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[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
..
369d514
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;
@@
-33,6
+33,7
@@
import java.util.Arrays;
import java.util.List;
import org.forester.io.parsers.PhylogenyParser;
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;
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();
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 ) {
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 );
}
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() + "]" );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( pccx.PRG_NAME, "failed to read \"" + infile + "\" [" + e.getMessage() + "]" );