inprogress

[jalview.git] / forester / java / src / org / forester / msa / MsaMethods.java

diff --git a/forester/java/src/org/forester/msa/MsaMethods.java b/forester/java/src/org/forester/msa/MsaMethods.java
index 9975ab2..1a94b74 100644 (file)
--- a/forester/java/src/org/forester/msa/MsaMethods.java
+++ b/forester/java/src/org/forester/msa/MsaMethods.java
@@ -111,7 +111,7 @@ public final class MsaMethods {
         return BasicMsa.createInstance( seqs );
     }
 
-    synchronized final public Msa removeGapColumns( final double max_allowed_gap_ratio,
+    synchronized final public Msa deleteGapColumns( final double max_allowed_gap_ratio,
                                                     final int min_allowed_length,
                                                     final Msa msa ) {
         init();
@@ -122,7 +122,7 @@ public final class MsaMethods {
         final boolean[] delete_cols = new boolean[ msa.getLength() ];
         int new_length = 0;
         for( int col = 0; col < msa.getLength(); ++col ) {
-            delete_cols[ col ] = ( ( double ) calcGapSumPerColumn( msa, col ) / msa.getNumberOfSequences() ) >= max_allowed_gap_ratio;
+            delete_cols[ col ] = ( ( double ) calcGapSumPerColumn( msa, col ) / msa.getNumberOfSequences() ) > max_allowed_gap_ratio;
             if ( !delete_cols[ col ] ) {
                 ++new_length;
             }
@@ -159,28 +159,24 @@ public final class MsaMethods {
         return BasicMsa.createInstance( seqs );
     }
 
-    synchronized final public static void removeGapColumns( final double max_allowed_gap_ratio, final DeleteableMsa msa ) {
-        if ( ( max_allowed_gap_ratio < 0 ) || ( max_allowed_gap_ratio > 1 ) ) {
-            throw new IllegalArgumentException( "max allowed gap ration is out of range: " + max_allowed_gap_ratio );
-        }
-        //   final boolean ignore_too_short_seqs = min_allowed_length > 0;
-        for( int col = msa.getLength() - 1; col >= 0 ; --col ) {
-            final boolean delete = ( ( double ) calcGapSumPerColumn( msa, col ) / msa.getNumberOfSequences() ) >= max_allowed_gap_ratio;
-            if ( delete ) {
-                msa.deleteColumn( col );
-            }
+    final public static DescriptiveStatistics calculateIdentityRatio( final int from, final int to, final Msa msa ) {
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+        for( int c = from; c <= to; ++c ) {
+            stats.addValue( calculateIdentityRatio( msa, c ) );
         }
+        return stats;
     }
 
-    public static DescriptiveStatistics calculateIdentityRatio( final int from, final int to, final Msa msa ) {
+    final public static DescriptiveStatistics calculateEffectiveLengthStatistics( final Msa msa ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
-        for( int c = from; c <= to; ++c ) {
-            stats.addValue( calculateIdentityRatio( msa, c ) );
+        for( int row = 0; row < msa.getNumberOfSequences(); ++row ) {
+            final Sequence s = msa.getSequence( row );
+            stats.addValue( s.getLength() - s.getNumberOfGapResidues() );
         }
         return stats;
     }
 
-    public static double calculateIdentityRatio( final Msa msa, final int column ) {
+    final public static double calculateIdentityRatio( final Msa msa, final int column ) {
         final SortedMap<Character, Integer> dist = calculateResidueDestributionPerColumn( msa, column );
         int majority_count = 0;
         final Iterator<Map.Entry<Character, Integer>> it = dist.entrySet().iterator();