Added initial functionality for Motif scanning and scoring via PWM class.

Will score simple motif, motif with variable length spacer, or motif with
a defined spacer of variable lengths
Moved source files from xcode directory to src for MotifScorer
Adding doxygen documentation to function within pwm source and header
Implementing functions within library to easily create class types

Create function to create track and sequences with minimal function
calls.

Also, tested and implemented some of the unimplemented seqTools(
ie shuffle sequence)
Added abiltity to import model from std::string

Created functions importFromString(...)
Merge branch 'master' into development
Updated StochHMM application to utilize the library for compiling
Fix makefile to work properly on OSX