X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FDeleteableMsa.java;h=172ce4dd5ef3491169d26e0c4af18bf6272a4f54;hb=fda4b2cd36f7c4d7edf6381268ebcf5fbbc77297;hp=350aae25cc4526b8907ca3fd93ec9b7fffd9dbf8;hpb=0465b8ebe16d57902022bba6f90f25dd1a18e656;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/DeleteableMsa.java b/forester/java/src/org/forester/msa/DeleteableMsa.java
index 350aae2..172ce4d 100644
--- a/forester/java/src/org/forester/msa/DeleteableMsa.java
+++ b/forester/java/src/org/forester/msa/DeleteableMsa.java
@@ -50,6 +50,27 @@ public final class DeleteableMsa extends BasicMsa {
         _seqs = msa.getNumberOfSequences();
     }
 
+    public final double[] calcGappiness() {
+        final int length = getLength();
+        final double gappiness[] = new double[ length ];
+        final int seqs = getNumberOfSequences();
+        for( int row = 0; row < seqs; ++row ) {
+            for( int col = 0; col < length; ++col ) {
+            }
+        }
+        return gappiness;
+    }
+
+    public static int calcGapSumPerColumn( final Msa msa, final int col ) {
+        int gap_rows = 0;
+        for( int j = 0; j < msa.getNumberOfSequences(); ++j ) {
+            if ( msa.isGapAt( j, col ) ) {
+                gap_rows++;
+            }
+        }
+        return gap_rows;
+    }
+
     public short determineMaxIdLength() {
         short max = 0;
         for( int row = 0; row < getNumberOfSequences(); ++row ) {