rem stringlengths 0 322k | add stringlengths 0 2.05M | context stringlengths 8 228k |
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response = ':%s %s %s :Welcome to the ugliest IRC server in the world.' % (self.server.servername, RPL_WELCOME, self.nick) | response = ':%s %s %s :%s' % (self.server.servername, RPL_WELCOME, self.nick, SRV_WELCOME) | def handle_nick(self, params): """ Handle the iniital setting of the user's nickname and nick changes. """ nick = params |
if len(self.children)==1: | if len(self.children)==1 and self.children[0] not in to_keep: | def prune(self, nodes): """ Prunes the topology of this node in order to conserve only a selected list of leaf or internal nodes. The algorithm deletes nodes until getting a consistent topology with a subset of nodes. Topology relationships among kept nodes is maintained. |
else: default_dist = spearman_dist | def square_euclidean_dist(v1,v2): if (v1 == v2).all(): return 0.0 valids = 0 distance= 0.0 for i in xrange(len(v1)): if numpy.isfinite(v1[i]) and numpy.isfinite(v2[i]): valids += 1 d = v1[i]-v2[i] distance += d*d if valids==0: raise ValueError, "Cannot calculate values" return distance/valids | |
col_lines = ['black'], extras=['']): | col_lines = ['black'], extras=[''], col_width=10): | def __init__(self, values, errors, colors=['white'], header='', \ fsize=11, height = 100, lines=[0.0], \ col_lines = ['black'], extras=['']): faces.Face.__init__(self) if colors == []: colors = ['grey']*len (values) if len (colors) != len (values): exit('ERROR: value and color arrays differ in length!!!\n') self.mean =... |
width = fm.size(QtCore.Qt.AlignTop, 'A'*(len (self.values))).width() | width = self.col_width * len(self.values) | def update_pixmap(self): ''' to refresh? ''' header_font_size = 8 # Calculates header's size header_font = QtGui.QFont("Arial", header_font_size) \ # could this be modified by the user? # Calculates size of main plot fm = QtGui.QFontMetrics(self.font) height = self.height width = fm.size(QtCore.Qt.AlignTop, 'A'*(len (... |
col_lines = ['black'],num=True, extras=['']): | col_lines = ['black'],num=True, extras=[''], col_width=10): | def __init__(self, values, errors, colors=['white'], header='', \ fsize=11, height = 100, lines=[0.0], \ col_lines = ['black'],num=True, extras=['']): faces.Face.__init__(self) if colors == []: colors = ['grey']*len (values) if len (colors) != len (values): exit('ERROR: value and color arrays differ in length!!!\n') se... |
width = fm.size(QtCore.Qt.AlignTop, 'A'*(len (self.values))).width() | width = self.col_width * len(self.values) | def update_pixmap(self): ''' to refresh? ''' header_font_size = 8 # Calculates header's size header_font = QtGui.QFont("Arial", header_font_size) \ # could this be modified by the user? # Calculates size of main plot fm = QtGui.QFontMetrics(self.font) if self.extras != ['']: self.height += 10 height = self.height widt... |
col_lines = ['black'],num=True, extras=['']): | col_lines = ['black'],num=True, extras=[''], col_width=10): | def __init__(self, values, errors, colors=['white'], header='', \ fsize=11, height = 100, lines=[0.0], \ col_lines = ['black'],num=True, extras=['']): faces.Face.__init__(self) if colors == []: colors = ['grey']*len (values) if len (colors) != len (values): exit('ERROR: value and color arrays differ in length!!!\n') se... |
width = fm.size(QtCore.Qt.AlignTop, 'A'*(len (self.values))).width() | width = self.col_width * len(self.values) | def update_pixmap(self): ''' to refresh? ''' |
if hasattr("_nid", n): tree_index[n._nid] = n | if hasattr(n, "_nid"): tree_index[str(n._nid)] = n | def _load_tree_from_path(self, treeid): tree_path = os.path.join(CONFIG["temp_dir"], treeid+".nw") t = self._treeid2tree[treeid] = self._tree(tree_path) tree_index = self._treeid2index[treeid] = {} for n in t.traverse(): if hasattr("_nid", n): tree_index[n._nid] = n return t, tree_index |
tree_index[str(n._nid)]=n | def _get_tree(self, tree=None, treeid=None, pre_drawing_action=None): if not treeid: treeid = hashlib.md5(str(time.time())).hexdigest() | |
for n in self.traverse(strategy="preorder"): | for n in self.traverse(strategy="levelorder"): | def iter_leaves(self): """ Returns an iterator over the leaves under this node. """ for n in self.traverse(strategy="preorder"): if n.is_leaf(): yield n |
''' | usage: tol = "((((((((Drosophila melanogaster,(Drosophila simulans,Drosophila secchellia)),(Drosophila yakuba,Drosophila erecta))[&&NHX:name=melanogaster subgroup],Drosophila ananassae)[&&NHX:name=melanogaster group],(Drosophila pseudoobscura,Drosophila persimilis)[&&NHX:name=obscura group])[&&NHX:name=Sophophora Old ... | def get_rooting(tol, seed_species, agename = False): ''' returns dict of species age for a given TOL and a given seed ''' tol = Tree (tol) try: node = tol.search_nodes (name=seed_species)[0] except IndexError: sys.exit ('ERROR: Seed species not found in tree\n') age = 1 ROOTING = {} if agename: age2name = {} while not ... |
sys.exit ('ERROR: Seed species not found in tree\n') | exit ('ERROR: Seed species not found in tree\n') | def get_rooting(tol, seed_species, agename = False): ''' returns dict of species age for a given TOL and a given seed ''' tol = Tree (tol) try: node = tol.search_nodes (name=seed_species)[0] except IndexError: sys.exit ('ERROR: Seed species not found in tree\n') age = 1 ROOTING = {} if agename: age2name = {} while not ... |
self.exportAttributes(outfile, level, namespace_, name_='Base') | self.exportAttributes(outfile, level, [], namespace_, name_='Base') | def export(self, outfile, level, namespace_='', name_='Base', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='Base') outfile.write('>') self.exportChildren(outfile, level ... |
def exportAttributes(self, outfile, level, namespace_='', name_='Base'): | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='Base'): | def exportAttributes(self, outfile, level, namespace_='', name_='Base'): for name, value in self.anyAttributes_.items(): outfile.write(' %s=%s' % (name, quote_attrib(value), )) pass |
self.exportAttributes(outfile, level, namespace_, name_='Meta') | self.exportAttributes(outfile, level, [], namespace_, name_='Meta') | def export(self, outfile, level, namespace_='', name_='Meta', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='Meta') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLS... |
def exportAttributes(self, outfile, level, namespace_='', name_='Meta'): super(Meta, self).exportAttributes(outfile, level, namespace_, name_='Meta') | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='Meta'): super(Meta, self).exportAttributes(outfile, level, already_processed, namespace_, name_='Meta') | def exportAttributes(self, outfile, level, namespace_='', name_='Meta'): super(Meta, self).exportAttributes(outfile, level, namespace_, name_='Meta') |
self.exportAttributes(outfile, level, namespace_, name_='ResourceMeta') | self.exportAttributes(outfile, level, [], namespace_, name_='ResourceMeta') | def export(self, outfile, level, namespace_='', name_='ResourceMeta', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='ResourceMeta') outfile.write(' xmlns:xsi="http://www.... |
def exportAttributes(self, outfile, level, namespace_='', name_='ResourceMeta'): super(ResourceMeta, self).exportAttributes(outfile, level, namespace_, name_='ResourceMeta') if self.href is not None: | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='ResourceMeta'): super(ResourceMeta, self).exportAttributes(outfile, level, already_processed, namespace_, name_='ResourceMeta') if self.href is not None and 'href' not in already_processed: already_processed.append('href') | def exportAttributes(self, outfile, level, namespace_='', name_='ResourceMeta'): super(ResourceMeta, self).exportAttributes(outfile, level, namespace_, name_='ResourceMeta') if self.href is not None: outfile.write(' href=%s' % (quote_attrib(self.href), )) outfile.write(' rel=%s' % (quote_attrib(self.rel), )) |
if value is not None: | if value is not None and 'href' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('href') if value is not None: already_processed.append('href') self.href = value value = attrs.get('rel') if value is not None: already_processed.append('rel') self.rel = value super(ResourceMeta, self).buildAttributes(node, attrs, already_pro... |
if value is not None: | if value is not None and 'rel' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('href') if value is not None: already_processed.append('href') self.href = value value = attrs.get('rel') if value is not None: already_processed.append('rel') self.rel = value super(ResourceMeta, self).buildAttributes(node, attrs, already_pro... |
childobj_ = Meta.factory() childobj_.build(child_) | type_name_ = child_.attrib.get('{http://www.w3.org/2001/XMLSchema-instance}type') if type_name_ is None: type_name_ = child_.attrib.get('type') if type_name_ is not None: type_names_ = type_name_.split(':') if len(type_names_) == 1: type_name_ = type_names_[0] else: type_name_ = type_names_[1] class_ = globals()[type_n... | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': childobj_ = Meta.factory() childobj_.build(child_) obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'meta', childobj_) self.content_.append(obj_) if hasattr(self, 'add_meta'): self.add_meta(obj_.valu... |
MixedContainer.TypeNone, 'meta', childobj_) | MixedContainer.TypeNone, 'meta', obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': childobj_ = Meta.factory() childobj_.build(child_) obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'meta', childobj_) self.content_.append(obj_) if hasattr(self, 'add_meta'): self.add_meta(obj_.valu... |
self.exportAttributes(outfile, level, namespace_, name_='LiteralMeta') | self.exportAttributes(outfile, level, [], namespace_, name_='LiteralMeta') | def export(self, outfile, level, namespace_='', name_='LiteralMeta', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='LiteralMeta') outfile.write(' xmlns:xsi="http://www.w3... |
def exportAttributes(self, outfile, level, namespace_='', name_='LiteralMeta'): super(LiteralMeta, self).exportAttributes(outfile, level, namespace_, name_='LiteralMeta') if self.datatype is not None: | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='LiteralMeta'): super(LiteralMeta, self).exportAttributes(outfile, level, already_processed, namespace_, name_='LiteralMeta') if self.datatype is not None and 'datatype' not in already_processed: already_processed.append('datatype') | def exportAttributes(self, outfile, level, namespace_='', name_='LiteralMeta'): super(LiteralMeta, self).exportAttributes(outfile, level, namespace_, name_='LiteralMeta') if self.datatype is not None: outfile.write(' datatype=%s' % (quote_attrib(self.datatype), )) if self.content is not None: outfile.write(' content=%s... |
if self.content is not None: | if self.content is not None and 'content' not in already_processed: already_processed.append('content') | def exportAttributes(self, outfile, level, namespace_='', name_='LiteralMeta'): super(LiteralMeta, self).exportAttributes(outfile, level, namespace_, name_='LiteralMeta') if self.datatype is not None: outfile.write(' datatype=%s' % (quote_attrib(self.datatype), )) if self.content is not None: outfile.write(' content=%s... |
if value is not None: | if value is not None and 'datatype' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('datatype') if value is not None: already_processed.append('datatype') self.datatype = value value = attrs.get('content') if value is not None: already_processed.append('content') self.content = value value = attrs.get('property') if value is ... |
if value is not None: | if value is not None and 'content' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('datatype') if value is not None: already_processed.append('datatype') self.datatype = value value = attrs.get('content') if value is not None: already_processed.append('content') self.content = value value = attrs.get('property') if value is ... |
if value is not None: | if value is not None and 'property' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('datatype') if value is not None: already_processed.append('datatype') self.datatype = value value = attrs.get('content') if value is not None: already_processed.append('content') self.content = value value = attrs.get('property') if value is ... |
self.exportAttributes(outfile, level, namespace_, name_='attrExtensions') | self.exportAttributes(outfile, level, [], namespace_, name_='attrExtensions') | def export(self, outfile, level, namespace_='', name_='attrExtensions', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='attrExtensions') if self.hasContent_(): outfile.wri... |
def exportAttributes(self, outfile, level, namespace_='', name_='attrExtensions'): | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='attrExtensions'): | def exportAttributes(self, outfile, level, namespace_='', name_='attrExtensions'): for name, value in self.anyAttributes_.items(): outfile.write(' %s=%s' % (name, quote_attrib(value), )) pass |
class ContinuousChar(GeneratedsSuper): | class AbstractMapping(Base): """The AbstractMapping type is the superclass for an ambiguity mapping. In an instance document, a subclass of this type will look like <member state="st1"/>, i.e. an element called "member" with an attribute called "state" whose value is an id reference that refers to an element that subcl... | def buildChildren(self, child_, nodeName_, from_subclass=False): pass |
superclass = None def __init__(self, states=None, tokens=None, codon=None, meta=None): | superclass = AbstractChar def __init__(self, about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None): super(ContinuousChar, self).__init__(about, meta, label, id, tokens, states, codon, ) | def buildChildren(self, child_, nodeName_, from_subclass=False): pass |
self.exportAttributes(outfile, level, namespace_, name_='ContinuousChar') | self.exportAttributes(outfile, level, [], namespace_, name_='ContinuousChar') | def export(self, outfile, level, namespace_='', name_='ContinuousChar', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='ContinuousChar') if self.hasContent_(): outfile.wri... |
def exportAttributes(self, outfile, level, namespace_='', name_='ContinuousChar'): | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='ContinuousChar'): super(ContinuousChar, self).exportAttributes(outfile, level, already_processed, namespace_, name_='ContinuousChar') | def exportAttributes(self, outfile, level, namespace_='', name_='ContinuousChar'): outfile.write(' states=%s' % (self.gds_format_string(quote_attrib(self.states).encode(ExternalEncoding), input_name='states'), )) outfile.write(' tokens=%s' % (quote_attrib(self.tokens), )) outfile.write(' codon=%s' % (quote_attrib(self.... |
if value is not None: | if value is not None and 'states' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('states') if value is not None: already_processed.append('states') self.states = value value = attrs.get('tokens') if value is not None: already_processed.append('tokens') self.tokens = value self.validate_MSTokenLength(self.tokens) # valid... |
if value is not None: | if value is not None and 'tokens' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('states') if value is not None: already_processed.append('states') self.states = value value = attrs.get('tokens') if value is not None: already_processed.append('tokens') self.tokens = value self.validate_MSTokenLength(self.tokens) # valid... |
if value is not None: | if value is not None and 'codon' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('states') if value is not None: already_processed.append('states') self.states = value value = attrs.get('tokens') if value is not None: already_processed.append('tokens') self.tokens = value self.validate_MSTokenLength(self.tokens) # valid... |
type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] | type_name_ = child_.attrib.get('{http://www.w3.org/2001/XMLSchema-instance}type') if type_name_ is None: type_name_ = child_.attrib.get('type') if type_name_ is not None: type_names_ = type_name_.split(':') if len(type_names_) == 1: type_name_ = type_names_[0] else: type_name_ = type_names_[1] class_ = globals()[type_n... | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] obj_ = class_.factory() obj_.build(child_) else: raise NotImplementedError( 'Class not implemented for <meta> element') self.meta.append(... |
class ContinuousFormat(GeneratedsSuper): """The ContinuousFormat class is the container of continuous column definitions.""" | class AbstractSet(IDTagged): | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] obj_ = class_.factory() obj_.build(child_) else: raise NotImplementedError( 'Class not implemented for <meta> element') self.meta.append(... |
superclass = None def __init__(self, char=None, set=None): if char is None: self.char = [] else: self.char = char if set is None: self.set = [] else: self.set = set def factory(*args_, **kwargs_): if ContinuousFormat.subclass: return ContinuousFormat.subclass(*args_, **kwargs_) else: return ContinuousFormat(*args_, **k... | superclass = IDTagged def __init__(self, about=None, meta=None, label=None, id=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] obj_ = class_.factory() obj_.build(child_) else: raise NotImplementedError( 'Class not implemented for <meta> element') self.meta.append(... |
if AbstractMapping.subclass: return AbstractMapping.subclass(*args_, **kwargs_) else: return AbstractMapping(*args_, **kwargs_) | if AbstractSet.subclass: return AbstractSet.subclass(*args_, **kwargs_) else: return AbstractSet(*args_, **kwargs_) | def factory(*args_, **kwargs_): if AbstractMapping.subclass: return AbstractMapping.subclass(*args_, **kwargs_) else: return AbstractMapping(*args_, **kwargs_) |
def get_state(self): return self.state def set_state(self, state): self.state = state | def get_state(self): return self.state | |
def export(self, outfile, level, namespace_='', name_='AbstractMapping', namespacedef_=''): | def export(self, outfile, level, namespace_='', name_='AbstractSet', namespacedef_=''): | def export(self, outfile, level, namespace_='', name_='AbstractMapping', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='AbstractMapping') outfile.write(' xmlns:xsi="http:... |
self.exportAttributes(outfile, level, namespace_, name_='AbstractMapping') | self.exportAttributes(outfile, level, [], namespace_, name_='AbstractSet') | def export(self, outfile, level, namespace_='', name_='AbstractMapping', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='AbstractMapping') outfile.write(' xmlns:xsi="http:... |
outfile.write(' xsi:type="AbstractMapping"') outfile.write('>') self.exportChildren(outfile, level + 1, namespace_, name_) outfile.write('</%s%s>\n' % (namespace_, name_)) def exportAttributes(self, outfile, level, namespace_='', name_='AbstractMapping'): super(AbstractMapping, self).exportAttributes(outfile, level, na... | outfile.write(' xsi:type="AbstractSet"') if self.hasContent_(): outfile.write('>\n') self.exportChildren(outfile, level + 1, namespace_, name_) showIndent(outfile, level) outfile.write('</%s%s>\n' % (namespace_, name_)) else: outfile.write('/>\n') def exportAttributes(self, outfile, level, already_processed, namespace_... | def export(self, outfile, level, namespace_='', name_='AbstractMapping', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='AbstractMapping') outfile.write(' xmlns:xsi="http:... |
super(AbstractMapping, self).hasContent_() | super(AbstractSet, self).hasContent_() | def hasContent_(self): if ( self.valueOf_ or super(AbstractMapping, self).hasContent_() ): return True else: return False |
def exportLiteral(self, outfile, level, name_='AbstractMapping'): | def exportLiteral(self, outfile, level, name_='AbstractSet'): | def exportLiteral(self, outfile, level, name_='AbstractMapping'): level += 1 self.exportLiteralAttributes(outfile, level, name_) if self.hasContent_(): self.exportLiteralChildren(outfile, level, name_) |
if self.state is not None: showIndent(outfile, level) outfile.write('state = "%s",\n' % (self.state,)) super(AbstractMapping, self).exportLiteralAttributes(outfile, level, name_) | super(AbstractSet, self).exportLiteralAttributes(outfile, level, name_) | def exportLiteralAttributes(self, outfile, level, name_): if self.state is not None: showIndent(outfile, level) outfile.write('state = "%s",\n' % (self.state,)) super(AbstractMapping, self).exportLiteralAttributes(outfile, level, name_) |
super(AbstractMapping, self).exportLiteralChildren(outfile, level, name_) | super(AbstractSet, self).exportLiteralChildren(outfile, level, name_) | def exportLiteralChildren(self, outfile, level, name_): super(AbstractMapping, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) |
value = attrs.get('state') if value is not None: already_processed.append('state') self.state = value super(AbstractMapping, self).buildAttributes(node, attrs, already_processed) | super(AbstractSet, self).buildAttributes(node, attrs, already_processed) | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('state') if value is not None: already_processed.append('state') self.state = value super(AbstractMapping, self).buildAttributes(node, attrs, already_processed) |
super(AbstractMapping, self).buildChildren(child_, nodeName_, True) | super(AbstractSet, self).buildChildren(child_, nodeName_, True) | def buildChildren(self, child_, nodeName_, from_subclass=False): if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) super(AbstractMapping, self).buildChildren(child_, nodeName_, True) pass |
class DNAMapping(GeneratedsSuper): """An IUPAC ambiguity mapping.""" | class TaxaLinked(IDTagged): """The TaxaLinked complexType is a super class for objects that that require an otus id reference.""" | def buildChildren(self, child_, nodeName_, from_subclass=False): if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) super(AbstractMapping, self).buildChildren(child_, nodeName_, True) pass |
superclass = None def __init__(self, valueOf_=None): | superclass = IDTagged def __init__(self, about=None, meta=None, label=None, id=None, otus=None, valueOf_=None, mixedclass_=None, content_=None): super(TaxaLinked, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.otus = _cast(None, otus) self.valueOf_ = valueOf_ if mixedclass_ is None: self... | def buildChildren(self, child_, nodeName_, from_subclass=False): if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) super(AbstractMapping, self).buildChildren(child_, nodeName_, True) pass |
if DNAMapping.subclass: return DNAMapping.subclass(*args_, **kwargs_) else: return DNAMapping(*args_, **kwargs_) | if TaxaLinked.subclass: return TaxaLinked.subclass(*args_, **kwargs_) else: return TaxaLinked(*args_, **kwargs_) | def factory(*args_, **kwargs_): if DNAMapping.subclass: return DNAMapping.subclass(*args_, **kwargs_) else: return DNAMapping(*args_, **kwargs_) |
def export(self, outfile, level, namespace_='', name_='DNAMapping', namespacedef_=''): | def export(self, outfile, level, namespace_='', name_='TaxaLinked', namespacedef_=''): | def export(self, outfile, level, namespace_='', name_='DNAMapping', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='DNAMapping') if self.hasContent_(): outfile.write('>') ... |
self.exportAttributes(outfile, level, namespace_, name_='DNAMapping') | self.exportAttributes(outfile, level, [], namespace_, name_='TaxaLinked') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="TaxaLinked"') if self.hasContent_(): outfile.write('>\n') self.exportChildren(outfile, level + 1, namespace_, name_) showIndent(outfile, level) outf... | def export(self, outfile, level, namespace_='', name_='DNAMapping', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='DNAMapping') if self.hasContent_(): outfile.write('>') ... |
def exportAttributes(self, outfile, level, namespace_='', name_='DNAMapping'): pass def exportChildren(self, outfile, level, namespace_='', name_='DNAMapping'): | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='RNAState'): super(RNAState, self).exportAttributes(outfile, level, already_processed, namespace_, name_='RNAState') outfile.write(' symbol=%s' % (quote_attrib(self.symbol), )) def exportChildren(self, outfile, level, namespace_='', name... | def exportAttributes(self, outfile, level, namespace_='', name_='DNAMapping'): pass |
def exportLiteral(self, outfile, level, name_='DNAMapping'): level += 1 self.exportLiteralAttributes(outfile, level, name_) if self.hasContent_(): self.exportLiteralChildren(outfile, level, name_) def exportLiteralAttributes(self, outfile, level, name_): pass def exportLiteralChildren(self, outfile, level, name_): show... | def exportLiteral(self, outfile, level, name_='RNAState'): | def exportLiteral(self, outfile, level, name_='DNAMapping'): level += 1 self.exportLiteralAttributes(outfile, level, name_) if self.hasContent_(): self.exportLiteralChildren(outfile, level, name_) |
if value is not None: | if value is not None and 'symbol' not in already_processed: | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('symbol') if value is not None: already_processed.append('symbol') self.symbol = value self.validate_DNAToken(self.symbol) # validate type DNAToken |
self.validate_DNAToken(self.symbol) | self.validate_RNAToken(self.symbol) super(RNAState, self).buildAttributes(node, attrs, already_processed) | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('symbol') if value is not None: already_processed.append('symbol') self.symbol = value self.validate_DNAToken(self.symbol) # validate type DNAToken |
class DNAUncertainStateSet(GeneratedsSuper): """The DNAUncertainStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.""" | class RestrictionChar(AbstractChar): """A concrete implementation of the char element, which requires a unique identifier and a state set reference.""" | def buildChildren(self, child_, nodeName_, from_subclass=False): pass |
superclass = None def __init__(self, symbol=None, member=None): self.symbol = _cast(None, symbol) if member is None: self.member = [] else: self.member = member | superclass = AbstractChar def __init__(self, about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None): super(RestrictionChar, self).__init__(about, meta, label, id, tokens, states, codon, ) self.tokens = _cast(None, tokens) self.states = _cast(None, states) self.codon = _cast(None, codon) self.... | def buildChildren(self, child_, nodeName_, from_subclass=False): pass |
if DNAUncertainStateSet.subclass: return DNAUncertainStateSet.subclass(*args_, **kwargs_) else: return DNAUncertainStateSet(*args_, **kwargs_) | if RestrictionChar.subclass: return RestrictionChar.subclass(*args_, **kwargs_) else: return RestrictionChar(*args_, **kwargs_) | def factory(*args_, **kwargs_): if DNAUncertainStateSet.subclass: return DNAUncertainStateSet.subclass(*args_, **kwargs_) else: return DNAUncertainStateSet(*args_, **kwargs_) |
def get_member(self): return self.member def set_member(self, member): self.member = member def add_member(self, value): self.member.append(value) def insert_member(self, index, value): self.member[index] = value def get_symbol(self): return self.symbol def set_symbol(self, symbol): self.symbol = symbol def validate_DN... | def get_meta(self): return self.meta def set_meta(self, meta): self.meta = meta def add_meta(self, value): self.meta.append(value) def insert_meta(self, index, value): self.meta[index] = value def get_tokens(self): return self.tokens def set_tokens(self, tokens): self.tokens = tokens def validate_MSTokenLength(self, va... | def get_member(self): return self.member |
def export(self, outfile, level, namespace_='', name_='DNAUncertainStateSet', namespacedef_=''): | def get_states(self): return self.states def set_states(self, states): self.states = states def get_codon(self): return self.codon def set_codon(self, codon): self.codon = codon def validate_CodonPosition(self, value): pass def get_id(self): return self.id def set_id(self, id): self.id = id def export(self, outfile, l... | def export(self, outfile, level, namespace_='', name_='DNAUncertainStateSet', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='DNAUncertainStateSet') if self.hasContent_():... |
self.exportAttributes(outfile, level, namespace_, name_='DNAUncertainStateSet') | self.exportAttributes(outfile, level, [], namespace_, name_='RestrictionChar') | def export(self, outfile, level, namespace_='', name_='DNAUncertainStateSet', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='DNAUncertainStateSet') if self.hasContent_():... |
def exportAttributes(self, outfile, level, namespace_='', name_='DNAUncertainStateSet'): outfile.write(' symbol=%s' % (quote_attrib(self.symbol), )) def exportChildren(self, outfile, level, namespace_='', name_='DNAUncertainStateSet'): for member_ in self.member: member_.export(outfile, level, namespace_, name_='member... | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='RestrictionChar'): super(RestrictionChar, self).exportAttributes(outfile, level, already_processed, namespace_, name_='RestrictionChar') outfile.write(' tokens=%s' % (quote_attrib(self.tokens), )) outfile.write(' states=%s' % (self.gds_... | def exportAttributes(self, outfile, level, namespace_='', name_='DNAUncertainStateSet'): outfile.write(' symbol=%s' % (quote_attrib(self.symbol), )) |
self.member | self.meta | def hasContent_(self): if ( self.member ): return True else: return False |
def exportLiteral(self, outfile, level, name_='DNAUncertainStateSet'): | def exportLiteral(self, outfile, level, name_='RestrictionChar'): | def exportLiteral(self, outfile, level, name_='DNAUncertainStateSet'): level += 1 self.exportLiteralAttributes(outfile, level, name_) if self.hasContent_(): self.exportLiteralChildren(outfile, level, name_) |
if self.symbol is not None: showIndent(outfile, level) outfile.write('symbol = %s,\n' % (self.symbol,)) | if self.tokens is not None: showIndent(outfile, level) outfile.write('tokens = %d,\n' % (self.tokens,)) if self.states is not None: showIndent(outfile, level) outfile.write('states = "%s",\n' % (self.states,)) if self.codon is not None: showIndent(outfile, level) outfile.write('codon = %d,\n' % (self.codon,)) if self.i... | def exportLiteralAttributes(self, outfile, level, name_): if self.symbol is not None: showIndent(outfile, level) outfile.write('symbol = %s,\n' % (self.symbol,)) |
outfile.write('member=[\n') level += 1 for member_ in self.member: showIndent(outfile, level) outfile.write('model_.DNAMapping(\n') member_.exportLiteral(outfile, level, name_='DNAMapping') | outfile.write('meta=[\n') level += 1 for meta_ in self.meta: showIndent(outfile, level) outfile.write('model_.Meta(\n') meta_.exportLiteral(outfile, level, name_='Meta') | def exportLiteralChildren(self, outfile, level, name_): showIndent(outfile, level) outfile.write('member=[\n') level += 1 for member_ in self.member: showIndent(outfile, level) outfile.write('model_.DNAMapping(\n') member_.exportLiteral(outfile, level, name_='DNAMapping') showIndent(outfile, level) outfile.write('),\n'... |
value = attrs.get('symbol') if value is not None: already_processed.append('symbol') self.symbol = value self.validate_DNAToken(self.symbol) | value = attrs.get('tokens') if value is not None and 'tokens' not in already_processed: already_processed.append('tokens') self.tokens = value self.validate_MSTokenLength(self.tokens) value = attrs.get('states') if value is not None and 'states' not in already_processed: already_processed.append('states') self.states =... | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('symbol') if value is not None: already_processed.append('symbol') self.symbol = value self.validate_DNAToken(self.symbol) # validate type DNAToken |
if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) class DNAPolymorphicStateSet(GeneratedsSuper): """The DNAPolymorphicStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.""" | if nodeName_ == 'meta': type_name_ = child_.attrib.get('{http://www.w3.org/2001/XMLSchema-instance}type') if type_name_ is None: type_name_ = child_.attrib.get('type') if type_name_ is not None: type_names_ = type_name_.split(':') if len(type_names_) == 1: type_name_ = type_names_[0] else: type_name_ = type_names_[1] c... | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) |
superclass = None def __init__(self, symbol=None, member=None, uncertain_state_set=None): self.symbol = _cast(None, symbol) if member is None: self.member = [] else: self.member = member if uncertain_state_set is None: self.uncertain_state_set = [] else: self.uncertain_state_set = uncertain_state_set | superclass = AbstractStates def __init__(self, about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None): super(RestrictionStates, self).__init__(about, meta, label, id, state, polymorphic_state_set, uncertain_state_set, set, ) if meta is None: self.meta = [... | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) |
if DNAPolymorphicStateSet.subclass: return DNAPolymorphicStateSet.subclass(*args_, **kwargs_) else: return DNAPolymorphicStateSet(*args_, **kwargs_) | if RestrictionStates.subclass: return RestrictionStates.subclass(*args_, **kwargs_) else: return RestrictionStates(*args_, **kwargs_) | def factory(*args_, **kwargs_): if DNAPolymorphicStateSet.subclass: return DNAPolymorphicStateSet.subclass(*args_, **kwargs_) else: return DNAPolymorphicStateSet(*args_, **kwargs_) |
def get_member(self): return self.member def set_member(self, member): self.member = member def add_member(self, value): self.member.append(value) def insert_member(self, index, value): self.member[index] = value def get_uncertain_state_set(self): return self.uncertain_state_set def set_uncertain_state_set(self, uncert... | def get_meta(self): return self.meta def set_meta(self, meta): self.meta = meta def add_meta(self, value): self.meta.append(value) def insert_meta(self, index, value): self.meta[index] = value def get_state(self): return self.state def set_state(self, state): self.state = state def add_state(self, value): self.state.ap... | def get_member(self): return self.member |
self.exportAttributes(outfile, level, namespace_, name_='DNAPolymorphicStateSet') | self.exportAttributes(outfile, level, [], namespace_, name_='RestrictionStates') | def export(self, outfile, level, namespace_='', name_='DNAPolymorphicStateSet', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='DNAPolymorphicStateSet') if self.hasContent... |
def exportAttributes(self, outfile, level, namespace_='', name_='DNAPolymorphicStateSet'): outfile.write(' symbol=%s' % (quote_attrib(self.symbol), )) def exportChildren(self, outfile, level, namespace_='', name_='DNAPolymorphicStateSet'): for member_ in self.member: member_.export(outfile, level, namespace_, name_='me... | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='RestrictionStates'): super(RestrictionStates, self).exportAttributes(outfile, level, already_processed, namespace_, name_='RestrictionStates') def exportChildren(self, outfile, level, namespace_='', name_='RestrictionStates'): for meta_... | def exportAttributes(self, outfile, level, namespace_='', name_='DNAPolymorphicStateSet'): outfile.write(' symbol=%s' % (quote_attrib(self.symbol), )) |
self.member or self.uncertain_state_set | self.meta or self.state or self.set | def hasContent_(self): if ( self.member or self.uncertain_state_set ): return True else: return False |
def exportLiteral(self, outfile, level, name_='DNAPolymorphicStateSet'): | def exportLiteral(self, outfile, level, name_='RestrictionStates'): | def exportLiteral(self, outfile, level, name_='DNAPolymorphicStateSet'): level += 1 self.exportLiteralAttributes(outfile, level, name_) if self.hasContent_(): self.exportLiteralChildren(outfile, level, name_) |
if self.symbol is not None: showIndent(outfile, level) outfile.write('symbol = %s,\n' % (self.symbol,)) | pass | def exportLiteralAttributes(self, outfile, level, name_): if self.symbol is not None: showIndent(outfile, level) outfile.write('symbol = %s,\n' % (self.symbol,)) |
outfile.write('member=[\n') level += 1 for member_ in self.member: showIndent(outfile, level) outfile.write('model_.DNAMapping(\n') member_.exportLiteral(outfile, level, name_='DNAMapping') | outfile.write('meta=[\n') level += 1 for meta_ in self.meta: showIndent(outfile, level) outfile.write('model_.Meta(\n') meta_.exportLiteral(outfile, level, name_='Meta') | def exportLiteralChildren(self, outfile, level, name_): showIndent(outfile, level) outfile.write('member=[\n') level += 1 for member_ in self.member: showIndent(outfile, level) outfile.write('model_.DNAMapping(\n') member_.exportLiteral(outfile, level, name_='DNAMapping') showIndent(outfile, level) outfile.write('),\n'... |
outfile.write('uncertain_state_set=[\n') level += 1 for uncertain_state_set_ in self.uncertain_state_set: showIndent(outfile, level) outfile.write('model_.DNAUncertainStateSet(\n') uncertain_state_set_.exportLiteral(outfile, level, name_='DNAUncertainStateSet') | outfile.write('state=[\n') level += 1 for state_ in self.state: showIndent(outfile, level) outfile.write('model_.RestrictionState(\n') state_.exportLiteral(outfile, level, name_='RestrictionState') showIndent(outfile, level) outfile.write('),\n') level -= 1 showIndent(outfile, level) outfile.write('],\n') showIndent(ou... | def exportLiteralChildren(self, outfile, level, name_): showIndent(outfile, level) outfile.write('member=[\n') level += 1 for member_ in self.member: showIndent(outfile, level) outfile.write('model_.DNAMapping(\n') member_.exportLiteral(outfile, level, name_='DNAMapping') showIndent(outfile, level) outfile.write('),\n'... |
self.validate_DNAToken(self.symbol) | self.validate_RestrictionToken(self.symbol) super(RestrictionState, self).buildAttributes(node, attrs, already_processed) | def buildAttributes(self, node, attrs, already_processed): value = attrs.get('symbol') if value is not None: already_processed.append('symbol') self.symbol = value self.validate_DNAToken(self.symbol) # validate type DNAToken |
if nodeName_ == 'member': obj_ = DNAMapping.factory() | pass class AAState(AbstractState): """This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to AAToken, i.e. a single IUPAC amino acid symbol, and optional mapping elements to refer to other states.""" subclass = None superclass = AbstractState def __init__(... | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) elif nodeName_ == 'uncertain_state_set': obj_ = DNAUncertainStateSet.factory() obj_.build(child_) self.uncertain_state_set.append(obj_) |
self.member.append(obj_) | self.state.append(obj_) elif nodeName_ == 'polymorphic_state_set': obj_ = AAPolymorphicStateSet.factory() obj_.build(child_) self.polymorphic_state_set.append(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) elif nodeName_ == 'uncertain_state_set': obj_ = DNAUncertainStateSet.factory() obj_.build(child_) self.uncertain_state_set.append(obj_) |
obj_ = DNAUncertainStateSet.factory() | obj_ = AAUncertainStateSet.factory() | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) elif nodeName_ == 'uncertain_state_set': obj_ = DNAUncertainStateSet.factory() obj_.build(child_) self.uncertain_state_set.append(obj_) |
class DNAStates(GeneratedsSuper): | elif nodeName_ == 'set': obj_ = StateSet.factory() obj_.build(child_) self.set.append(obj_) class AAChar(AbstractChar): """A concrete implementation of the AbstractChar element.""" subclass = None superclass = AbstractChar def __init__(self, about=None, meta=None, label=None, id=None, tokens=None, states=None, codon... | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) elif nodeName_ == 'uncertain_state_set': obj_ = DNAUncertainStateSet.factory() obj_.build(child_) self.uncertain_state_set.append(obj_) |
superclass = None def __init__(self, meta=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None): | superclass = AbstractStates def __init__(self, about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None): super(DNAStates, self).__init__(about, meta, label, id, state, polymorphic_state_set, uncertain_state_set, set, ) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': obj_ = DNAMapping.factory() obj_.build(child_) self.member.append(obj_) elif nodeName_ == 'uncertain_state_set': obj_ = DNAUncertainStateSet.factory() obj_.build(child_) self.uncertain_state_set.append(obj_) |
self.exportAttributes(outfile, level, namespace_, name_='DNAStates') | self.exportAttributes(outfile, level, [], namespace_, name_='DNAStates') | def export(self, outfile, level, namespace_='', name_='DNAStates', namespacedef_=''): showIndent(outfile, level) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) self.exportAttributes(outfile, level, namespace_, name_='DNAStates') if self.hasContent_(): outfile.write('>\n') ... |
def exportAttributes(self, outfile, level, namespace_='', name_='DNAStates'): pass | def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='DNAStates'): super(DNAStates, self).exportAttributes(outfile, level, already_processed, namespace_, name_='DNAStates') | def exportAttributes(self, outfile, level, namespace_='', name_='DNAStates'): pass |
pass | super(DNAStates, self).buildAttributes(node, attrs, already_processed) | def buildAttributes(self, node, attrs, already_processed): pass |
type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] | type_name_ = child_.attrib.get('{http://www.w3.org/2001/XMLSchema-instance}type') if type_name_ is None: type_name_ = child_.attrib.get('type') if type_name_ is not None: type_names_ = type_name_.split(':') if len(type_names_) == 1: type_name_ = type_names_[0] else: type_name_ = type_names_[1] class_ = globals()[type_n... | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] obj_ = class_.factory() obj_.build(child_) else: raise NotImplementedError( 'Class not implemented for <meta> element') self.meta.append(... |
class DNAChar(GeneratedsSuper): """A concrete implementation of the AbstractChar element.""" | class DNAState(AbstractState): """This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to DNAToken, i.e. a single IUPAC nucleotide symbol, and optional mapping elements to refer to other states.""" | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] obj_ = class_.factory() obj_.build(child_) else: raise NotImplementedError( 'Class not implemented for <meta> element') self.meta.append(... |
superclass = None def __init__(self, tokens=None, states=None, codon=None, id=None, meta=None): self.tokens = _cast(None, tokens) self.states = _cast(None, states) self.codon = _cast(None, codon) self.id = _cast(None, id) if meta is None: self.meta = [] else: self.meta = meta | superclass = AbstractState def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, valueOf_=None): super(DNAState, self).__init__(about, meta, label, id, symbol, valueOf_, ) self.symbol = _cast(None, symbol) self.valueOf_ = valueOf_ | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'meta': type_name = child_.attrib.get('type') if type_name is not None: class_ = globals()[type_name] obj_ = class_.factory() obj_.build(child_) else: raise NotImplementedError( 'Class not implemented for <meta> element') self.meta.append(... |
if DNAChar.subclass: return DNAChar.subclass(*args_, **kwargs_) else: return DNAChar(*args_, **kwargs_) | if DNAState.subclass: return DNAState.subclass(*args_, **kwargs_) else: return DNAState(*args_, **kwargs_) | def factory(*args_, **kwargs_): if DNAChar.subclass: return DNAChar.subclass(*args_, **kwargs_) else: return DNAChar(*args_, **kwargs_) |
def get_meta(self): return self.meta def set_meta(self, meta): self.meta = meta def add_meta(self, value): self.meta.append(value) def insert_meta(self, index, value): self.meta[index] = value def get_tokens(self): return self.tokens def set_tokens(self, tokens): self.tokens = tokens def validate_MSTokenLength(self, va... | def get_meta(self): return self.meta | |
def validate_AAToken(self, value): | def validate_DNAToken(self, value): | def validate_AAToken(self, value): # Validate type AAToken, a restriction on AbstractSymbol. pass |
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