compactor work

[jalview.git] / forester / java / src / org / forester / msa_compactor / MsaProperties.java

diff --git a/forester/java/src/org/forester/msa_compactor/MsaProperties.java b/forester/java/src/org/forester/msa_compactor/MsaProperties.java
index 5343aec..1abc638 100644 (file)
--- a/forester/java/src/org/forester/msa_compactor/MsaProperties.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaProperties.java
@@ -34,7 +34,7 @@ public final class MsaProperties {
     final private double _gap_ratio;
     final private int    _length;
     final private int    _number_of_sequences;
-    final private double _avg_number_of_gaps_per_100;
+    final private double _avg_number_of_gaps;
     final private String _removed_seq;
 
     public MsaProperties( final int number_of_sequences,
@@ -42,14 +42,14 @@ public final class MsaProperties {
                           final double gap_ratio,
                           final double entropy7,
                           final double entropy21,
-                          final double avg_number_of_gaps_per_100,
+                          final double avg_number_of_gaps,
                           final String removed_seq ) {
         _number_of_sequences = number_of_sequences;
         _length = length;
         _gap_ratio = gap_ratio;
         _entropy7 = entropy7;
         _entropy21 = entropy21;
-        _avg_number_of_gaps_per_100 = avg_number_of_gaps_per_100;
+        _avg_number_of_gaps = avg_number_of_gaps;
         _removed_seq = removed_seq;
     }
 
@@ -58,7 +58,7 @@ public final class MsaProperties {
         _length = msa.getLength();
         _gap_ratio = MsaMethods.calcGapRatio( msa );
         _removed_seq = removed_seq;
-        _avg_number_of_gaps_per_100 = MsaMethods.calcNumberOfGapsPer100Stats( msa ).arithmeticMean();
+        _avg_number_of_gaps = MsaMethods.calcNumberOfGapsStats( msa ).arithmeticMean();
         if ( calculate_normalized_shannon_entropy ) {
             _entropy7 = MsaMethods.calcNormalizedShannonsEntropy( 7, msa );
             _entropy21 = MsaMethods.calcNormalizedShannonsEntropy( 21, msa );
@@ -81,8 +81,8 @@ public final class MsaProperties {
         return _gap_ratio;
     }
 
-    public final double getAvgNumberOfGapsPer100() {
-        return _avg_number_of_gaps_per_100;
+    public final double getAvgNumberOfGaps() {
+        return _avg_number_of_gaps;
     }
     
     public final int getLength() {