Refs #3203: Replaced calls to getIndicesFromSpectra() where possible.

Code/Mantid/Framework/API/inc/MantidAPI/MatrixWorkspace.h

Code/Mantid/Framework/API/src/MatrixWorkspace.cpp

Code/Mantid/Framework/API/test/MatrixWorkspaceTest.h

...Mantid/Framework/Algorithms/src/CalculateTransmission.cpp

...work/Algorithms/src/CalculateTransmissionBeamSpreader.cpp

...Mantid/Framework/Algorithms/src/SANSDirectBeamScaling.cpp