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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
evoinference
/
TestPhylogenyReconstruction.java
diff --git
a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
index
7726735
..
3529d1e
100644
(file)
--- a/
forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
+++ b/
forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java
@@
-23,7
+23,7
@@
// 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.evoinference;
package org.forester.evoinference;
@@
-1925,7
+1925,6
@@
public class TestPhylogenyReconstruction {
m.setIdentifier( 4, "E" );
m.setIdentifier( 5, "F" );
final NeighborJoining nj = NeighborJoining.createInstance();
m.setIdentifier( 4, "E" );
m.setIdentifier( 5, "F" );
final NeighborJoining nj = NeighborJoining.createInstance();
- nj.setVerbose( false );
nj.execute( m );
m = new BasicSymmetricalDistanceMatrix( 7 );
m.setIdentifier( 0, "Bovine" );
nj.execute( m );
m = new BasicSymmetricalDistanceMatrix( 7 );
m.setIdentifier( 0, "Bovine" );
@@
-2347,10
+2346,14
@@
public class TestPhylogenyReconstruction {
private static void timeNeighborJoining() {
final NeighborJoining nj = NeighborJoining.createInstance();
private static void timeNeighborJoining() {
final NeighborJoining nj = NeighborJoining.createInstance();
- for( int n = 3; n <= 12; ++n ) {
+ for( int n = 3; n <= 13; ++n ) {
final int x = ( int ) Math.pow( 2, n );
final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
mt.randomize( new Date().getTime() );
final int x = ( int ) Math.pow( 2, n );
final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x );
mt.randomize( new Date().getTime() );
+ // for( int i = 0; i < mt.getSize(); i++ ) {
+ // mt.setIdentifier( i, i + "i" );
+ // }
+ // System.out.println( mt.toStringBuffer( Format.PHYLIP ) );
final long start_time = new Date().getTime();
nj.execute( mt );
System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms." );
final long start_time = new Date().getTime();
nj.execute( mt );
System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms." );