X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmcc.java;h=70b520f1364cb27c4c9ecc209debad0e0bb24ff5;hb=9bad57b1ba0f75075ab8c6bda1dedb906f8c6280;hp=77c9a7ff9bef517d9615eefc9f0cf3afc8ae7458;hpb=6a8e6ec5f2cebcb8ec901add6fb64033fcd572da;p=jalview.git

diff --git a/forester/java/src/org/forester/application/mcc.java b/forester/java/src/org/forester/application/mcc.java
index 77c9a7f..70b520f 100644
--- a/forester/java/src/org/forester/application/mcc.java
+++ b/forester/java/src/org/forester/application/mcc.java
@@ -27,7 +27,9 @@ 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 );
             }
@@ -90,7 +98,13 @@ public class mcc {
     }
 
     private static void printHelp() {
-        ForesterUtil.printProgramInformation( PRG_NAME, PRG_DESC, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+        ForesterUtil.printProgramInformation( PRG_NAME,
+                                              PRG_DESC,
+                                              PRG_VERSION,
+                                              PRG_DATE,
+                                              E_MAIL,
+                                              WWW,
+                                              ForesterUtil.getForesterLibraryInformation() );
         System.out.println( "Usage:" );
         System.out.println();
         System.out.println( PRG_NAME + " <options> <msa input file>" );
@@ -115,15 +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;
             }