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removed clustalo
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
nhx_too.java
diff --git
a/forester/java/src/org/forester/application/nhx_too.java
b/forester/java/src/org/forester/application/nhx_too.java
index
32acbc8
..
1061c5c
100644
(file)
--- a/
forester/java/src/org/forester/application/nhx_too.java
+++ b/
forester/java/src/org/forester/application/nhx_too.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;
@@
-31,8
+31,10
@@
import java.util.ArrayList;
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.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.util.CommandLineArguments;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.util.CommandLineArguments;
@@
-79,7
+81,7
@@
public class nhx_too {
Phylogeny p = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
Phylogeny p = 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 ) {
@@
-88,7
+90,7
@@
public class nhx_too {
}
if ( int_node_name_is_support ) {
try {
}
if ( int_node_name_is_support ) {
try {
- ForesterUtil.transferInternalNodeNamesToConfidence( p );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( p );
}
catch ( final Exception e ) {
ForesterUtil.unexpectedFatalError( nhx_too.PRG_NAME,
}
catch ( final Exception e ) {
ForesterUtil.unexpectedFatalError( nhx_too.PRG_NAME,