Package schrodinger :: Package application :: Package msv :: Package domain :: Module undoable_alignment :: Class ProteinAlignment

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Class ProteinAlignment

       object --+                    
                |                    
sip.simplewrapper --+                
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          sip.wrapper --+            
                        |            
     PyQt4.QtCore.QObject --+        
                            |        
      alignment.BaseAlignment --+    
                                |    
       alignment.ProteinAlignment --+
                                    |
                                   ProteinAlignment

A ProteinAlignment class that presents the same interface as a regular ProteinAlignment but optionally accomplishes mutating operations via a command stack.

If no command stack is set on the object, commands are executed but cannot be undone.

Instance Methods

[hide private]

setUndoStack(self, undo_stack)

addSeqs(self, seqs, index=None)
Add multiple sequences to the alignment

removeSeq(self, seq)
Remove a sequence from the alignment

removeSeqByIndex(self, index)
Remove a Sequence from the alignment

removeAllSeqs(self)
Clears the entire alignment of sequences

addGaps(self, gap_indices)
Adds gaps to the alignment

setGaps(self, gap_indices)
Sets gaps on the alignment

removeGaps(self, gap_indices)

removeTerminalGaps(self)
Removes the gaps from the ends of every sequence in the alignment

removeAllGaps(self)
Removes all the gaps of the sequences in the alignment.

_getInsertCommand(self, aln, start)

insertSubalignment(self, aln, start)
Insert an alignment into the current alignment at the specified index

removeSubalignment(self, start, end)
Remove a block of the subalignment from the start to end points, including column locks in that region

appendSubalignment(self, aln)
Append an alignment to this one

replaceSubalignment(self, aln, start, end)
Replace a subsection of the alignment indicated by start and end indices with the specified alignment

setLockedColumns(self, columns, lock=True)
Sets the specified columns to the specified lock state

setAllLocks(self, lock=True)
Convenience method to set all the locks to the specified lock state at once

minimizeAlignment(self)
Minimizes the alignment, i.e.

Inherited from alignment.ProteinAlignment: __init__

Inherited from alignment.BaseAlignment: __add__, __contains__, __deepcopy__, __getitem__, __iter__, __len__, __repr__, __str__, addSeq, alignmentLocked, calculateMatrix, columns, createConsensusSequence, findPattern, getAlignedBlocks, getColumn, getEntropy, getFrequencies, getGaps, getGlobalAnnotationData, getIdentities, getRedundantSequences, getResidueData, getResidueIndices, getSeqIndex, getSimilarityScore, getSubalignment, getTerminalGaps, lockedColumns, removeSeqs

Inherited from alignment.BaseAlignment (private): _adjustGapsInSubalignments, _checkAlignmentLength, _getAlignmentDescription, _getGapOnlyColumns, _getRegions, _getTextFormattedAlignment, _monitorSequence, _recalculateLength, _sequenceLengthAboutToChange, _sequenceLengthChanged, _setLockedColumns, _stopMonitoringSequence, _validateGapIndices

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, parent, 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__, __setattr__, __sizeof__, __subclasshook__

Class Methods

[hide private]

Inherited from alignment.BaseAlignment: mergePairwiseAlignments, padAlignment

Inherited from alignment.BaseAlignment (private): _insertGaps

Class Variables

[hide private]

Inherited from PyQt4.QtCore.QObject: staticMetaObject

Instance Variables

[hide private]

Inherited from alignment.BaseAlignment: alignmentLengthAboutToChange, alignmentLengthChanged, sequenceNameChanged, sequenceResiduesChanged, sequencesAboutToBeInserted, sequencesAboutToBeRemoved, sequencesInserted, sequencesRemoved

Properties

[hide private]

Inherited from alignment.ProteinAlignment: global_annotations, seq_annotations

Inherited from alignment.BaseAlignment: all_annotations

Inherited from object: __class__

Method Details

[hide private]

setUndoStack(self, undo_stack)

Parameters:

undo_stack (PyQt4.QtGui.QUndoStack Set the undo stack on the object) - The undo stack on which to push commands

addSeqs(self, seqs, index=None)

Add multiple sequences to the alignment

Parameters:

sequences - Sequences to add
start - The index at which to insert; if None, seq is appended

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.addSeqs

(inherited documentation)

removeSeq(self, seq)

Remove a sequence from the alignment

Parameters:

seq - The sequence to remove

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.removeSeq

(inherited documentation)

removeSeqByIndex(self, index)

Remove a Sequence from the alignment

Parameters:

index - The index of the sequence to remove

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.removeSeqByIndex

(inherited documentation)

removeAllSeqs(self)

Clears the entire alignment of sequences

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.removeAllSeqs

(inherited documentation)

addGaps(self, gap_indices)

Adds gaps to the alignment

Parameters:

gap_indices - A list of lists of gap indices, one for each sequence in the alignment.
Note that the length of the gap_indices list must match the number of sequences in the alignment.

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.addGaps

(inherited documentation)

setGaps(self, gap_indices)

Sets gaps on the alignment

Parameters:

gap_indices - A list of lists of gap indices, one for each sequence in the alignment.

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.setGaps

(inherited documentation)

removeGaps(self, gap_indices)

Parameters:

gap_indices - Indices of gaps to remove

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.removeGaps

(inherited documentation)

removeTerminalGaps(self)

Removes the gaps from the ends of every sequence in the alignment

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.removeTerminalGaps

(inherited documentation)

removeAllGaps(self)

Removes all the gaps of the sequences in the alignment. This also unlocks all columns

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.removeAllGaps

(inherited documentation)

insertSubalignment(self, aln, start)

Insert an alignment into the current alignment at the specified index

Parameters:

aln - The alignment to insert
start - The index at which to insert the alignment

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.insertSubalignment

(inherited documentation)

removeSubalignment(self, start, end)

Remove a block of the subalignment from the start to end points, including column locks in that region

Parameters:

start - The start index of the columns to remove
end - The end index of the columns to remove

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.removeSubalignment

(inherited documentation)

appendSubalignment(self, aln)

Append an alignment to this one

Parameters:

aln - The alignment to append

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.appendSubalignment

(inherited documentation)

replaceSubalignment(self, aln, start, end)

Replace a subsection of the alignment indicated by start and end indices with the specified alignment

Parameters:

aln - The alignment to insert
start - The index at which to insert the alignment

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.replaceSubalignment

(inherited documentation)

setLockedColumns(self, columns, lock=True)

Sets the specified columns to the specified lock state

In undoable subclasses, this is an undoable method. We offer a private version of the method so that other undoable methods can call it without calling a second undoable method.

Parameters:

columns - an iterable of columns to set, specified by index
lock - Whether to lock or unlock columns
reset - Whether to reset the locks or add to existing ones

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.setLockedColumns

(inherited documentation)

setAllLocks(self, lock=True)

Convenience method to set all the locks to the specified lock state at once

Parameters:

lock - Whether to lock or unlock the specified columns

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.setAllLocks

(inherited documentation)

minimizeAlignment(self)

Minimizes the alignment, i.e. removes all gaps from the gap-only columns.

Decorators:

@command.do_command

Overrides: alignment.BaseAlignment.minimizeAlignment

(inherited documentation)