @@ public class AAFrequency
       String maxRes = profile.getModalResidue();
       if (maxRes.length() > 1)
       {
-        sb.append("[").append(maxRes).append("] ");
-        maxRes = "+";
+        sb.append("[").append(maxRes).append("]");
       }
       else
       {
-        sb.append(maxRes).append(" ");
+        sb.append(maxRes);
+      }
+      if (maxRes.length() > 0)
+      {
+        sb.append(" ");
+        Format.appendPercentage(sb, pid, dp);
+        sb.append("%");
       }
-      Format.appendPercentage(sb, pid, dp);
-      sb.append("%");
       description = sb.toString();
     }
     return description;