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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
count_support.java
diff --git
a/forester/java/src/org/forester/application/count_support.java
b/forester/java/src/org/forester/application/count_support.java
index
e094f69
..
b57f3c5
100644
(file)
--- a/
forester/java/src/org/forester/application/count_support.java
+++ b/
forester/java/src/org/forester/application/count_support.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;
@@
-32,6
+32,7
@@
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.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
@@
-49,11
+50,18
@@
public class count_support {
final static private String PRG_NAME = "count_support";
final static private String PRG_VERSION = "1.0";
final static private String PRG_DATE = "2008.03.04";
final static private String PRG_NAME = "count_support";
final static private String PRG_VERSION = "1.0";
final static private String PRG_DATE = "2008.03.04";
+ final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String WWW = "www.phylosoft.org/forester/";
private final static boolean WRITE_EVALUATORS_AS_NHX = false;
public static void main( final String args[] ) {
private final static boolean WRITE_EVALUATORS_AS_NHX = false;
public static void main( final String args[] ) {
- ForesterUtil
- .printProgramInformation( count_support.PRG_NAME, count_support.PRG_VERSION, count_support.PRG_DATE );
+ ForesterUtil.printProgramInformation( PRG_NAME,
+ null,
+ PRG_VERSION,
+ PRG_DATE,
+ E_MAIL,
+ WWW,
+ ForesterUtil.getForesterLibraryInformation() );
if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
System.out.println();
System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
System.out.println();
System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
@@
-104,7
+112,7
@@
public class count_support {
Phylogeny[] ev = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
Phylogeny[] ev = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( phylogeny_infile, true );
p = factory.create( phylogeny_infile, pp )[ 0 ];
}
catch ( final Exception e ) {
p = factory.create( phylogeny_infile, pp )[ 0 ];
}
catch ( final Exception e ) {
@@
-113,7
+121,7
@@
public class count_support {
}
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
}
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( evaluators_infile, true );
+ final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( evaluators_infile, true );
ev = factory.create( evaluators_infile, pp );
}
catch ( final Exception e ) {
ev = factory.create( evaluators_infile, pp );
}
catch ( final Exception e ) {