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Thank you, Oracle!
[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
44839c9
..
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
// 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;
package org.forester.application;
@@
-176,7
+176,7
@@
public class pccx {
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( pccx.PRG_NAME, error );
}
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( pccx.PRG_NAME, error );
}
- intable = BasicTableParser.parse( infile, " ", false, false );
+ intable = BasicTableParser.parse( infile, ' ', false, false );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( pccx.PRG_NAME, "failed to read \"" + infile + "\" [" + e.getMessage() + "]" );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( pccx.PRG_NAME, "failed to read \"" + infile + "\" [" + e.getMessage() + "]" );
@@
-263,7
+263,7
@@
public class pccx {
}
catch ( final IOException e ) {
ForesterUtil.fatalError( pccx.PRG_NAME, "Failed to write to \"" + annotated_phylogenies_outfile
}
catch ( final IOException e ) {
ForesterUtil.fatalError( pccx.PRG_NAME, "Failed to write to \"" + annotated_phylogenies_outfile
- + "\" [" + e.getMessage() + "]" );
+ + "\" [" + e.getMessage() + "]" );
}
}
}
}
}
}
@@
-283,7
+283,7
@@
public class pccx {
System.out.println( "Usage:" );
System.out.println();
System.out.println( pccx.PRG_NAME
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();
System.out.println();
System.out.println( " Options: " );
System.out.println();
@@
-294,7
+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
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();
}
System.out.println( " phylogeny in phylogenies infile is used)" );
System.out.println();
}