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updated __all__ tags for 1.00a2 release

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jchang
jchang committed Jul 5, 2001
1 parent 56eb624 commit a7a332bde7a5fec75c808d478607b3ad545aa681
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@@ -1 +1,7 @@
# Align directory
+
+__all__ = [
+ 'AlignInfo',
+ 'FormatConvert',
+ 'Generic'
+ ]
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@@ -1,5 +1,9 @@
import string, re
+__all__ = [
+ 'IUPAC',
+ ]
+
# This is used by sequences which contain a finite number of similar
# words.
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@@ -3,4 +3,8 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-__all__ = ['NCBIStandalone', 'NCBIWWW', 'Record']
+__all__ = [
+ 'NCBIStandalone',
+ 'NCBIWWW',
+ 'Record',
+ ]
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@@ -21,6 +21,10 @@
o _AlignCreator
o MultipleAlignCL"""
+__all__ = [
+ 'clustal_format',
+ ]
+
# standard library
import os
import string
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@@ -1 +1,6 @@
# This is a Python module
+
+__all__ = [
+ 'CodonTable',
+ 'IUPACData'
+ ]
@@ -1 +1,6 @@
# This is a Python module.
+
+__all__ = [
+ 'IUPACEncoding',
+ ]
+
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@@ -28,6 +28,10 @@
import string
import os
+__all__ = [
+ 'FastaAlign',
+ ]
+
from Bio import File
from Bio import Index
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@@ -34,6 +34,11 @@
download_many Download many GenBank records.
"""
+__all__ = [
+ 'LocationParser',
+ 'Record',
+ 'genbank_format',
+ ]
# standard library
import string
import os
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@@ -3,6 +3,11 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
+__all__ = [
+ 'Record',
+ 'kabat_format'
+ ]
+
# standard library
import string
import array
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@@ -38,7 +38,10 @@
_extract_pattern_hits Extract Prosite patterns from a web page.
"""
-__all__ = ['Prodoc', 'Pattern']
+__all__ = [
+ 'Pattern',
+ 'Prodoc',
+ ]
from types import *
import string
import re
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@@ -3,4 +3,8 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-__all__ = ['Dom', 'Lin', 'Location']
+__all__ = [
+ 'Dom',
+ 'Lin',
+ 'Location'
+ ]
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@@ -7,3 +7,6 @@
# Note that once a parser is given an input string, it is free to read
# as much of the data as it wants to read, unless otherwise mentioned.
+__all__ = [
+ 'FASTA'
+ ]
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@@ -1,3 +1,8 @@
+__all__ = [
+ 'FreqTable',
+ 'MatrixInfo'
+ ]
+
import re
import string
import sys
@@ -3,4 +3,7 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-__all__ = ['SProt', 'KeyWList']
+__all__ = [
+ 'KeyWList',
+ 'SProt',
+ ]
@@ -2,3 +2,7 @@
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
+
+__init__ = [
+ 'kMeans',
+ ]
@@ -0,0 +1,10 @@
+# Copyright 2001 by Jeffrey Chang. All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+__all__ = [
+ 'Scheduler',
+ 'Task',
+ 'copen'
+ ]
@@ -1 +1,5 @@
# make files in this directory importable
+
+__all__ = [
+ 'spark',
+ ]
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@@ -1,5 +1,11 @@
# This is a Python module
+__all__ = [
+ 'ExPASy',
+ 'NCBI,
+ 'SCOP',
+ ]
+
import time
class RequestLimiter:
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@@ -11,17 +11,20 @@
"Data",
"Encodings",
"Enzyme",
+ "FSSP",
"Fasta",
"File",
"GenBank",
"Gobase",
"Index",
+ "Kabat",
"Medline",
"PDB",
"ParserSupport",
"PropertyManager",
"Prosite",
"Rebase",
+ "RecordFile",
"SCOP",
"Seq",
"SeqFeature",
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@@ -20,6 +20,13 @@ recursive-include Tests *
global-exclude CVS
global-exclude CVS/*
+# Don't include obsolete regression testing frameworks.
+exclude Tests/br_regrtest.py
+recursive-exclude Tests/UnitTests *
+
+# Don't include obsolete Sequence.py
+exclude Bio/Sequence.py
+
exclude Tests/Amino
exclude Tests/Blast
exclude Tests/Enzymes
@@ -30,9 +37,6 @@ exclude Tests/Prosite
exclude Tests/Prosite/Doc
exclude Tests/Rebase
exclude Tests/SwissProt
-exclude Tests/UnitTests
-exclude Tests/UnitTests/Prosite
-exclude Tests/UnitTests/Save
-exclude Tests/UnitTests/Seq
exclude Tests/output
exclude Tests/Blast/bt008* # file too large
+
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2 README
@@ -131,8 +131,6 @@ setup.py -- Installation file.
- microarray data
-- deprecate Sequence.py
-
If you see something here you would like to work on, please send mail
to biopython@biopython.org!

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