16 #include "halCountedPtr.h"
25 #define HAL_VERSION 2.1
31 typedef int64_t hal_index_t;
36 typedef uint64_t hal_offset_t;
41 typedef uint64_t hal_size_t;
46 typedef std::runtime_error hal_exception;
50 extern const hal_index_t NULL_INDEX;
53 #define HAL_FORWARD_DEC_CLASS(T) \
55 typedef counted_ptr<T> T ## Ptr;\
56 typedef counted_ptr<const T> T ## ConstPtr;
58 HAL_FORWARD_DEC_CLASS(Alignment)
59 HAL_FORWARD_DEC_CLASS(CLParser)
60 HAL_FORWARD_DEC_CLASS(Genome)
61 HAL_FORWARD_DEC_CLASS(MetaData)
62 HAL_FORWARD_DEC_CLASS(TopSegment)
63 HAL_FORWARD_DEC_CLASS(BottomSegment)
64 HAL_FORWARD_DEC_CLASS(Segment)
65 HAL_FORWARD_DEC_CLASS(Sequence)
66 HAL_FORWARD_DEC_CLASS(SlicedSegment)
67 HAL_FORWARD_DEC_CLASS(MappedSegment)
68 HAL_FORWARD_DEC_CLASS(SegmentIterator)
69 HAL_FORWARD_DEC_CLASS(GappedSegmentIterator)
70 HAL_FORWARD_DEC_CLASS(TopSegmentIterator)
71 HAL_FORWARD_DEC_CLASS(GappedTopSegmentIterator)
72 HAL_FORWARD_DEC_CLASS(BottomSegmentIterator)
73 HAL_FORWARD_DEC_CLASS(GappedBottomSegmentIterator)
74 HAL_FORWARD_DEC_CLASS(DNAIterator)
75 HAL_FORWARD_DEC_CLASS(SequenceIterator)
76 HAL_FORWARD_DEC_CLASS(ColumnIterator)
77 HAL_FORWARD_DEC_CLASS(Rearrangement)