Class ProteinAlignment

       object --+                
                |                
sip.simplewrapper --+            
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          sip.wrapper --+        
                        |        
     PyQt5.QtCore.QObject --+    
                            |    
                BaseAlignment --+
                                |
                               ProteinAlignment

Known Subclasses:

gui.undoable_alignment.ProteinAlignment

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
x.__init__(...) initializes x; see help(type(x)) for signature

toClustalFile(self, file_name, use_unique_names=True)
Writes aln to a Clustal alignment file.

toFastaString(self, use_unique_names=True, maxl=50)
Convert ProteinAlignment object to list of sequence strings

list

toFastaStringList(self)
Convert self to list of fasta sequence strings

toFastaFile(self, file_name, use_unique_names=True, maxl=50)
Write self to specified FASTA file

Inherited from BaseAlignment: __add__, __contains__, __deepcopy__, __getitem__, __iter__, __len__, __repr__, __str__, addGaps, addOrReplaceSeqs, addResidues, addSeq, addSeqs, addSeqsByIndices, alignmentLengthAboutToChange, alignmentLengthChanged, alignmentLocked, appendSubalignment, calculateMatrix, columnHasAllSameResidues, columns, createConsensusSequence, findPattern, getAlignedBlocks, getColumn, getEntropy, getFrequencies, getGapIndicesByKeyFunc, getGaps, getGapsByKeyFunc, getGlobalAnnotationData, getHiddenSeqIndices, getIdentities, getQuerySeq, getRedundantSequences, getResidueData, getResidueIndices, getSeqIndex, getSimilarityScore, getSubalignment, getTerminalGaps, getVisibleSeqIndices, insertSubalignment, isQuerySeq, iterResidues, lockedColumns, makeResidueSelection, minimizeAlignment, mutateResidues, notifyResDisplayChanged, notifyResidueSelection, notifySequenceVisibilityChanged, querySequenceUpdated, removeAllGaps, removeAllSeqs, removeGaps, removeResidues, removeSeq, removeSeqByIndex, removeSeqs, removeSubalignment, removeTerminalGaps, reorderSequences, replaceResiduesWithGaps, replaceSeq, replaceSubalignment, residueVisibilityChanged, residuesAdded, residuesRemoved, residuesSelected, sequenceNameChanged, sequenceResiduesChanged, sequenceVisibilityChanged, sequencesAboutToBeInserted, sequencesAboutToBeRemoved, sequencesAboutToBeReordered, sequencesInserted, sequencesRemoved, sequencesReordered, setAllLocks, setGaps, setLockedColumns, setQuerySeq

Inherited from BaseAlignment (private): _addSeq, _adjustGapsInSubalignments, _checkAlignmentLength, _getAddOrReplaceSeqs, _getAlignmentDescription, _getGapOnlyColumns, _getQuerySeqReordering, _getRegions, _getTextFormattedAlignment, _monitorSequence, _recalculateLength, _removeResidues, _removeSeq, _removeSeqByIndex, _reorderSequences, _sequenceLengthAboutToChange, _sequenceLengthChanged, _setLockedColumns, _stopMonitoringSequence, _updateColumnSameResCache, _validateGapIndices

Inherited from PyQt5.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, event, eventFilter, findChild, findChildren, inherits, installEventFilter, isSignalConnected, isWidgetType, isWindowType, killTimer, metaObject, moveToThread, objectName, objectNameChanged, parent, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setParent, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr