rem stringlengths 0 322k | add stringlengths 0 2.05M | context stringlengths 8 228k |
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def __init__(self, about=None, meta=None, label=None, id=None, otus=None, network=None, tree=None, set=None, valueOf_=None, mixedclass_=None, content_=None): super(Trees, self).__init__(about, meta, label, id, otus, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, network=None, tree=None, set=None): super(Trees, self).__init__(about, meta, label, id, otus, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, network=None, tree=None, set=None, valueOf_=None, mixedclass_=None, content_=None): super(Trees, self).__init__(about, meta, label, id, otus, valueOf_, mixedclass_, content_, ) if network is None: self.network = [] else: self.network = network if... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, network=None, tree=None, set=None, valueOf_=None, mixedclass_=None, content_=None): super(Trees, self).__init__(about, meta, label, id, otus, valueOf_, mixedclass_, content_, ) if network is None: self.network = [] else: self.network = network if... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | for network_ in self.get_network(): network_.export(outfile, level, namespace_, name_='network') for tree_ in self.get_tree(): tree_.export(outfile, level, namespace_, name_='tree') for set_ in self.set: set_.export(outfile, level, namespace_, name_='set') | def exportChildren(self, outfile, level, namespace_='', name_='Trees'): super(Trees, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.network or self.tree or self.set or self.valueOf_ or super(Trees, self).hasContent_() ): return True else: return False | |
outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.wri... | outfile.write('network=[\n') level += 1 for network_ in self.network: showIndent(outfile, level) outfile.write('model_.AbstractNetwork(\n') network_.exportLiteral(outfile, level, name_='AbstractNetwork') showIndent(outfile, level) outfile.write('),\n') level -= 1 showIndent(outfile, level) outfile.write('],\n') showInd... | def exportLiteralChildren(self, outfile, level, name_): super(Trees, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, l... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'network', obj_) self.content_.append(obj_) if hasattr(self, 'add_network'): self.add_network(obj_.value) elif hasattr(self, 'set_network'): self.set_network(obj_.value) elif nodeName_ == 'tree': | self.network.append(obj_) elif nodeName_ == 'tree': | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'network': 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_) =... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'tree', obj_) self.content_.append(obj_) if hasattr(self, 'add_tree'): self.add_tree(obj_.value) elif hasattr(self, 'set_tree'): self.set_tree(obj_.value) elif nodeName_ == 'set': | self.tree.append(obj_) elif nodeName_ == 'set': | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'network': 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_) =... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'set', obj_) self.content_.append(obj_) if hasattr(self, 'add_set'): self.add_set(obj_.value) elif hasattr(self, 'set_set'): self.set_set(obj_.value) if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.... | self.set.append(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'network': 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_) =... |
def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractBlock, self).__init__(about, meta, label, id, otus, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None): super(AbstractBlock, self).__init__(about, meta, label, id, otus, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractBlock, self).__init__(about, meta, label, id, otus, valueOf_, mixedclass_, content_, ) self.format = format self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedcla... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractBlock, self).__init__(about, meta, label, id, otus, valueOf_, mixedclass_, content_, ) self.format = format self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedcla... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | format_.export(outfile, level, namespace_, name_='format') | def exportChildren(self, outfile, level, namespace_='', name_='AbstractBlock'): super(AbstractBlock, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.format is not None or self.valueOf_ or super(AbstractBlock, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | if self.AbstractFormat is not None: showIndent(outfile, level) outfile.write('AbstractFormat=model_.AbstractFormat(\n') self.AbstractFormat.exportLiteral(outfile, level) showIndent(outfile, level) outfile.write('),\n') | def exportLiteralChildren(self, outfile, level, name_): super(AbstractBlock, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(ou... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'format', obj_) self.content_.append(obj_) if hasattr(self, 'add_format'): self.add_format(obj_.value) elif hasattr(self, 'set_format'): self.set_format(obj_.value) if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(... | self.set_format(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'format': 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_) ==... |
def __init__(self, about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractObsRow, self).__init__(about, meta, label, id, otu, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None): super(AbstractObsRow, self).__init__(about, meta, label, id, otu, ) | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractObsRow, self).__init__(about, meta, label, id, otu, valueOf_, mixedclass_, content_, ) if cell is None: self.cell = [] else: self.cell = cell if set is None: self.... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractObsRow, self).__init__(about, meta, label, id, otu, valueOf_, mixedclass_, content_, ) if cell is None: self.cell = [] else: self.cell = cell if set is None: self.... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | for cell_ in self.get_cell(): cell_.export(outfile, level, namespace_, name_='cell') for set_ in self.set: set_.export(outfile, level, namespace_, name_='set') | def exportChildren(self, outfile, level, namespace_='', name_='AbstractObsRow'): super(AbstractObsRow, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.cell or self.set or self.valueOf_ or super(AbstractObsRow, self).hasContent_() ): return True else: return False | |
outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.wri... | outfile.write('cell=[\n') level += 1 for cell_ in self.cell: showIndent(outfile, level) outfile.write('model_.AbstractObs(\n') cell_.exportLiteral(outfile, level, name_='AbstractObs') showIndent(outfile, level) outfile.write('),\n') level -= 1 showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) ... | def exportLiteralChildren(self, outfile, level, name_): super(AbstractObsRow, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(o... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'cell', obj_) self.content_.append(obj_) if hasattr(self, 'add_cell'): self.add_cell(obj_.value) elif hasattr(self, 'set_cell'): self.set_cell(obj_.value) elif nodeName_ == 'set': | self.cell.append(obj_) elif nodeName_ == 'set': | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'cell': 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... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'set', obj_) self.content_.append(obj_) if hasattr(self, 'add_set'): self.add_set(obj_.value) elif hasattr(self, 'set_set'): self.set_set(obj_.value) if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.... | self.set.append(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'cell': 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... |
def __init__(self, about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractSeqRow, self).__init__(about, meta, label, id, otu, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, seq=None): super(AbstractSeqRow, self).__init__(about, meta, label, id, otu, ) | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractSeqRow, self).__init__(about, meta, label, id, otu, valueOf_, mixedclass_, content_, ) self.seq = seq self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = Mixe... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractSeqRow, self).__init__(about, meta, label, id, otu, valueOf_, mixedclass_, content_, ) self.seq = seq self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = Mixe... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | if self.seq is not None: showIndent(outfile, level) outfile.write('<%sseq>%s</%sseq>\n' % (namespace_, self.gds_format_string(quote_xml(self.seq).encode(ExternalEncoding), input_name='seq'), namespace_)) | def exportChildren(self, outfile, level, namespace_='', name_='AbstractSeqRow'): super(AbstractSeqRow, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.seq is not None or self.valueOf_ or super(AbstractSeqRow, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | if self.seq is not None: showIndent(outfile, level) outfile.write('seq=%s,\n' % quote_python(self.seq).encode(ExternalEncoding)) | def exportLiteralChildren(self, outfile, level, name_): super(AbstractSeqRow, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(o... |
if nodeName_ == 'seq' and child_.text is not None: valuestr_ = child_.text obj_ = self.mixedclass_(MixedContainer.CategorySimple, MixedContainer.TypeString, 'seq', valuestr_) self.content_.append(obj_) if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.... | if nodeName_ == 'seq': seq_ = child_.text self.seq = seq_ | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'seq' and child_.text is not None: valuestr_ = child_.text obj_ = self.mixedclass_(MixedContainer.CategorySimple, MixedContainer.TypeString, 'seq', valuestr_) self.content_.append(obj_) if not from_subclass and child_.tail is not None: obj... |
def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractUncertainStateSet, self).__init__(about, meta, label, id, symbol, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None): super(AbstractUncertainStateSet, self).__init__(about, meta, label, id, symbol, ) | def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractUncertainStateSet, self).__init__(about, meta, label, id, symbol, valueOf_, mixedclass_, content_, ) if member is None: self.member = [] else: self.member = member self... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractUncertainStateSet, self).__init__(about, meta, label, id, symbol, valueOf_, mixedclass_, content_, ) if member is None: self.member = [] else: self.member = member self... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | for member_ in self.get_member(): member_.export(outfile, level, namespace_, name_='member') | def exportChildren(self, outfile, level, namespace_='', name_='AbstractUncertainStateSet'): super(AbstractUncertainStateSet, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.member or self.valueOf_ or super(AbstractUncertainStateSet, self).hasContent_() ): return True else: return False | |
outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | outfile.write('member=[\n') level += 1 for member_ in self.member: showIndent(outfile, level) outfile.write('model_.AbstractMapping(\n') member_.exportLiteral(outfile, level, name_='AbstractMapping') showIndent(outfile, level) outfile.write('),\n') level -= 1 showIndent(outfile, level) outfile.write('],\n') | def exportLiteralChildren(self, outfile, level, name_): super(AbstractUncertainStateSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') s... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'member', obj_) self.content_.append(obj_) if hasattr(self, 'add_member'): self.add_member(obj_.value) elif hasattr(self, 'set_member'): self.set_member(obj_.value) if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(... | self.member.append(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'member': 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_) ==... |
def __init__(self, about=None, meta=None, label=None, id=None, node=None, edge=None, rootedge=None, valueOf_=None, mixedclass_=None, content_=None): super(NodeAndRootEdgeAndEdgeSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, node=None, edge=None, rootedge=None): super(NodeAndRootEdgeAndEdgeSet, self).__init__(about, meta, label, id, ) | def __init__(self, about=None, meta=None, label=None, id=None, node=None, edge=None, rootedge=None, valueOf_=None, mixedclass_=None, content_=None): super(NodeAndRootEdgeAndEdgeSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.node = _cast(None, node) self.edge = _cast(None, edge) self... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | pass | def __init__(self, about=None, meta=None, label=None, id=None, node=None, edge=None, rootedge=None, valueOf_=None, mixedclass_=None, content_=None): super(NodeAndRootEdgeAndEdgeSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.node = _cast(None, node) self.edge = _cast(None, edge) self... |
self.valueOf_ or | def hasContent_(self): if ( self.valueOf_ or super(NodeAndRootEdgeAndEdgeSet, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | def exportLiteralChildren(self, outfile, level, name_): super(NodeAndRootEdgeAndEdgeSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | |
if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | 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(NodeAndRootEdgeAndEdgeSet, self).buildChildren(child_, nodeName_, True) pass | |
def __init__(self, about=None, meta=None, label=None, id=None, tree=None, network=None, valueOf_=None, mixedclass_=None, content_=None): super(TreeAndNetworkSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, tree=None, network=None): super(TreeAndNetworkSet, self).__init__(about, meta, label, id, ) | def __init__(self, about=None, meta=None, label=None, id=None, tree=None, network=None, valueOf_=None, mixedclass_=None, content_=None): super(TreeAndNetworkSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.tree = _cast(None, tree) self.network = _cast(None, network) self.valueOf_ = va... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | pass | def __init__(self, about=None, meta=None, label=None, id=None, tree=None, network=None, valueOf_=None, mixedclass_=None, content_=None): super(TreeAndNetworkSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.tree = _cast(None, tree) self.network = _cast(None, network) self.valueOf_ = va... |
self.valueOf_ or | def hasContent_(self): if ( self.valueOf_ or super(TreeAndNetworkSet, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | def exportLiteralChildren(self, outfile, level, name_): super(TreeAndNetworkSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | |
if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | 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(TreeAndNetworkSet, self).buildChildren(child_, nodeName_, True) pass | |
def __init__(self, about=None, meta=None, label=None, id=None, cell=None, valueOf_=None, mixedclass_=None, content_=None): super(CellSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, cell=None): super(CellSet, self).__init__(about, meta, label, id, ) | def __init__(self, about=None, meta=None, label=None, id=None, cell=None, valueOf_=None, mixedclass_=None, content_=None): super(CellSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.cell = _cast(None, cell) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedConta... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | pass | def __init__(self, about=None, meta=None, label=None, id=None, cell=None, valueOf_=None, mixedclass_=None, content_=None): super(CellSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.cell = _cast(None, cell) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedConta... |
self.valueOf_ or | def hasContent_(self): if ( self.valueOf_ or super(CellSet, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | def exportLiteralChildren(self, outfile, level, name_): super(CellSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | |
if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | 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(CellSet, self).buildChildren(child_, nodeName_, True) pass | |
def __init__(self, about=None, meta=None, label=None, id=None, row=None, valueOf_=None, mixedclass_=None, content_=None): super(RowSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, row=None): super(RowSet, self).__init__(about, meta, label, id, ) | def __init__(self, about=None, meta=None, label=None, id=None, row=None, valueOf_=None, mixedclass_=None, content_=None): super(RowSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.row = _cast(None, row) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | pass | def __init__(self, about=None, meta=None, label=None, id=None, row=None, valueOf_=None, mixedclass_=None, content_=None): super(RowSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.row = _cast(None, row) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer... |
self.valueOf_ or | def hasContent_(self): if ( self.valueOf_ or super(RowSet, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | def exportLiteralChildren(self, outfile, level, name_): super(RowSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | |
if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | 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(RowSet, self).buildChildren(child_, nodeName_, True) pass | |
def __init__(self, about=None, meta=None, label=None, id=None, char=None, valueOf_=None, mixedclass_=None, content_=None): super(CharSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, char=None): super(CharSet, self).__init__(about, meta, label, id, ) | def __init__(self, about=None, meta=None, label=None, id=None, char=None, valueOf_=None, mixedclass_=None, content_=None): super(CharSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.char = _cast(None, char) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedConta... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | pass | def __init__(self, about=None, meta=None, label=None, id=None, char=None, valueOf_=None, mixedclass_=None, content_=None): super(CharSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.char = _cast(None, char) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedConta... |
self.valueOf_ or | def hasContent_(self): if ( self.valueOf_ or super(CharSet, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | def exportLiteralChildren(self, outfile, level, name_): super(CharSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | |
if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | 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(CharSet, self).buildChildren(child_, nodeName_, True) pass | |
def __init__(self, about=None, meta=None, label=None, id=None, uncertain_state_set=None, state=None, polymorphic_state_set=None, valueOf_=None, mixedclass_=None, content_=None): super(StateSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, uncertain_state_set=None, state=None, polymorphic_state_set=None): super(StateSet, self).__init__(about, meta, label, id, ) | def __init__(self, about=None, meta=None, label=None, id=None, uncertain_state_set=None, state=None, polymorphic_state_set=None, valueOf_=None, mixedclass_=None, content_=None): super(StateSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.uncertain_state_set = _cast(None, uncertain_sta... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | pass | def __init__(self, about=None, meta=None, label=None, id=None, uncertain_state_set=None, state=None, polymorphic_state_set=None, valueOf_=None, mixedclass_=None, content_=None): super(StateSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.uncertain_state_set = _cast(None, uncertain_sta... |
self.valueOf_ or | def hasContent_(self): if ( self.valueOf_ or super(StateSet, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | def exportLiteralChildren(self, outfile, level, name_): super(StateSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | |
if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | 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(StateSet, self).buildChildren(child_, nodeName_, True) pass | |
def __init__(self, about=None, meta=None, label=None, id=None, otu=None, valueOf_=None, mixedclass_=None, content_=None): super(TaxonSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, otu=None): super(TaxonSet, self).__init__(about, meta, label, id, ) | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, valueOf_=None, mixedclass_=None, content_=None): super(TaxonSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.otu = _cast(None, otu) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContain... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | pass | def __init__(self, about=None, meta=None, label=None, id=None, otu=None, valueOf_=None, mixedclass_=None, content_=None): super(TaxonSet, self).__init__(about, meta, label, id, valueOf_, mixedclass_, content_, ) self.otu = _cast(None, otu) self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContain... |
self.valueOf_ or | def hasContent_(self): if ( self.valueOf_ or super(TaxonSet, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | def exportLiteralChildren(self, outfile, level, name_): super(TaxonSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | |
if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(MixedContainer.CategoryText, MixedContainer.TypeNone, '', child_.tail) self.content_.append(obj_) | 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(TaxonSet, self).buildChildren(child_, nodeName_, True) pass | |
def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractCells, self).__init__(about, meta, label, id, otus, format, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None): super(AbstractCells, self).__init__(about, meta, label, id, otus, format, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractCells, self).__init__(about, meta, label, id, otus, format, valueOf_, mixedclass_, content_, ) self.matrix = matrix self.valueOf_ = valueOf_ if mixedclass_ i... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractCells, self).__init__(about, meta, label, id, otus, format, valueOf_, mixedclass_, content_, ) self.matrix = matrix self.valueOf_ = valueOf_ if mixedclass_ i... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | matrix_.export(outfile, level, namespace_, name_='matrix') | def exportChildren(self, outfile, level, namespace_='', name_='AbstractCells'): super(AbstractCells, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.matrix is not None or self.valueOf_ or super(AbstractCells, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | if self.AbstractObsMatrix is not None: showIndent(outfile, level) outfile.write('AbstractObsMatrix=model_.AbstractObsMatrix(\n') self.AbstractObsMatrix.exportLiteral(outfile, level) showIndent(outfile, level) outfile.write('),\n') | def exportLiteralChildren(self, outfile, level, name_): super(AbstractCells, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(ou... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'matrix', obj_) self.content_.append(obj_) if hasattr(self, 'add_matrix'): self.add_matrix(obj_.value) elif hasattr(self, 'set_matrix'): self.set_matrix(obj_.value) if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(... | self.set_matrix(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'matrix': 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_) ==... |
def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractSeqs, self).__init__(about, meta, label, id, otus, format, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None): super(AbstractSeqs, self).__init__(about, meta, label, id, otus, format, ) | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractSeqs, self).__init__(about, meta, label, id, otus, format, valueOf_, mixedclass_, content_, ) self.matrix = matrix self.valueOf_ = valueOf_ if mixedclass_ is... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractSeqs, self).__init__(about, meta, label, id, otus, format, valueOf_, mixedclass_, content_, ) self.matrix = matrix self.valueOf_ = valueOf_ if mixedclass_ is... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | matrix_.export(outfile, level, namespace_, name_='matrix') | def exportChildren(self, outfile, level, namespace_='', name_='AbstractSeqs'): super(AbstractSeqs, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.matrix is not None or self.valueOf_ or super(AbstractSeqs, self).hasContent_() ): return True else: return False | |
showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | if self.AbstractSeqMatrix is not None: showIndent(outfile, level) outfile.write('AbstractSeqMatrix=model_.AbstractSeqMatrix(\n') self.AbstractSeqMatrix.exportLiteral(outfile, level) showIndent(outfile, level) outfile.write('),\n') | def exportLiteralChildren(self, outfile, level, name_): super(AbstractSeqs, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(out... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'matrix', obj_) self.content_.append(obj_) if hasattr(self, 'add_matrix'): self.add_matrix(obj_.value) elif hasattr(self, 'set_matrix'): self.set_matrix(obj_.value) if not from_subclass and child_.tail is not None: obj_ = self.mixedclass_(... | self.set_matrix(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'matrix': 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_) ==... |
def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractPolymorphicStateSet, self).__init__(about, meta, label, id, symbol, member, valueOf_, mixedclass_, content_, ) | def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None): super(AbstractPolymorphicStateSet, self).__init__(about, meta, label, id, symbol, member, ) | def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractPolymorphicStateSet, self).__init__(about, meta, label, id, symbol, member, valueOf_, mixedclass_, content_, ) if uncertain_state_set is None:... |
self.valueOf_ = valueOf_ if mixedclass_ is None: self.mixedclass_ = MixedContainer else: self.mixedclass_ = mixedclass_ if content_ is None: self.content_ = [] else: self.content_ = content_ self.valueOf_ = valueOf_ | def __init__(self, about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None, mixedclass_=None, content_=None): super(AbstractPolymorphicStateSet, self).__init__(about, meta, label, id, symbol, member, valueOf_, mixedclass_, content_, ) if uncertain_state_set is None:... | |
for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) | for uncertain_state_set_ in self.get_uncertain_state_set(): uncertain_state_set_.export(outfile, level, namespace_, name_='uncertain_state_set') | def exportChildren(self, outfile, level, namespace_='', name_='AbstractPolymorphicStateSet'): super(AbstractPolymorphicStateSet, self).exportChildren(outfile, level, namespace_, name_) for item_ in self.content_: item_.export(outfile, level, item_.name, namespace_) |
self.valueOf_ or | def hasContent_(self): if ( self.uncertain_state_set or self.valueOf_ or super(AbstractPolymorphicStateSet, self).hasContent_() ): return True else: return False | |
outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n') showIndent(outfile, level) outfile.write('valueOf_ = """%s""",\n' % (self.valueOf_,)) | outfile.write('uncertain_state_set=[\n') level += 1 for uncertain_state_set_ in self.uncertain_state_set: showIndent(outfile, level) outfile.write('model_.AbstractUncertainStateSet(\n') uncertain_state_set_.exportLiteral(outfile, level, name_='AbstractUncertainStateSet') showIndent(outfile, level) outfile.write('),\n')... | def exportLiteralChildren(self, outfile, level, name_): super(AbstractPolymorphicStateSet, self).exportLiteralChildren(outfile, level, name_) showIndent(outfile, level) outfile.write('content_ = [\n') for item_ in self.content_: item_.exportLiteral(outfile, level, name_) showIndent(outfile, level) outfile.write('],\n')... |
obj_ = self.mixedclass_(MixedContainer.CategoryComplex, MixedContainer.TypeNone, 'uncertain_state_set', obj_) self.content_.append(obj_) if hasattr(self, 'add_uncertain_state_set'): self.add_uncertain_state_set(obj_.value) elif hasattr(self, 'set_uncertain_state_set'): self.set_uncertain_state_set(obj_.value) if not fr... | self.uncertain_state_set.append(obj_) | def buildChildren(self, child_, nodeName_, from_subclass=False): if nodeName_ == 'uncertain_state_set': 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(ty... |
node.SEdN = vals[13] if 'dN' in line else None node.SEdS = vals[18] if 'dS' in line else None | node.add_feature ('SEdN', float (vals[vals.index ('dN') + 4])\ if 'dN' in line else None) node.add_feature ('SEdS', float (vals[vals.index ('dS') + 4])\ if 'dS' in line else None) | def parse_paml (pamout, model, codon_freq=True): ''' parser function for codeml files, with values of w,dN,dS etc... dependending of the model tested. ''' # if multiple dataset in same file we divide the outfile and model.name+x if not '*' in str (model.params['ndata']): divide_data (pamout, model, codon_freq=True) ret... |
down_branch_connector.support = buffered_support | def set_outgroup(self, outgroup): """ Sets a descendant node as the outgroup of a tree. This function can be used to root a tree or even an internal node. | |
to label tree as paml | to label tree as paml, nearly walking man over the tree algorithm | def _label_as_paml (self): ''' to label tree as paml WARNING: sorted names in same order that sequence ''' paml_id = 1 for leaf in sorted (self, key=lambda x: x.name): leaf.add_feature ('paml_id', paml_id) paml_id += 1 self.add_feature ('paml_id', paml_id) # left members for node in self.get_descendants()[::2]: if hasa... |
for node in self.get_descendants()[::2]: if hasattr (node, 'paml_id'): if node.is_leaf() and not node.get_sisters()[0].is_leaf(): paml_id += 1 node.get_sisters()[0].add_feature ('paml_id', paml_id) continue paml_id += 1 node.add_feature ('paml_id', paml_id) for node in self.get_descendants()[1::2]: if hasattr (node, '... | node = self while True: node = node.get_children()[0] if node.is_leaf(): node = node.up while hasattr (node.get_children()[1], 'paml_id'): node = node.up if not node: break if not node: break node = node.get_children()[1] if not hasattr (node, 'paml_id'): paml_id += 1 node.add_feature ('paml_id', paml_id) | def _label_as_paml (self): ''' to label tree as paml WARNING: sorted names in same order that sequence ''' paml_id = 1 for leaf in sorted (self, key=lambda x: x.name): leaf.add_feature ('paml_id', paml_id) paml_id += 1 self.add_feature ('paml_id', paml_id) # left members for node in self.get_descendants()[::2]: if hasa... |
rst = re.sub('out$', 'rst', pamout) | rst = '/'.join (pamout.split('/')[:-1])+'/rst' | def divide_data (pamout, model, codon_freq=True): ''' for multiple dataset, divide outfile. ''' for num in range (1, int (model.params['ndata'])): model.name = model.name + '_' + str(num) out = open (pamout + '_' + str(num), 'w') copy = False for line in open (pamout): if copy == False and \ line.startswith('Data set '... |
print >> sys.stderr, 'labelling does not correspond!! check' | print >> sys.stderr, \ 'WARNING: labelling does not correspond!!\n' + \ 'Getting them from ' + pamout | def _get_paml_labels(model, tree, paml_labels, line, pamout): ''' map tree to paml labels, and place w and bL values ''' bL = line.split()[:len (paml_labels)] w = line.split()[len (paml_labels)+1:] try: relations = sorted (map (lambda x: map( int, x.split('..')), paml_labels), key=lambda x: x[1]) except IndexError: re... |
if len (line.strip().split()[i+1])> | def parse_paml(pamout, model, rst=None, ndata=1, codon_freq=True): ''' parser function for codeml files, returns a diccionary with values of w,dN,dS etc... dependending of the model tested. ''' if ndata != 1: dic = {} for num in range (1, ndata): out = open (pamout + '_' + str(num), 'w') copy = False for line in open (... | |
p.drawRect(self.rect().x(),self.rect().y(),self.rect().width(),self.rect().height()) return | p.drawRect(self.rect()) return | def paint(self, p, option, widget): p.setPen(self.Color) p.drawRect(self.rect().x(),self.rect().y(),self.rect().width(),self.rect().height()) return # Draw info text font = QtGui.QFont("Arial",13) text = "%d selected." % len(self.get_selected_nodes()) textR = QtGui.QFontMetrics(font).boundingRect(text) if self.rect()... |
self.selector.setRect(e.scenePos().x(),e.scenePos().y(),0,0) self.selector.startPoint = QtCore.QPointF(e.scenePos().x(),e.scenePos().y()) | pos = self.selector.mapFromScene(e.scenePos()) self.selector.setRect(pos.x(),pos.y(),4,4) self.selector.startPoint = QtCore.QPointF(pos.x(), pos.y()) | def mousePressEvent(self,e): self.selector.setRect(e.scenePos().x(),e.scenePos().y(),0,0) self.selector.startPoint = QtCore.QPointF(e.scenePos().x(),e.scenePos().y()) self.selector.setActive(True) self.selector.setVisible(True) QtGui.QGraphicsScene.mousePressEvent(self,e) |
curr_pos = e.scenePos() | curr_pos = self.selector.mapFromScene(e.scenePos()) | def mouseReleaseEvent(self,e): curr_pos = e.scenePos() x = min(self.selector.startPoint.x(),curr_pos.x()) y = min(self.selector.startPoint.y(),curr_pos.y()) w = max(self.selector.startPoint.x(),curr_pos.x()) - x h = max(self.selector.startPoint.y(),curr_pos.y()) - y if self.selector.startPoint == curr_pos: self.selecto... |
curr_pos = e.scenePos() | curr_pos = self.selector.mapFromScene(e.scenePos()) | def mouseMoveEvent(self,e): curr_pos = e.scenePos() if self.selector.isActive(): x = min(self.selector.startPoint.x(),curr_pos.x()) y = min(self.selector.startPoint.y(),curr_pos.y()) w = max(self.selector.startPoint.x(),curr_pos.x()) - x h = max(self.selector.startPoint.y(),curr_pos.y()) - y self.selector.setRect(x,y,w... |
while node: | while node is not None: | def _iter_descendants_preorder(self): """ Iterator over all desdecendant nodes. """ to_visit = [] node = self while node: yield node to_visit = node.children + to_visit try: node = to_visit.pop(0) except IndexError: node = None |
except IndexError: | except: | def _iter_descendants_preorder(self): """ Iterator over all desdecendant nodes. """ to_visit = [] node = self while node: yield node to_visit = node.children + to_visit try: node = to_visit.pop(0) except IndexError: node = None |
down_branch_connector.support = buffered_support | def set_outgroup(self, outgroup): """ Sets a descendant node as the outgroup of a tree. This function can be used to root a tree or even an internal node. |
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