From c7cc98b96407b16d62bb50f5927bc08cf663333b Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 9 Oct 2024 02:23:21 +0200
Subject: [PATCH] Implement `__len__` for `HMMPressedFile` using the SSI index
---
pyhmmer/plan7.pxd | 1 +
pyhmmer/plan7.pyi | 1 +
pyhmmer/plan7.pyx | 7 +++++++
pyhmmer/tests/test_plan7/test_hmmfile.py | 10 ++++++++++
4 files changed, 19 insertions(+)
diff --git a/pyhmmer/plan7.pxd b/pyhmmer/plan7.pxd
index 2b2e5977..f0200666 100644
--- a/pyhmmer/plan7.pxd
+++ b/pyhmmer/plan7.pxd
@@ -173,6 +173,7 @@ cdef class HMMPressedFile:
cdef P7_HMMFILE* _hfp
cdef Alphabet _alphabet
cdef HMMFile _hmmfile
+ cdef size_t _position
cpdef void close(self) except *
cpdef void rewind(self) except *
diff --git a/pyhmmer/plan7.pyi b/pyhmmer/plan7.pyi
index 4393079d..e6c67a08 100644
--- a/pyhmmer/plan7.pyi
+++ b/pyhmmer/plan7.pyi
@@ -453,6 +453,7 @@ class HMMPressedFile(typing.Iterator[OptimizedProfile]):
) -> bool: ...
def __iter__(self) -> HMMPressedFile: ...
def __next__(self) -> OptimizedProfile: ...
+ def __len__(self) -> int: ...
@property
def closed(self) -> bool: ...
@property
diff --git a/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index 2f7e1fc1..9137461c 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -3750,6 +3750,7 @@ cdef class HMMPressedFile:
self._alphabet = None
self._hmmfile = None
self._hfp = NULL
+ self._position = 0
def __init__(self, object file):
"""__init__(self, file)\n--\n
@@ -3790,6 +3791,10 @@ cdef class HMMPressedFile:
def __exit__(self, exc_type, exc_value, traceback):
self.close()
+ def __len__(self):
+ assert self._hfp.ssi != NULL
+ return self._hfp.ssi.nprimary - self._position
+
# --- Properties ---------------------------------------------------------
@property
@@ -3822,6 +3827,7 @@ cdef class HMMPressedFile:
"""Rewind the file back to the beginning.
"""
self._hmmfile.rewind()
+ self._position = 0
cpdef OptimizedProfile read(self):
"""Read the next optimized profile from the file.
@@ -3856,6 +3862,7 @@ cdef class HMMPressedFile:
if status == libeasel.eslOK:
om.alphabet = self._alphabet
+ self._position += 1
return om
elif status == libeasel.eslEOF:
return None
diff --git a/pyhmmer/tests/test_plan7/test_hmmfile.py b/pyhmmer/tests/test_plan7/test_hmmfile.py
index 900aa247..a71fea8f 100644
--- a/pyhmmer/tests/test_plan7/test_hmmfile.py
+++ b/pyhmmer/tests/test_plan7/test_hmmfile.py
@@ -93,6 +93,16 @@ class _TestHMMPath:
with self.open_hmm(path) as f:
self.check_hmmfile(f.optimized_profiles())
+ def test_optimized_profiles_length(self):
+ path = os.path.join(self.hmms_folder, "db", "{}.hmm".format(self.ID))
+ with self.open_hmm(path) as f:
+ profiles = f.optimized_profiles()
+ self.assertEqual(len(profiles), len(self.NAMES))
+ profiles.read()
+ self.assertEqual(len(profiles), len(self.NAMES) - 1)
+ profiles.rewind()
+ self.assertEqual(len(profiles), len(self.NAMES))
+
def test_rewind(self):
path = os.path.join(self.hmms_folder, "txt", "{}.hmm".format(self.ID))
with self.open_hmm(path) as f:
--
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