removed clustalo

[jalview.git] / forester / java / src / org / forester / application / strip.java

diff --git a/forester/java/src/org/forester/application/strip.java b/forester/java/src/org/forester/application/strip.java
index 7af9ff8..14aa69e 100644 (file)
--- a/forester/java/src/org/forester/application/strip.java
+++ b/forester/java/src/org/forester/application/strip.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;
 
@@ -29,12 +29,12 @@ import java.io.File;
 import java.io.IOException;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.util.ForesterUtil;
 
 public class strip {
 
@@ -55,7 +55,7 @@ public class strip {
         Phylogeny p = null;
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( infile, true );
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( infile, true );
             p = factory.create( infile, pp )[ 0 ];
         }
         catch ( final Exception e ) {
@@ -84,7 +84,7 @@ public class strip {
         }
         else {
             names = new String[ args.length - 3 ];
-            for( int i = 0; i < args.length - 3; ++i ) {
+            for( int i = 0; i < ( args.length - 3 ); ++i ) {
                 names[ i ] = args[ i + 3 ];
             }
         }
@@ -109,7 +109,7 @@ public class strip {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final File f = new File( file );
-            final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( f, true );
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( f, true );
             p0 = factory.create( f, pp )[ 0 ];
         }
         catch ( final Exception e ) {