Class ProteinSequence

       object --+                        
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sip.simplewrapper --+                    
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          sip.wrapper --+                
                        |                
     PyQt4.QtCore.QObject --+            
                            |            
            Qt.QtCore.QObject --+        
                                |        
                sequence.Sequence --+    
                                    |    
             sequence.ProteinSequence --+
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                                       ProteinSequence

Nested Classes

[hide private]

Inherited from sequence.ProteinSequence: AnnotationClass

Inherited from sequence.Sequence: ORIGIN

Instance Methods

[hide private]

setUndoStack(self, undo_stack)

setName(self, name)
Set the name on the instance and emit a notification

addGaps(self, gaps)
Add gaps to the sequence at the specified indices

removeGaps(self, gaps)
Removes the specified gaps from the sequence

setGaps(self, gaps)
Sets gaps on the sequence from a list of gap indices, relative to the ungapped sequence

removeAllGaps(self)
Remove gaps from the sequence

extend(self, elements)
Extends the sequence with elements from a list

insert(self, index, elements)
Insert a list of elements or sequence element into this sequence

mutate(self, start, end, elements)
Mutate sequence elements starting at the given index to the provided elements

remove(self, start, end=None)
Removes elements from the sequence from the index start and returns the removed elements as a new sequence

sanitize(self, start=0, end=None)
Remove gaps and unknown sequence elements from sequence

Inherited from sequence.ProteinSequence: __init__, append, getGapCount, getTerminalGaps, makeSeqElement, removeStructurelessResidues, removeTerminalGaps

Inherited from sequence.ProteinSequence (private): _makeSeqElements

Inherited from sequence.Sequence: __add__, __contains__, __copy__, __deepcopy__, __getitem__, __iter__, __len__, __repr__, __str__, get, getGapIndicesByKeyFunc, getGaps, getGapsByKeyFunc, getHomology, getIdentity, getNextResidue, getNextResidueIndex, getNumResidues, getPreviousResidue, getPreviousResidueIndex, getSimilarity, getSimilarityScore, getSubsequence, index, lengthAboutToChange, lengthChanged, nameChanged, removeFromSequence, replaceAllElements, residuesChanged, residuesDeleted

Inherited from sequence.Sequence (private): _addGaps, _getScore, _removeAllGaps, _validateGapRemoval

Inherited from Qt.QtCore.QObject: connect, emit

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