From 5433c1a81b31b7806bab9b5c6eb022202bd24ea1 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 9 Oct 2024 01:08:00 +0200
Subject: [PATCH] Use faster `PyUnicode` functions to decode fixed-sized
strings of `HMM` and `Profile`
---
pyhmmer/plan7.pyx | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index 212f9147..2f7e1fc1 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -31,6 +31,7 @@ from cpython.unicode cimport (
PyUnicode_KIND,
PyUnicode_READ,
PyUnicode_GET_LENGTH,
+ PyUnicode_FromStringAndSize,
)
from cpython.pythread cimport (
PyThread_type_lock,
@@ -2676,7 +2677,7 @@ cdef class HMM:
if not (self._hmm.flags & libhmmer.p7_hmm.p7H_CONS):
return None
assert self._hmm.consensus != NULL
- return (&self._hmm.consensus[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._hmm.consensus[1], self._hmm.M)
@property
def consensus_structure(self):
@@ -2689,7 +2690,7 @@ cdef class HMM:
if not (self._hmm.flags & libhmmer.p7_hmm.p7H_CS):
return None
assert self._hmm.cs != NULL
- return (&self._hmm.cs[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._hmm.cs[1], self._hmm.M)
@property
def consensus_accessibility(self):
@@ -2702,7 +2703,7 @@ cdef class HMM:
if not (self._hmm.flags & libhmmer.p7_hmm.p7H_CA):
return None
assert self._hmm.ca != NULL
- return (&self._hmm.ca[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._hmm.ca[1], self._hmm.M)
@property
def reference(self):
@@ -2719,7 +2720,7 @@ cdef class HMM:
if not (self._hmm.flags & libhmmer.p7_hmm.p7H_RF):
return None
assert self._hmm.rf != NULL
- return (&self._hmm.rf[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._hmm.rf[1], self._hmm.M)
@property
def model_mask(self):
@@ -2732,7 +2733,7 @@ cdef class HMM:
if not (self._hmm.flags & libhmmer.p7_hmm.p7H_MM):
return None
assert self._hmm.mm != NULL
- return (&self._hmm.mm[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._hmm.mm[1], self._hmm.M)
@property
def description(self):
@@ -4200,7 +4201,7 @@ cdef class OptimizedProfile:
assert self._om != NULL
if self._om.consensus[0] == b'\0':
return None
- return (&self._om.consensus[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._om.consensus[1], self._om.M)
@property
def consensus_structure(self):
@@ -4212,7 +4213,7 @@ cdef class OptimizedProfile:
assert self._om != NULL
if self._om.cs[0] == b'\0':
return None
- return (&self._om.cs[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._om.cs[1], self._om.M)
@property
def reference(self):
@@ -4229,7 +4230,7 @@ cdef class OptimizedProfile:
assert self._om.rf != NULL
if self._om.rf[0] == b'\0':
return None
- return (&self._om.rf[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._om.rf[1], self._om.M)
@property
def model_mask(self):
@@ -4242,7 +4243,7 @@ cdef class OptimizedProfile:
assert self._om.mm != NULL
if self._om.mm[0] == b'\0':
return None
- return (&self._om.mm[1]).decode("ascii")
+ return PyUnicode_FromStringAndSize(&self._om.mm[1], self._om.M)
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