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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
mcc.java
diff --git
a/forester/java/src/org/forester/application/mcc.java
b/forester/java/src/org/forester/application/mcc.java
index
e31679a
..
23320fc
100644
(file)
--- 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
// 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;
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;
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;
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 );
}
if ( cla.isOptionSet( FROM_OPTION ) ) {
singleCalc( in, from, to, msa );
}
@@
-90,7
+98,13
@@
public class mcc {
}
private static void printHelp() {
}
private static void printHelp() {
- ForesterUtil.printProgramInformation( PRG_NAME, PRG_DESC, PRG_VERSION, PRG_DATE, E_MAIL, WWW, ForesterUtil.getForesterLibraryInformation() );
+ 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>" );
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() ];
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;
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;
}
if ( to > ( msa.getLength() - 1 ) ) {
to = msa.getLength() - 1;
}