From 7476d4a39fc5840955b57289b862bf08b8419fd7 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 17 May 2012 05:10:38 +0000
Subject: [PATCH] in progress

---
 .../src/org/forester/application/msa_quality.java   |    8 ++++----
 forester/java/src/org/forester/msa/MsaMethods.java  |   19 +++++++++++++++++--
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/forester/java/src/org/forester/application/msa_quality.java b/forester/java/src/org/forester/application/msa_quality.java
index 0ffd63d..3f3d745 100644
--- a/forester/java/src/org/forester/application/msa_quality.java
+++ b/forester/java/src/org/forester/application/msa_quality.java
@@ -5,12 +5,13 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.SortedMap;
 
 import org.forester.io.parsers.GeneralMsaParser;
 import org.forester.msa.Msa;
 import org.forester.msa.MsaMethods;
+import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.CommandLineArguments;
+import org.forester.util.DescriptiveStatistics;
 
 public class msa_quality {
 
@@ -41,10 +42,9 @@ public class msa_quality {
         }
         final int end = 2;
         final int start = 6;
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( int c = start; c <= end; ++c ) {
-            final SortedMap<Character, Integer> dist = MsaMethods.calculateResidueDestributionPerColumn( msa, c );
-            final char majority_char = ' ';
-            final int majority_count = 0;
+            stats.addValue( MsaMethods.calculateIdentityRatio( msa, c ) );
         }
     }
 }
diff --git a/forester/java/src/org/forester/msa/MsaMethods.java b/forester/java/src/org/forester/msa/MsaMethods.java
index e252efe..716c843 100644
--- a/forester/java/src/org/forester/msa/MsaMethods.java
+++ b/forester/java/src/org/forester/msa/MsaMethods.java
@@ -26,7 +26,9 @@
 package org.forester.msa;
 
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
@@ -118,9 +120,22 @@ public final class MsaMethods {
         return BasicMsa.createInstance( seqs );
     }
 
-    public static SortedMap<Character, Integer> calculateResidueDestributionPerColumn( final Msa msa, final int c ) {
+    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();
+        while ( it.hasNext() ) {
+            final Map.Entry<Character, Integer> pair = it.next();
+            if ( pair.getValue() > majority_count ) {
+                majority_count = pair.getValue();
+            }
+        }
+        return ( double ) majority_count / msa.getNumberOfSequences();
+    }
+
+    public static SortedMap<Character, Integer> calculateResidueDestributionPerColumn( final Msa msa, final int column ) {
         final SortedMap<Character, Integer> map = new TreeMap<Character, Integer>();
-        for( final Character r : msa.getColumnAt( c ) ) {
+        for( final Character r : msa.getColumnAt( column ) ) {
             if ( !map.containsKey( r ) ) {
                 map.put( r, 1 );
             }
-- 
1.7.10.2