Class AlignmentMetricsProxyModel

         object --+                                
                  |                                
  sip.simplewrapper --+                            
                      |                            
            sip.wrapper --+                        
                          |                        
       PyQt4.QtCore.QObject --+                    
                              |                    
PyQt4.QtCore.QAbstractItemModel --+                
                                  |                
    PyQt4.QtGui.QAbstractProxyModel --+            
                                      |            
          Qt.QtCore.QAbstractProxyModel --+        
                                          |        
                             NonNestedProxy --+    
                                              |    
                BaseAdjacentAlignmentProxyModel --+
                                                  |
                                                 AlignmentMetricsProxyModel

A proxy model that contains the alignment metrics, such as percentage of identity, similarity, homology and score to the reference sequence.

Instance Methods

[hide private]

__init__(self, include_gaps=False, parent=None)
x.__init__(...) initializes x; see help(type(x)) for signature

bool

getIncludeGaps(self)
Returns: Whether to include gaps.

setIncludeGaps(self, include_gaps)

_getData(self, index, source_index, role)

Inherited from BaseAdjacentAlignmentProxyModel: columnCount, data, mapFromSource, mapToSource, rowCount, setSourceModel

Inherited from NonNestedProxy: index, parent, resetCountCache

Inherited from Qt.QtCore.QAbstractProxyModel: reset, setRoleNames, setSupportedDragActions

Inherited from PyQt4.QtGui.QAbstractProxyModel: buddy, canFetchMore, fetchMore, flags, hasChildren, headerData, itemData, mapSelectionFromSource, mapSelectionToSource, mimeData, mimeTypes, revert, setData, setHeaderData, setItemData, sort, sourceModel, span, submit, supportedDropActions

Inherited from PyQt4.QtCore.QAbstractItemModel: beginInsertColumns, beginInsertRows, beginMoveColumns, beginMoveRows, beginRemoveColumns, beginRemoveRows, beginResetModel, changePersistentIndex, changePersistentIndexList, columnsAboutToBeInserted, columnsAboutToBeMoved, columnsAboutToBeRemoved, columnsInserted, columnsMoved, columnsRemoved, createIndex, dataChanged, decodeData, dropMimeData, encodeData, endInsertColumns, endInsertRows, endMoveColumns, endMoveRows, endRemoveColumns, endRemoveRows, endResetModel, hasIndex, headerDataChanged, insertColumn, insertColumns, insertRow, insertRows, layoutAboutToBeChanged, layoutChanged, match, modelAboutToBeReset, modelReset, persistentIndexList, removeColumn, removeColumns, removeRow, removeRows, resetInternalData, roleNames, rowsAboutToBeInserted, rowsAboutToBeMoved, rowsAboutToBeRemoved, rowsInserted, rowsMoved, rowsRemoved, sibling, supportedDragActions

Inherited from PyQt4.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connect, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, emit, event, eventFilter, findChild, findChildren, inherits, installEventFilter, isWidgetType, killTimer, metaObject, moveToThread, objectName, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setParent, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr, trUtf8

Inherited from sip.simplewrapper: __new__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

tuple of 2-tuples of (str, enum.Enum) COL_DATA = (('Identity', <CustomRole.AlignmentIdentity: 44>), ...
Tuple of header and display role information to be defined by subclasses.

Inherited from PyQt4.QtCore.QObject: staticMetaObject

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, include_gaps=False, parent=None)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

include_gaps (bool) - Whether to include gaps in calculating metrics.

Overrides: object.__init__

getIncludeGaps(self)

Returns: bool: Whether to include gaps.

setIncludeGaps(self, include_gaps)

Parameters:

include_gaps (bool) - Whether to include gaps in alignment

_getData(self, index, source_index, role)

Overrides: BaseAdjacentAlignmentProxyModel._getData

Class Variable Details

[hide private]

COL_DATA

Tuple of header and display role information to be defined by subclasses. The tuple should consist of 2-tuples, each consisting of a column header string and data role to use for information to be displayed in this column.

Type:: tuple of 2-tuples of (str, enum.Enum)

Value:

(('Identity', <CustomRole.AlignmentIdentity: 44>),
 ('Similarity', <CustomRole.AlignmentSimilarity: 45>),
 ('Homology', <CustomRole.AlignmentHomology: 46>),
 ('Score', <CustomRole.AlignmentScore: 47>))

Class AlignmentMetricsProxyModel

__init__(self, include_gaps=False, parent=None) (Constructor)

getIncludeGaps(self)

setIncludeGaps(self, include_gaps)

_getData(self, index, source_index, role)

COL_DATA

init(self, include_gaps=False, parent=None)
(Constructor)