X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FResidueCount.java;h=4ca4c807e291ce5fbf9e3e10c737823b742c3bc9;hb=45d7b8f24253fa1c49977feedfe8a0f2f7cea85e;hp=aaf698880529e5b827e2d760cde6488c0f59335a;hpb=56e8c00dcdc6aa8596830451e4419e64628c77f8;p=jalview.git

diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java
index aaf6988..4ca4c80 100644
--- a/src/jalview/datamodel/ResidueCount.java
+++ b/src/jalview/datamodel/ResidueCount.java
@@ -72,7 +72,7 @@ public class ResidueCount
    */
   private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY";
 
-  private static final int GAP_COUNT = 0;
+  static final int GAP_COUNT = 0;
 
   /*
    * fast lookup tables holding the index into our count
@@ -232,7 +232,12 @@ public class ResidueCount
         counts[offset] = (short) ++newValue;
       }
     }
-    maxCount = Math.max(maxCount, newValue);
+
+    if (offset != GAP_COUNT)
+    {
+      // update modal residue count
+      maxCount = Math.max(maxCount, newValue);
+    }
     return newValue;
   }
 
@@ -321,15 +326,7 @@ public class ResidueCount
    */
   public int addGap()
   {
-    int newValue;
-    if (useIntCounts)
-    {
-      newValue = ++intCounts[GAP_COUNT];
-    }
-    else
-    {
-      newValue = ++counts[GAP_COUNT];
-    }
+    int newValue = increment(GAP_COUNT);
     return newValue;
   }
 
@@ -666,7 +663,7 @@ public class ResidueCount
    * 
    * @return
    */
-  public int getTotalCount()
+  public int getTotalResidueCount()
   {
     int total = 0;
     for (char symbol : this.getSymbolCounts().symbols)