import java.util.TreeSet;
import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.distance.NeighborJoiningF;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
final MsaInferrer mafft = Mafft
.createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" );
final List<String> opts = new ArrayList<String>();
- // opts.add( "--maxiterate" );
- // opts.add( "1000" );
- // opts.add( "--localpair" );
+ opts.add( "--maxiterate" );
+ opts.add( "1000" );
+ opts.add( "--localpair" );
opts.add( "--quiet" );
_msa = mafft.infer( _msa.asSequenceList(), opts );
}
}
}
- Phylogeny pi() {
- final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa );
+ Phylogeny pi( final String matrix ) {
+ final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, true, matrix );
final int seed = 15;
final int n = 100;
final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
final Phylogeny[] eval_phys = new Phylogeny[ n ];
for( int i = 0; i < n; ++i ) {
resampleable_msa.resample( resampled_column_positions[ i ] );
- eval_phys[ i ] = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, resampleable_msa );
+ eval_phys[ i ] = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, resampleable_msa, false, null );
}
ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
PhylogenyMethods.extractFastaInformation( master_phy );
return master_phy;
}
- private Phylogeny inferNJphylogeny( PWD_DISTANCE_METHOD pwd_distance_method, final Msa msa ) {
+ private Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method,
+ final Msa msa,
+ final boolean write_matrix,
+ final String matrix_name ) {
BasicSymmetricalDistanceMatrix m = null;
switch ( pwd_distance_method ) {
case KIMURA_DISTANCE:
default:
throw new IllegalArgumentException( "invalid pwd method" );
}
- final NeighborJoining nj = NeighborJoining.createInstance();
+ if ( write_matrix ) {
+ try {
+ m.write( ForesterUtil.createBufferedWriter( matrix_name ) );
+ }
+ catch ( final IOException e ) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
final Phylogeny phy = nj.execute( m );
return phy;
}
final int step,
final boolean realign,
final boolean norm ) throws IOException, InterruptedException {
- final Phylogeny a = pi();
+ final Phylogeny a = pi( "a.pwd" );
Archaeopteryx.createApplication( a );
final GapContribution stats[] = calcGapContribtionsStats( norm );
final List<String> to_remove_ids = new ArrayList<String>();
if ( realign ) {
mafft();
}
- final Phylogeny b = pi();
+ final Phylogeny b = pi( "b.pwd" );
Archaeopteryx.createApplication( b );
}