Out of memory when constructing alignment from sequence to associated PDB chain

jalview.structure.StructureSelectionManager.setMapping method does not gracefully handle out of memory errors. This is a problem when working with very large structures - see attached virus particle.

Reproduce:
1. load PDB file onto Jalview (with 1G VM)
2. Opening the structure raises an unhandled error.

In this case, the mapping should be reclaimed from the initial sequence extraction, rather than by realigning the structure.

Alternatively, a more memory efficient alignment could be carried out (either by tiling the alignment matrix, or memory mapping the matrix from disk for a the applet's case).

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Example provided by Barry Kesner (kesner@med.unc.edu).