Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / Encodings / IUPACEncoding.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Encodings/IUPACEncoding.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Encodings/IUPACEncoding.py
deleted file mode 100644 (file)
index a4089a3..0000000
--- a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Encodings/IUPACEncoding.py
+++ /dev/null
@@ -1,126 +0,0 @@
-# Set up the IUPAC alphabet properties
-
-
-from Bio.PropertyManager import default_manager
-from Bio import Alphabet
-from Bio.Alphabet import IUPAC
-from Bio.Data import IUPACData
-
-from Bio import Transcribe, Translate
-
-set_prop = default_manager.class_property
-
-# weight tables
-set_prop[IUPAC.IUPACUnambiguousDNA]["weight_table"] = \
-             IUPACData.unambiguous_dna_weights
-set_prop[IUPAC.IUPACAmbiguousDNA]["weight_table"] = \
-             IUPACData.avg_ambiguous_dna_weights
-set_prop[IUPAC.IUPACUnambiguousRNA]["weight_table"] = \
-             IUPACData.unambiguous_rna_weights
-set_prop[IUPAC.IUPACAmbiguousRNA]["weight_table"] = \
-             IUPACData.avg_ambiguous_rna_weights
-set_prop[IUPAC.IUPACProtein]["weight_table"] = \
-             IUPACData.protein_weights
-set_prop[IUPAC.ExtendedIUPACProtein]["weight_table"] = \
-             IUPACData.avg_extended_protein_weights
-
-set_prop[IUPAC.IUPACUnambiguousDNA]["weight_range_table"] = \
-             IUPACData.unambiguous_dna_weight_ranges
-set_prop[IUPAC.IUPACAmbiguousDNA]["weight_range_table"] = \
-             IUPACData.ambiguous_dna_weight_ranges
-set_prop[IUPAC.IUPACUnambiguousRNA]["weight_range_table"] = \
-             IUPACData.unambiguous_rna_weight_ranges
-set_prop[IUPAC.IUPACAmbiguousRNA]["weight_range_table"] = \
-             IUPACData.ambiguous_rna_weight_ranges
-set_prop[IUPAC.IUPACProtein]["weight_range_table"] = \
-             IUPACData.protein_weight_ranges
-set_prop[IUPAC.ExtendedIUPACProtein]["weight_range_table"] = \
-             IUPACData.extended_protein_weight_ranges
-
-
-
-#  transcriber objects
-
-set_prop[Alphabet.DNAAlphabet]["transcriber"] = \
-             Transcribe.generic_transcriber
-
-set_prop[IUPAC.IUPACAmbiguousDNA]["transcriber"] = \
-             Transcribe.ambiguous_transcriber
-
-set_prop[IUPAC.IUPACUnambiguousDNA]["transcriber"] = \
-             Transcribe.unambiguous_transcriber
-
-
-set_prop[Alphabet.RNAAlphabet]["transcriber"] = \
-             Transcribe.generic_transcriber
-
-set_prop[IUPAC.IUPACAmbiguousRNA]["transcriber"] = \
-             Transcribe.ambiguous_transcriber
-
-set_prop[IUPAC.IUPACUnambiguousRNA]["transcriber"] = \
-             Transcribe.unambiguous_transcriber
-
-
-# translator objects
-for name, obj in Translate.unambiguous_dna_by_name.items():
-    property = "translator.name." + name
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-
-for name, obj in Translate.unambiguous_rna_by_name.items():
-    property = "translator.name." + name
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    property = "rna_translator.name." + name
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-
-
-for id, obj in Translate.unambiguous_dna_by_id.items():
-    property = "translator.id.%d" % id
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-    if id == 1:
-        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
-        set_prop[obj.table.protein_alphabet.__class__]["translator"] = obj
-
-
-for id, obj in Translate.unambiguous_rna_by_id.items():
-    property = "translator.id.%d" % id
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    property = "rna_translator.id.%d" % id
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-    if id == 1:
-        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
-        set_prop[obj.table.protein_alphabet.__class__]["rna_translator"] = obj
-
-# ambiguous translator objects
-for name, obj in Translate.ambiguous_dna_by_name.items():
-    property = "translator.name." + name
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    property = "ambiguous_translator.name." + name
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-
-for name, obj in Translate.ambiguous_rna_by_name.items():
-    property = "translator.name." + name
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    property = "ambiguous_rna_translator.name." + name
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-
-
-for id, obj in Translate.ambiguous_dna_by_id.items():
-    property = "translator.id.%d" % id
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    property = "ambiguous_translator.id.%d" % id
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-    if id == 1:
-        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
-        set_prop[obj.table.protein_alphabet.__class__]["ambiguous_translator"] = obj
-
-
-for id, obj in Translate.ambiguous_rna_by_id.items():
-    property = "translator.id.%d" % id
-    set_prop[obj.table.nucleotide_alphabet.__class__][property] = obj
-    property = "ambiguous_rna_translator.id.%d" % id
-    set_prop[obj.table.protein_alphabet.__class__][property] = obj
-    if id == 1:
-        set_prop[obj.table.nucleotide_alphabet.__class__]["translator"] = obj
-        set_prop[obj.table.protein_alphabet.__class__]["ambiguous_rna_translator"] = obj