X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fpccx.java;h=369d51449ac65b5be134cc179a4de9c5c8192cb8;hb=94fab44b4568a8c49d9766c7f49eefac2d8f22ff;hp=d46d18f22cd54c3541cbf603716d4259805758a3;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git

diff --git a/forester/java/src/org/forester/application/pccx.java b/forester/java/src/org/forester/application/pccx.java
index d46d18f..369d514 100644
--- a/forester/java/src/org/forester/application/pccx.java
+++ b/forester/java/src/org/forester/application/pccx.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
@@ -15,13 +15,13 @@
 // 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
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.application;
 
@@ -33,6 +33,7 @@ import java.util.Arrays;
 import java.util.List;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.pccx.BasicExternalNodeBasedCoverageExtender;
 import org.forester.pccx.Coverage;
@@ -144,7 +145,7 @@ public class pccx {
         Phylogeny[] phylogenies = null;
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogenies_infile, true );
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogenies_infile, true );
             phylogenies = factory.create( phylogenies_infile, pp );
         }
         catch ( final IOException e ) {
@@ -175,7 +176,7 @@ public class pccx {
                 if ( !ForesterUtil.isEmpty( error ) ) {
                     ForesterUtil.fatalError( pccx.PRG_NAME, error );
                 }
-                intable = BasicTableParser.parse( infile, " ", false );
+                intable = BasicTableParser.parse( infile, ' ', false, false );
             }
             catch ( final IOException e ) {
                 ForesterUtil.fatalError( pccx.PRG_NAME, "failed to read \"" + infile + "\" [" + e.getMessage() + "]" );