change to name an classes

q2_types/profile_hmms/__init__.py

@@ -6,15 +6,13 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 from ._format import (
-    ProteinHmmMultipleProfilesFileFmt,
-    DnaHmmMultipleProfilesFileFmt,
-    RnaHmmMultipleProfilesFileFmt,
-    ProteinHmmMultipleProfilesDirectoryFormat,
-    DnaHmmMultipleProfilesDirectoryFormat,
-    RnaHmmMultipleProfilesDirectoryFormat,
-    ProteinHmmFileFmt, DnaHmmFileFmt, RnaHmmFileFmt,
-    ProteinHmmDirectoryFormat, DnaHmmDirectoryFormat, RnaHmmDirectoryFormat,
-    BaseHmmPressedDirFmt
+    PressedProfileHmmsDirectoryFmt,
+    ProteinSingleProfileHmmDirectoryFmt,
+    ProteinMultipleProfileHmmDirectoryFmt,
+    DnaSingleProfileHmmDirectoryFmt,
+    DnaMultipleProfileHmmDirectoryFmt,
+    RnaSingleProfileHmmDirectoryFmt,
+    RnaMultipleProfileHmmDirectoryFmt
 )
 from ._type import (
     ProfileHMM,
@@ -24,17 +22,15 @@
 )
 
 __all__ = [
-    "ProteinHmmMultipleProfilesFileFmt",
-    "DnaHmmMultipleProfilesFileFmt",
-    "RnaHmmMultipleProfilesFileFmt",
-    "ProteinHmmMultipleProfilesDirectoryFormat",
-    "DnaHmmMultipleProfilesDirectoryFormat",
-    "RnaHmmMultipleProfilesDirectoryFormat",
-    "ProteinHmmFileFmt", "DnaHmmFileFmt", "RnaHmmFileFmt",
-    "ProteinHmmDirectoryFormat",
-    "DnaHmmDirectoryFormat",
-    "RnaHmmDirectoryFormat",
-    "BaseHmmPressedDirFmt",
+    "ProfileHmmBinaryFileFmt",
+    "PressedProfileHmmsDirectoryFmt",
+    "ProfileHmmFileFmt",
+    "ProteinSingleProfileHmmDirectoryFmt",
+    "ProteinMultipleProfileHmmDirectoryFmt",
+    "DnaSingleProfileHmmDirectoryFmt",
+    "DnaMultipleProfileHmmDirectoryFmt",
+    "RnaSingleProfileHmmDirectoryFmt",
+    "RnaMultipleProfileHmmDirectoryFmt",
     "ProfileHMM",
     "SingleProtein", "SingleDNA", "SingleRNA",
     "MultipleProtein", "MultipleDNA", "MultipleRNA",

q2_types/profile_hmms/_format.py

@@ -11,12 +11,12 @@
 from q2_types.plugin_setup import plugin
 
 
-class HmmBinaryFileFmt(model.BinaryFileFormat):
+class ProfileHmmBinaryFileFmt(model.BinaryFileFormat):
     def _validate_(self, level):
         pass
 
 
-class BaseHmmPressedDirFmt(model.DirectoryFormat):
+class PressedProfileHmmsDirectoryFmt(model.DirectoryFormat):
     """
     The  <hmmfile>.h3m file contains the profile HMMs
     and their annotation in a binary format. The <hmmfile>.h3i file is an
@@ -25,16 +25,14 @@ class BaseHmmPressedDirFmt(model.DirectoryFormat):
     (the MSV filter).  The <hmmfile>.h3p file contains precomputed data
     structures for the rest of each profile.
     """
-    h3m = model.File(r'.*\.hmm\.h3m', format=HmmBinaryFileFmt)
-    h3i = model.File(r'.*\.hmm\.h3i', format=HmmBinaryFileFmt)
-    h3f = model.File(r'.*\.hmm\.h3f', format=HmmBinaryFileFmt)
-    h3p = model.File(r'.*\.hmm\.h3p', format=HmmBinaryFileFmt)
+    h3m = model.File(r'.*\.hmm\.h3m', format=ProfileHmmBinaryFileFmt)
+    h3i = model.File(r'.*\.hmm\.h3i', format=ProfileHmmBinaryFileFmt)
+    h3f = model.File(r'.*\.hmm\.h3f', format=ProfileHmmBinaryFileFmt)
+    h3p = model.File(r'.*\.hmm\.h3p', format=ProfileHmmBinaryFileFmt)
 
 
-class HmmBaseFileFmt(model.TextFileFormat):
-    def _validate_file_fmt(
-            self, level: str, alphabet: str, single_profile: bool
-    ):
+class ProfileHmmFileFmt(model.TextFileFormat):
+    def _validate_(self, level: str):
         """
         Check http://eddylab.org/software/hmmer/Userguide.pdf
         section "HMMER profile HMM files" for full description of
@@ -52,92 +50,88 @@ def _validate_file_fmt(
                     f"{e}"
                 )
 
-            if len(hmm_profiles) > 1 and single_profile:
+            if len(hmm_profiles) > 1 and self.single_profile:
                 raise ValidationError(
                         f"Expected 1 profile, found {len(hmm_profiles)}."
                     )
 
             for hmm_profile in hmm_profiles[:parse_n_profiles]:
                 hmm_profile.validate(tolerance=tolerance)
 
-                if hmm_profile.alphabet.type.lower() != alphabet:
+                if hmm_profile.alphabet.type.lower() != self.alphabet:
                     raise ValidationError(
                         "Found profile with alphabet "
                         f"{hmm_profile.alphabet.type.lower()}\n"
-                        f"{self.__class__} only accepts {alphabet} profiles."
+                        f"Expected alphabet: {self.alphabet}."
                     )
 
 
-class ProteinHmmFileFmt(HmmBaseFileFmt):
+class ProteinProfileHmmFileFmt(ProfileHmmFileFmt):
     alphabet = "amino"
 
-    def _validate_(self, level):
-        self._validate_file_fmt(level, self.alphabet, True)
 
+class ProteinSingleProfileHmmFileFmt(ProteinProfileHmmFileFmt):
+    single_profile = True
+
+
+class ProteinMultipleProfileHmmFileFmt(ProteinProfileHmmFileFmt):
+    single_profile = False
 
-class DnaHmmFileFmt(HmmBaseFileFmt):
+
+class DnaProfileHmmFileFmt(ProfileHmmFileFmt):
     alphabet = "dna"
 
-    def _validate_(self, level):
-        self._validate_file_fmt(level, self.alphabet, True)
 
+class DnaSingleProfileHmmFileFmt(DnaProfileHmmFileFmt):
+    single_profile = True
 
-class RnaHmmFileFmt(HmmBaseFileFmt):
+
+class DnaMultipleProfileHmmFileFmt(DnaProfileHmmFileFmt):
+    single_profile = False
+
+
+class RnaProfileHmmFileFmt(ProfileHmmFileFmt):
     alphabet = "rna"
 
-    def _validate_(self, level):
-        self._validate_file_fmt(level, self.alphabet, True)
 
+class RnaSingleProfileHmmFileFmt(RnaProfileHmmFileFmt):
+    single_profile = True
 
-ProteinHmmDirectoryFormat = model.SingleFileDirectoryFormat(
-    'AminoHmmFileFmt', r'.*\..hmm', ProteinHmmFileFmt)
 
-DnaHmmDirectoryFormat = model.SingleFileDirectoryFormat(
-    'DnaHmmFileFmt', r'.*\..hmm', DnaHmmFileFmt)
+class RnaMultipleProfileHmmFileFmt(RnaProfileHmmFileFmt):
+    single_profile = False
 
-RnaHmmDirectoryFormat = model.SingleFileDirectoryFormat(
-    'RnaHmmFileFmt', r'.*\..hmm', RnaHmmFileFmt)
 
+class ProteinSingleProfileHmmDirectoryFmt(model.DirectoryFormat):
+    profile = model.File(r'.*\.hmm', format=ProteinSingleProfileHmmFileFmt)
 
-class ProteinHmmMultipleProfilesFileFmt(ProteinHmmFileFmt):
-    def _validate_(self, level):
-        self._validate_file_fmt(level, self.alphabet, False)
 
+class ProteinMultipleProfileHmmDirectoryFmt(model.DirectoryFormat):
+    profiles = model.File(r'.*\.hmm', format=ProteinMultipleProfileHmmFileFmt)
 
-class DnaHmmMultipleProfilesFileFmt(DnaHmmFileFmt):
-    def _validate_(self, level):
-        self._validate_file_fmt(level, self.alphabet, False)
 
+class DnaSingleProfileHmmDirectoryFmt(model.DirectoryFormat):
+    profile = model.File(r'.*\.hmm', format=DnaSingleProfileHmmFileFmt)
 
-class RnaHmmMultipleProfilesFileFmt(RnaHmmFileFmt):
-    def _validate_(self, level):
-        self._validate_file_fmt(level, self.alphabet, False)
 
+class DnaMultipleProfileHmmDirectoryFmt(model.DirectoryFormat):
+    profiles = model.File(r'.*\.hmm', format=DnaMultipleProfileHmmFileFmt)
 
-ProteinHmmMultipleProfilesDirectoryFormat = model.SingleFileDirectoryFormat(
-    'AminoHmmMultipleProfilesDirectoryFormat',
-    r'.*\..hmm',
-    ProteinHmmMultipleProfilesFileFmt
-)
 
-DnaHmmMultipleProfilesDirectoryFormat = model.SingleFileDirectoryFormat(
-    'DnaHmmMultipleProfilesDirectoryFormat',
-    r'.*\..hmm',
-    DnaHmmMultipleProfilesFileFmt,
-)
+class RnaSingleProfileHmmDirectoryFmt(model.DirectoryFormat):
+    profile = model.File(r'.*\.hmm', format=RnaSingleProfileHmmFileFmt)
+
+
+class RnaMultipleProfileHmmDirectoryFmt(model.DirectoryFormat):
+    profiles = model.File(r'.*\.hmm', format=RnaMultipleProfileHmmFileFmt)
 
-RnaHmmMultipleProfilesDirectoryFormat = model.SingleFileDirectoryFormat(
-    'RnaHmmMultipleProfilesDirectoryFormat',
-    r'.*\..hmm',
-    RnaHmmMultipleProfilesFileFmt,
-)
 
 plugin.register_formats(
-    ProteinHmmMultipleProfilesFileFmt,
-    DnaHmmMultipleProfilesFileFmt,
-    RnaHmmMultipleProfilesFileFmt,
-    ProteinHmmMultipleProfilesDirectoryFormat,
-    DnaHmmMultipleProfilesDirectoryFormat,
-    RnaHmmMultipleProfilesDirectoryFormat,
-    ProteinHmmDirectoryFormat, DnaHmmDirectoryFormat, RnaHmmDirectoryFormat
+    PressedProfileHmmsDirectoryFmt,
+    ProteinSingleProfileHmmDirectoryFmt,
+    ProteinMultipleProfileHmmDirectoryFmt,
+    DnaSingleProfileHmmDirectoryFmt,
+    DnaMultipleProfileHmmDirectoryFmt,
+    RnaSingleProfileHmmDirectoryFmt,
+    RnaMultipleProfileHmmDirectoryFmt
 )

q2_types/profile_hmms/_type.py

@@ -8,11 +8,13 @@
 from qiime2.plugin import SemanticType
 from q2_types.plugin_setup import plugin
 from q2_types.profile_hmms._format import (
-    ProteinHmmMultipleProfilesDirectoryFormat,
-    DnaHmmMultipleProfilesDirectoryFormat,
-    RnaHmmMultipleProfilesDirectoryFormat,
-    ProteinHmmDirectoryFormat, DnaHmmDirectoryFormat, RnaHmmDirectoryFormat,
-    BaseHmmPressedDirFmt
+    PressedProfileHmmsDirectoryFmt,
+    DnaSingleProfileHmmDirectoryFmt,
+    DnaMultipleProfileHmmDirectoryFmt,
+    RnaSingleProfileHmmDirectoryFmt,
+    RnaMultipleProfileHmmDirectoryFmt,
+    ProteinSingleProfileHmmDirectoryFmt,
+    ProteinMultipleProfileHmmDirectoryFmt
 )
 
 
@@ -54,7 +56,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[PressedProtein],
-    directory_format=BaseHmmPressedDirFmt,
+    directory_format=PressedProfileHmmsDirectoryFmt,
     description=(
         "A collection of profile Hidden Markov Models for amino acid "
         "sequences in binary format and indexed."
@@ -63,7 +65,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[PressedDNA],
-    directory_format=BaseHmmPressedDirFmt,
+    directory_format=PressedProfileHmmsDirectoryFmt,
     description=(
         "A collection of profile Hidden Markov Models for DNA "
         "sequences in binary format and indexed."
@@ -72,7 +74,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[PressedRNA],
-    directory_format=BaseHmmPressedDirFmt,
+    directory_format=PressedProfileHmmsDirectoryFmt,
     description=(
         "A collection of profile Hidden Markov Models for RNA "
         "sequences in binary format and indexed."
@@ -81,7 +83,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[SingleProtein],
-    directory_format=ProteinHmmDirectoryFormat,
+    directory_format=ProteinSingleProfileHmmDirectoryFmt,
     description=(
         "One single profile Hidden Markov Model representing a group "
         "of related proteins."
@@ -90,7 +92,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[SingleDNA],
-    directory_format=DnaHmmDirectoryFormat,
+    directory_format=DnaSingleProfileHmmDirectoryFmt,
     description=(
         "One single profile Hidden Markov Model representing a group "
         "of related DNA sequences."
@@ -99,7 +101,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[SingleRNA],
-    directory_format=RnaHmmDirectoryFormat,
+    directory_format=RnaSingleProfileHmmDirectoryFmt,
     description=(
         "One single profile Hidden Markov Model representing a group "
         "of related RNA sequences."
@@ -108,7 +110,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[MultipleProtein],
-    directory_format=ProteinHmmMultipleProfilesDirectoryFormat,
+    directory_format=ProteinMultipleProfileHmmDirectoryFmt,
     description=(
         "A collection of profile Hidden Markov Models, "
         "each representing a group of related proteins."
@@ -117,7 +119,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[MultipleDNA],
-    directory_format=DnaHmmMultipleProfilesDirectoryFormat,
+    directory_format=DnaMultipleProfileHmmDirectoryFmt,
     description=(
         "A collection of profile Hidden Markov Models, "
         "each representing a group of related DNA sequences."
@@ -126,7 +128,7 @@
 
 plugin.register_artifact_class(
     ProfileHMM[MultipleRNA],
-    directory_format=RnaHmmMultipleProfilesDirectoryFormat,
+    directory_format=RnaMultipleProfileHmmDirectoryFmt,
     description=(
         "A collection of profile Hidden Markov Models, "
         "each representing a group of related RNA sequences."