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in progress....
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
nj.java
diff --git
a/forester/java/src/org/forester/application/nj.java
b/forester/java/src/org/forester/application/nj.java
index
6bce553
..
dca5d08
100644
(file)
--- a/
forester/java/src/org/forester/application/nj.java
+++ b/
forester/java/src/org/forester/application/nj.java
@@
-22,7
+22,7
@@
// 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;
@@
-119,7
+119,7
@@
public class nj {
+ matrices[ 0 ].getSize() );
}
final List<Phylogeny> ps = new ArrayList<Phylogeny>();
+ matrices[ 0 ].getSize() );
}
final List<Phylogeny> ps = new ArrayList<Phylogeny>();
- final NeighborJoining nj = NeighborJoining.createInstance( verbose );
+ final NeighborJoining nj = NeighborJoining.createInstance( verbose, 6 );
final long start_time = new Date().getTime();
for( final DistanceMatrix matrix : matrices ) {
ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
final long start_time = new Date().getTime();
for( final DistanceMatrix matrix : matrices ) {
ps.add( nj.execute( ( BasicSymmetricalDistanceMatrix ) matrix ) );
@@
-142,7
+142,7
@@
public class nj {
System.out.println( "Usage:" );
System.out.println();
System.out.println( "% java -cp forester.jar org.forester.applications." + PRG_NAME
System.out.println( "Usage:" );
System.out.println();
System.out.println( "% java -cp forester.jar org.forester.applications." + PRG_NAME
- + " [options] <pairwise distances infile> <out file>" );
+ + " [options] <pairwise distances infile> <out file>" );
System.out.println();
System.out.println( " Options: " );
System.out.println( VERBOSE_OPTION + ": verbose on" );
System.out.println();
System.out.println( " Options: " );
System.out.println( VERBOSE_OPTION + ": verbose on" );