11 #ifndef AP_SEQUENCE_HXX
12 #define AP_SEQUENCE_HXX
27 #define ap_assert(cond) arb_assert(cond)
44 if (is_set != has_sequence) {
46 has_sequence = is_set;
51 virtual void set(
const char *sequence) = 0;
52 virtual void unset() = 0;
103 static long global_combineCount;
121 virtual uint32_t
checksum()
const = 0;
132 global_combineCount--;
143 #error AP_sequence.hxx included twice
144 #endif // AP_SEQUENCE_HXX
AP_combinableSeq(const AliView *aliview)
virtual ~AP_combinableSeq()
virtual AP_FLOAT count_weighted_bases() const =0
const AP_weights * get_weights() const
static long combine_count()
GBDATA * get_bound_species_data() const
virtual int cmp_combined(const AP_combinableSeq *other) const =0
void ensure_sequence_loaded() const
AP_sequence(const AliView *aliview)
void do_lazy_load() const
const AP_filter * get_filter() const
virtual AP_sequence * dup() const =0
virtual AP_combinableSeq * dup() const =0
bool is_bound_to_species() const
virtual void partial_match(const AP_combinableSeq *part, long *overlap, long *penalty) const =0
void mark_sequence_set(bool is_set)
virtual uint32_t checksum() const =0
const AP_weights * get_weights() const
Mutations noncounting_combine_seq(const AP_combinableSeq *lefts, const AP_combinableSeq *rights)
void unbind_from_species()
const AP_filter * get_filter() const
bool combinedEquals(const AP_combinableSeq *other) const
const AliView * get_aliview() const
size_t get_sequence_length() const
AP_FLOAT weighted_base_count() const
void lazy_load_sequence() const
virtual Mutations combine_seq(const AP_combinableSeq *lefts, const AP_combinableSeq *rights, char *mutation_per_site=NULp)=0
GB_ERROR bind_to_species(GBDATA *gb_species)
size_t get_length() const
virtual void set(const char *sequence)=0
virtual Mutations mutations_if_combined_with(const AP_combinableSeq *other)=0
static void inc_combine_count()