rio - gsdir work...

[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 308878f..f374154 100644 (file)
--- a/forester/java/src/org/forester/application/strip.java
+++ b/forester/java/src/org/forester/application/strip.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -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 ) {