update spikes/mungo from JAL-3076 patch branch

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

diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java
index 047b7e7..74eb887 100644 (file)
--- a/src/jalview/datamodel/ResidueCount.java
+++ b/src/jalview/datamodel/ResidueCount.java
@@ -25,8 +25,6 @@ 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.
@@ -150,24 +148,6 @@ 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.
@@ -660,19 +640,4 @@ 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;
-  }
 }