private static void timeNeighborJoining() { final NeighborJoiningR njr = NeighborJoiningR.createInstance(); for( int n = 3; n <= 10; ++n ) { final int x = ( int ) Math.pow( 2, n ); final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x ); mt.randomize( new Date().getTime() ); final long start_time = new Date().getTime(); njr.execute( mt ); System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } final NeighborJoiningF njf = NeighborJoiningF.createInstance(); for( int n = 3; n <= 10; ++n ) { final int x = ( int ) Math.pow( 2, n ); final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x ); mt.randomize( new Date().getTime() ); final long start_time = new Date().getTime(); njf.execute( mt ); System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } final NeighborJoining nj = NeighborJoining.createInstance(); for( int n = 3; n <= 10; ++n ) { final int x = ( int ) Math.pow( 2, n ); final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x ); mt.randomize( new Date().getTime() ); final long start_time = new Date().getTime(); nj.execute( mt ); System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } } }
private BasicSymmetricalDistanceMatrix calcKimuraDistances() { final int s = _msa.getNumberOfSequences(); final BasicSymmetricalDistanceMatrix d = new BasicSymmetricalDistanceMatrix( s ); copyIdentifiers( s, d ); calcKimuraDistances( s, d ); return d; }
private BasicSymmetricalDistanceMatrix calcPoissonDistances() { final int s = _msa.getNumberOfSequences(); final BasicSymmetricalDistanceMatrix d = new BasicSymmetricalDistanceMatrix( s ); copyIdentifiers( s, d ); calcPoissonDistances( s, d ); return d; }
private BasicSymmetricalDistanceMatrix calcFractionalDissimilarities() { final int s = _msa.getNumberOfSequences(); final BasicSymmetricalDistanceMatrix d = new BasicSymmetricalDistanceMatrix( s ); copyIdentifiers( s, d ); calcFractionalDissimilarities( s, d ); return d; }
/** * Creates a guide tree for use during progressive multiple sequence alignment. * * @param sequences the {@link List} of {@link Sequence}s to align * @param scorers list of sequence pair scorers, one for each pair of sequences given */ public GuideTree(List<S> sequences, List<PairwiseSequenceScorer<S, C>> scorers) { this.sequences = Collections.unmodifiableList(sequences); this.scorers = Collections.unmodifiableList(scorers); distances = new BasicSymmetricalDistanceMatrix(sequences.size()); for (int i = 0, n = 0; i < sequences.size(); i++) { AccessionID id = sequences.get(i).getAccession(); String str = (id == null) ? Integer.toString(i + 1) : id.getID(); distances.setIdentifier(i, str); for (int j = i+1; j < sequences.size(); j++) { double dist = scorers.get(n++).getDistance(); distances.setValue(i, j, dist); } } BasicSymmetricalDistanceMatrix distclone = ForesterWrapper.cloneDM(distances); Phylogeny phylogeny = TreeConstructor.distanceTree(distclone, TreeConstructorType.NJ); newick = phylogeny.toString(); root = new Node(phylogeny.getRoot(), null); }
DistanceMatrix DM = new BasicSymmetricalDistanceMatrix(n);
DistanceMatrix DM = new BasicSymmetricalDistanceMatrix(n);
DistanceMatrix DM = new BasicSymmetricalDistanceMatrix(n);
/** * Creates a guide tree for use during progressive multiple sequence alignment. * * @param sequences the {@link List} of {@link Sequence}s to align * @param scorers list of sequence pair scorers, one for each pair of sequences given */ public GuideTree(List<S> sequences, List<PairwiseSequenceScorer<S, C>> scorers) { this.sequences = Collections.unmodifiableList(sequences); this.scorers = Collections.unmodifiableList(scorers); distances = new BasicSymmetricalDistanceMatrix(sequences.size()); for (int i = 0, n = 0; i < sequences.size(); i++) { AccessionID id = sequences.get(i).getAccession(); String str = (id == null) ? Integer.toString(i + 1) : id.getID(); distances.setIdentifier(i, str); for (int j = i+1; j < sequences.size(); j++) { double dist = scorers.get(n++).getDistance(); distances.setValue(i, j, dist); } } BasicSymmetricalDistanceMatrix distclone = ForesterWrapper.cloneDM(distances); Phylogeny phylogeny = TreeConstructor.distanceTree(distclone, TreeConstructorType.NJ); newick = phylogeny.toString(); root = new Node(phylogeny.getRoot(), null); }
jacknife_ratio, generator ); final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes ); final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes ); for( int i = 0; i < number_of_genomes; ++i ) { final String species_i = species[ i ].getSpeciesId();
/** * Helper function to clone a forester symmetrical DistanceMatrix. * * @param distM * forester symmetrical DistanceMatrix * @return identical copy of the forester symmetrical DistanceMatrix */ public static BasicSymmetricalDistanceMatrix cloneDM( BasicSymmetricalDistanceMatrix distM) { int n = distM.getSize(); BasicSymmetricalDistanceMatrix cloneDM = new BasicSymmetricalDistanceMatrix(n); for (int i = 0; i < n; i++) { cloneDM.setIdentifier(i, distM.getIdentifier(i)); for (int j = i + 1; j < n; j++) { cloneDM.setValue(i, j, distM.getValue(i, j)); } } return cloneDM; }
/** * Helper function to clone a forester symmetrical DistanceMatrix. * * @param distM * forester symmetrical DistanceMatrix * @return identical copy of the forester symmetrical DistanceMatrix */ public static BasicSymmetricalDistanceMatrix cloneDM( BasicSymmetricalDistanceMatrix distM) { int n = distM.getSize(); BasicSymmetricalDistanceMatrix cloneDM = new BasicSymmetricalDistanceMatrix(n); for (int i = 0; i < n; i++) { cloneDM.setIdentifier(i, distM.getIdentifier(i)); for (int j = i + 1; j < n; j++) { cloneDM.setValue(i, j, distM.getValue(i, j)); } } return cloneDM; }
/** * Helper function to clone a forester symmetrical DistanceMatrix. * * @param distM * forester symmetrical DistanceMatrix * @return identical copy of the forester symmetrical DistanceMatrix */ public static BasicSymmetricalDistanceMatrix cloneDM( BasicSymmetricalDistanceMatrix distM) { int n = distM.getSize(); BasicSymmetricalDistanceMatrix cloneDM = new BasicSymmetricalDistanceMatrix(n); for (int i = 0; i < n; i++) { cloneDM.setIdentifier(i, distM.getIdentifier(i)); for (int j = i + 1; j < n; j++) { cloneDM.setValue(i, j, distM.getValue(i, j)); } } return cloneDM; }
DistanceMatrix distance = new BasicSymmetricalDistanceMatrix(n); int totalloopcount = (n / 2) * (n + 1);
DistanceMatrix distance = new BasicSymmetricalDistanceMatrix(n); int totalloopcount = (n / 2) * (n + 1);
DistanceMatrix distance = new BasicSymmetricalDistanceMatrix(n); int totalloopcount = (n / 2) * (n + 1);
DistanceMatrix DM = new BasicSymmetricalDistanceMatrix(n); int totalloopcount = (n / 2) * (n + 1); int end = msa.getLength();
DistanceMatrix DM = new BasicSymmetricalDistanceMatrix(n); int totalloopcount = (n / 2) * (n + 1); int end = msa.getLength();
DistanceMatrix DM = new BasicSymmetricalDistanceMatrix(n); int totalloopcount = (n / 2) * (n + 1); int end = msa.getLength();
+ table.getNumberOfColumns() + ", rows: " + table.getNumberOfRows() + "]" ); final DistanceMatrix distance_matrix = new BasicSymmetricalDistanceMatrix( table.getNumberOfColumns() - 1 ); int start_row = 0; if ( first_line_is_size ) {