Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java
index efab97c..154af20 100644 (file)
--- 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.
@@ -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.
@@ -637,4 +657,19 @@ public class ResidueCount
     sb.append("]");
     return sb.toString();
   }
+
+  /**
+   * Answers the total count for all symbols (excluding gaps)
+   * 
+   * @return
+   */
+  public int getTotalResidueCount()
+  {
+    int total = 0;
+    for (char symbol : this.getSymbolCounts().symbols)
+    {
+      total += getCount(symbol);
+    }
+    return total;
+  }
 }