/**
* Gets a sub-matrix for only those taxa in the collection (all of which should be present in this
* matrix).
*
* @param taxonSubset
* @return the new submatrix
*/
public DistanceMatrix getSubmatrix(Collection<Taxon> taxonSubset) {
double[][] newDistances = new double[taxonSubset.size()][taxonSubset.size()];
int i = 0;
for (Taxon taxonRow : taxonSubset) {
int row = taxa.indexOf(taxonRow);
if (row == -1) {
throw new IllegalArgumentException(
"The taxon, " + taxonRow.getName() + " is not found in this matrix");
}
int j = 0;
for (Taxon taxonColumn : taxonSubset) {
int column = taxa.indexOf(taxonColumn);
if (column == -1) {
throw new IllegalArgumentException(
"The taxon, " + taxonColumn.getName() + " is not found in this matrix");
}
newDistances[i][j] = getDistance(row, column);
}
i++;
}
return new BasicDistanceMatrix(taxonSubset, newDistances);
}
/**
* Gets the distance between 2 taxa
*
* @param taxonRow
* @param taxonColumn
* @return the distance
*/
public double getDistance(Taxon taxonRow, Taxon taxonColumn) {
int row = taxa.indexOf(taxonRow);
if (row == -1) {
throw new IllegalArgumentException(
"The row taxon, " + taxonRow.getName() + " is not found in this matrix");
}
int column = taxa.indexOf(taxonColumn);
if (column == -1) {
throw new IllegalArgumentException(
"The column taxon, " + taxonColumn.getName() + " is not found in this matrix");
}
return getDistance(row, column);
}