SConstruct: Enable C++11

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
SequenceComparator: Use standard shared pointers

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
Work on enumerated alphabet instead of ascii characters

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
Some stylistic fixes

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
SimilarityMatrix: Implement support for custom similarity matrix

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
Misc: Add header to all source files

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
Add support for loading Similarity Matrix from file

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
SConstruct: Enable all compilation warnings

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
main: Fix compilation warning

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>
Add more documentation

Signed-off-by: Tomasz Figa <tomasz.figa@gmail.com>