Updated the follwoing integration tests:
1. splice_out_generic
2. splice_out
3. splice_in_genric
4. splice_in
5. splice_seq_const
These ofcourse will fail compared to previous commits
In Splice.cc:
1.Add Carbonyl coordiante constraints
2. Changed the current segment behvaiour so it reads the current segment from the XML rather than the pdb
3. In SpliceSegments the occurrence data for H3 loops with no occurrence data is filled in by Rosetta (previously this caused a segmentation fault)
4. In SequenceProfile I added getter and setter functions for accessing the occurrence_data array
5. In SeqprofCons I added tracer lines to check correctness of occurrence_data array