X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmcc.java;h=23320fc8210667a6304644f1179fe97c5453e6bb;hb=e779d10d20ff0b7b7e3e95b39297e4d69fe5268b;hp=3ee440fbff49335be4a11862823b132680091d9f;hpb=e174d62534f7fc6f3de133d523a402a87735b27f;p=jalview.git

diff --git a/forester/java/src/org/forester/application/mcc.java b/forester/java/src/org/forester/application/mcc.java
index 3ee440f..23320fc 100644
--- a/forester/java/src/org/forester/application/mcc.java
+++ b/forester/java/src/org/forester/application/mcc.java
@@ -21,13 +21,15 @@
 // 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;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.InputStream;
 
+import org.forester.io.parsers.FastaParser;
 import org.forester.io.parsers.GeneralMsaParser;
 import org.forester.msa.Msa;
 import org.forester.msa.MsaMethods;
@@ -76,7 +78,13 @@ public class mcc {
                 System.exit( 0 );
             }
             Msa msa = null;
-            msa = GeneralMsaParser.parse( new FileInputStream( in ) );
+            final InputStream is = new FileInputStream( in );
+            if ( FastaParser.isLikelyFasta( in ) ) {
+                msa = FastaParser.parseMsa( is );
+            }
+            else {
+                msa = GeneralMsaParser.parse( is );
+            }
             if ( cla.isOptionSet( FROM_OPTION ) ) {
                 singleCalc( in, from, to, msa );
             }
@@ -121,15 +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;
             }