X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FResidueCount.java;h=4ca4c807e291ce5fbf9e3e10c737823b742c3bc9;hb=45d7b8f24253fa1c49977feedfe8a0f2f7cea85e;hp=612969f1cfbb62c9086c24f2d422bd327ec49d9d;hpb=28d2a0b7dde7f6751d9e063fc2e11da065d284a4;p=jalview.git

diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java
index 612969f..4ca4c80 100644
--- a/src/jalview/datamodel/ResidueCount.java
+++ b/src/jalview/datamodel/ResidueCount.java
@@ -25,6 +25,8 @@ import jalview.util.Format;
 import jalview.util.QuickSort;
 import jalview.util.SparseCount;
 
+import java.util.List;
+
 /**
  * A class to count occurrences of residues in a profile, optimised for speed
  * and memory footprint.
@@ -70,7 +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
@@ -148,6 +150,24 @@ public class ResidueCount
   }
 
   /**
+   * A constructor that counts frequency of all symbols (including gaps) in the
+   * sequences (not case-sensitive)
+   * 
+   * @param sequences
+   */
+  public ResidueCount(List<SequenceI> sequences)
+  {
+    this();
+    for (SequenceI seq : sequences)
+    {
+      for (int i = 0; i < seq.getLength(); i++)
+      {
+        add(seq.getCharAt(i));
+      }
+    }
+  }
+
+  /**
    * Increments the count for the given character. The supplied character may be
    * upper or lower case but counts are for the upper case only. Gap characters
    * (space, ., -) are all counted together.
@@ -212,7 +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;
   }
 
@@ -301,15 +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;
   }
 
@@ -641,15 +658,17 @@ public class ResidueCount
     return sb.toString();
   }
 
-  public int getTotalCount()
+  /**
+   * Answers the total count for all symbols (excluding gaps)
+   * 
+   * @return
+   */
+  public int getTotalResidueCount()
   {
     int total = 0;
     for (char symbol : this.getSymbolCounts().symbols)
     {
-      if (!Comparison.isGap(symbol))
-      {
-        total += getCount(symbol);
-      }
+      total += getCount(symbol);
     }
     return total;
   }