X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmcc.java;h=23320fc8210667a6304644f1179fe97c5453e6bb;hb=656be28debec520e0e35a8b311114398a40ea366;hp=c0c72b04e2e168a1eae02068a5ec067bffcefa4b;hpb=b1a74bd076c917d428002284a53a2c6f390226fb;p=jalview.git

diff --git a/forester/java/src/org/forester/application/mcc.java b/forester/java/src/org/forester/application/mcc.java
index c0c72b0..23320fc 100644
--- a/forester/java/src/org/forester/application/mcc.java
+++ b/forester/java/src/org/forester/application/mcc.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.application;
 
@@ -129,15 +129,15 @@ public class mcc {
             step = 1;
         }
         final double id_ratios[] = new double[ msa.getLength() ];
-        for( int i = 0; i <= msa.getLength() - 1; ++i ) {
+        for( int i = 0; i <= ( msa.getLength() - 1 ); ++i ) {
             id_ratios[ i ] = MsaMethods.calculateIdentityRatio( msa, i );
         }
         String min_pos = "";
         String max_pos = "";
         double min = 1;
         double max = 0;
-        for( int i = 0; i <= msa.getLength() - 1; i += step ) {
-            int to = i + window - 1;
+        for( int i = 0; i <= ( msa.getLength() - 1 ); i += step ) {
+            int to = ( i + window ) - 1;
             if ( to > ( msa.getLength() - 1 ) ) {
                 to = msa.getLength() - 1;
             }