The MATLAB and Java facade exports the boundary matrix of the complex a result was computed from, for your own linear algebra (an optimal-cycle solver, harmonic smoothing, ...):

PersistenceResult result = TDA4j.computeFromPoints(points, new String[]{"maxDimension", "1"});
int n = result.numCells();               // cells, not bars
int[] rows = result.boundaryRows();      // 0-based
int[] cols = result.boundaryCols();
double[] values = result.boundaryValues();
int dim7 = result.columnDimension(7);
int[] vertices7 = result.columnVertices(7);
double value7 = result.columnFiltrationValue(7);

n = result.numCells();
M = sparse(double(result.boundaryRows())+1, double(result.boundaryCols())+1, result.boundaryValues(), n, n);

Columns are the cells of the complex in filtration order, so a face's row comes before its coface's column. The matrix is the same whichever engine computed the bars, and is built the first time you ask for it. Column j describes cell j, which is unrelated to bar j of toArray(). Not available from the command line.

From Scala, the cells of any stream are stream.iterator in filtration order, with stream.filtrationValue(cell) and cell.boundary[C].