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Use p7_tophits_Clone to implement TopHits.copy
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@althonos
althonos committed Aug 16, 2023
1 parent 06e3914 commit 122bbde
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Showing 2 changed files with 14 additions and 82 deletions.
1 change: 1 addition & 0 deletions include/libhmmer/p7_tophits.pxd
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Expand Up @@ -29,6 +29,7 @@ cdef extern from "hmmer.h" nogil:
ctypedef p7_tophits_s P7_TOPHITS

P7_TOPHITS *p7_tophits_Create()
P7_TOPHITS *p7_tophits_Clone(const P7_TOPHITS* h)
int p7_tophits_Grow(P7_TOPHITS *h)
int p7_tophits_CreateNextHit(P7_TOPHITS *h, P7_HIT **ret_hit)
int p7_tophits_Add(P7_TOPHITS *h,
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95 changes: 13 additions & 82 deletions pyhmmer/plan7.pyx
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Expand Up @@ -7922,96 +7922,27 @@ cdef class TopHits:
assert self._th != NULL
assert self._th.N >= 0

cdef size_t i
cdef size_t j
cdef ptrdiff_t diff
cdef P7_DOMAIN* dom_orig
cdef P7_DOMAIN* dom_copy
cdef TopHits copy = TopHits.__new__(TopHits)
cdef TopHits copy = TopHits.__new__(TopHits)

# record query name and accession
copy._qname = self._qname
copy._qacc = self._qacc

# WARN(@althonos): there is no way to do this in the HMMER codebase
# so this is a manual implementation; make sure
# that it stays consistent if P7_TOPHITS changes!
# TODO(@althonos): Replace with `p7_tophits_Clone` as implemented
# in EddyRivasLab/hmmer#273 when formally released.
with nogil:
# copy pipeline configuration
memcpy(&copy._pli, &self._pli, sizeof(P7_PIPELINE))

# don't use `p7_tophits_Create` here otherwise it will allocate
# using a default size, while we already know how large we want
# our buffers to be.
copy._th = <P7_TOPHITS*> malloc(sizeof(P7_TOPHITS))
if copy._th == NULL:
raise AllocationError("P7_TOPHITS", sizeof(P7_TOPHITS))

# copy attributes that don't need any allocation
copy._th.nreported = self._th.nreported
copy._th.nincluded = self._th.nincluded
copy._th.is_sorted_by_sortkey = self._th.is_sorted_by_sortkey
copy._th.is_sorted_by_seqidx = self._th.is_sorted_by_seqidx

# we allocate an exact size array here since we don't expect new
# data to be added to the copy; this means we can use the real `N`
# as the `Nalloc`
copy._th.Nalloc = copy._th.N = self._th.N
copy._th.unsrt = <P7_HIT*> calloc(self._th.N, sizeof(P7_HIT))
if copy._th.unsrt == NULL:
raise AllocationError("P7_HIT", sizeof(P7_HIT), self._th.N)

# here we have to copy the sorted array, which is basically an
# array of pointers to `unsrt`; for each sorted hit we retrieve
# its position in the old array and use it to set the position
# in the new array
copy._th.hit = <P7_HIT**> calloc(self._th.N, sizeof(P7_HIT*))
if copy._th.hit == NULL:
raise AllocationError("P7_HIT*", sizeof(P7_HIT*), self._th.N)
for i in range(<size_t> self._th.N):
diff = self._th.hit[i] - self._th.unsrt
copy._th.hit[i] = copy._th.unsrt + diff

# now copy the hits themselves, making sure to duplicate any
# memory owned by them get's duplicated in the process (this
# is a deepcopy to avoid any double free)
memcpy(copy._th.unsrt, self._th.unsrt, sizeof(P7_HIT) * self._th.N)
for i in range(<size_t> self._th.N):
# reallocate an owned string for the hit name, accession and description
if self._th.unsrt[i].name != NULL:
copy._th.unsrt[i].name = strdup(self._th.unsrt[i].name)
if copy._th.unsrt[i].name == NULL:
raise AllocationError("char*", sizeof(char*), strlen(self._th.unsrt[i].name))
if self._th.unsrt[i].acc != NULL:
copy._th.unsrt[i].acc = strdup(self._th.unsrt[i].acc)
if copy._th.unsrt[i].acc == NULL:
raise AllocationError("char*", sizeof(char*), strlen(self._th.unsrt[i].acc))
if self._th.unsrt[i].desc != NULL:
copy._th.unsrt[i].desc = strdup(self._th.unsrt[i].desc)
if copy._th.unsrt[i].desc == NULL:
raise AllocationError("char*", sizeof(char*), strlen(self._th.unsrt[i].desc))
# copy the domain list
copy._th.unsrt[i].dcl = <P7_DOMAIN*> calloc(sizeof(P7_DOMAIN), copy._th.unsrt[i].ndom)
if copy._th.unsrt[i].dcl == NULL:
raise AllocationError("P7_DOMAIN", sizeof(P7_DOMAIN), self._th.unsrt[i].ndom)
memcpy(copy._th.unsrt[i].dcl, self._th.unsrt[i].dcl, sizeof(P7_DOMAIN) * self._th.unsrt[i].ndom)
# copy domain memory
for j in range(<size_t> self._th.unsrt[i].ndom):
dom_orig = &self._th.unsrt[i].dcl[j]
dom_copy = &copy._th.unsrt[i].dcl[j]
# copy scores per position
if dom_orig.scores_per_pos != NULL:
dom_copy.scores_per_pos = <float*> calloc(sizeof(float), dom_orig.ad.N)
if dom_copy.scores_per_pos == NULL:
raise AllocationError("float", sizeof(float), dom_orig.ad.N)
memcpy(dom_copy.scores_per_pos, dom_orig.scores_per_pos, sizeof(float) * dom_orig.ad.N)
# copy alidisplay
dom_copy.ad = libhmmer.p7_alidisplay.p7_alidisplay_Clone(dom_orig.ad)
if dom_copy.ad == NULL:
raise AllocationError("P7_ALIDISPLAY", sizeof(P7_ALIDISPLAY))

# copy top hits
# WARN(@althonos): `p7_tophits_Clone` will fail when called
# on an empty P7_TOPHITS as it attempts a
# zero-allocation of the target arrays, it
# should be reported as a bug at some point.
if self._th.N > 0:
copy._th = libhmmer.p7_tophits.p7_tophits_Clone(self._th)
else:
copy._th = libhmmer.p7_tophits.p7_tophits_Create()
if copy._th == NULL:
raise AllocationError("P7_TOPHITS", sizeof(P7_TOPHITS))

return copy

cpdef int compare_ranking(self, KeyHash ranking) except -1:
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