in progress...

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

diff --git a/forester/java/src/org/forester/application/pccx.java b/forester/java/src/org/forester/application/pccx.java
index 0cb6577..e3c8167 100644 (file)
--- a/forester/java/src/org/forester/application/pccx.java
+++ b/forester/java/src/org/forester/application/pccx.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;
 
@@ -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() + "]" );
@@ -262,7 +263,7 @@ public class pccx {
                 }
                 catch ( final IOException e ) {
                     ForesterUtil.fatalError( pccx.PRG_NAME, "Failed to write to \"" + annotated_phylogenies_outfile
-                            + "\" [" + e.getMessage() + "]" );
+                                             + "\" [" + e.getMessage() + "]" );
                 }
             }
         }
@@ -282,7 +283,7 @@ public class pccx {
         System.out.println( "Usage:" );
         System.out.println();
         System.out.println( pccx.PRG_NAME
-                + "  [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
+                            + "  [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
         System.out.println();
         System.out.println( " Options: " );
         System.out.println();
@@ -293,7 +294,7 @@ public class pccx {
         System.out.println( " -o=<file> : write output to <file>" );
         System.out.println( " -i=<file> : read (new-line separated) external node names from <file>" );
         System.out.println( " -" + pccx.OUTPUT_ANNOTATED_PHYLOGENIES_OPTION
-                + "=<file> : write output as annotated phylogeny to <file> (only first" );
+                            + "=<file> : write output as annotated phylogeny to <file> (only first" );
         System.out.println( "             phylogeny in phylogenies infile is used)" );
         System.out.println();
     }