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

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Class ProteinAlignment

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

reorderSequences(self, seq_indices)
Reorder the sequences in the alignment using the specified list of indices

setQuerySeq(self, seq=None)
Set the specified sequence as the query sequence.

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

addSeqsByIndices(self, seq_map)
Insert a sequences at the specified indices in the alignment.

removeSeq(self, seq)
See _removeSeq for documentation.

removeSeqByIndex(self, index)
See _removeSeqByIndex for documentation.

removeSeqs(self, seqs)
Remove multiple sequences from the alignment

replaceSeq(self, seq, index)
Replace the sequence at the specified index with the elements in the specified sequence

addOrReplaceSeqs(self, seqs, identifier_func)
Given seqs and an identifier_func, replaces seqs in the alignment matching the identifier_func and appends any additional seqs to the alignment

removeAllSeqs(self)
Clears the entire alignment of sequences

removeResidues(self, residues)
Removes the specified residues from the alignment and emits the residuesRemoved signal with the selection

mutateResidues(self, mutations)
Mutate the residues at the specified locations in the alignment

addResidues(self, selection)
Adds the specified residues to the alignment

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 domain.alignment.ProteinAlignment: __init__, toClustalFile, toFastaFile, toFastaString, toFastaStringList

Inherited from domain.alignment.BaseAlignment: __add__, __contains__, __deepcopy__, __getitem__, __iter__, __len__, __repr__, __str__, addSeq, alignmentLengthAboutToChange, alignmentLengthChanged, alignmentLocked, calculateMatrix, columnHasAllSameResidues, columns, createConsensusSequence, findPattern, getAlignedBlocks, getColumn, getEntropy, getFrequencies, getGapIndicesByKeyFunc, getGaps, getGapsByKeyFunc, getGlobalAnnotationData, getHiddenSeqIndices, getIdentities, getQuerySeq, getRedundantSequences, getResidueData, getResidueIndices, getSeqIndex, getSimilarityScore, getSubalignment, getTerminalGaps, getVisibleSeqIndices, isQuerySeq, iterResidues, lockedColumns, makeResidueSelection, notifyResDisplayChanged, notifyResidueSelection, notifySequenceVisibilityChanged, querySequenceUpdated, replaceResiduesWithGaps, residueVisibilityChanged, residuesAdded, residuesRemoved, residuesSelected, sequenceNameChanged, sequenceResiduesChanged, sequenceVisibilityChanged, sequencesAboutToBeInserted, sequencesAboutToBeRemoved, sequencesAboutToBeReordered, sequencesInserted, sequencesRemoved, sequencesReordered

Inherited from domain.alignment.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

Inherited from sip.simplewrapper: __new__

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

Class Methods

[hide private]

Inherited from domain.alignment.BaseAlignment: mergePairwiseAlignments, padAlignment

Inherited from domain.alignment.BaseAlignment (private): _insertGaps

Static Methods

[hide private]

Inherited from domain.alignment.ProteinAlignment: fromClustalFile, fromFastaFile, fromFastaString, fromFastaStringList

Inherited from domain.alignment.BaseAlignment: getReversedSequenceOrdering

Class Variables

[hide private]

Inherited from PyQt5.QtCore.QObject: staticMetaObject

Properties

[hide private]

Inherited from domain.alignment.ProteinAlignment: global_annotations, seq_annotations

Inherited from domain.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

reorderSequences(self, seq_indices)

Reorder the sequences in the alignment using the specified list of indices

Parameters:

seq_indices - A list with the new indices for sequences

Decorators:

@command.do_command

Raises:

ValueError - In the event that the list of indices does not match the length of the alignment

Overrides: domain.alignment.BaseAlignment.reorderSequences

setQuerySeq(self, seq=None)

Set the specified sequence as the query sequence. If None is passed, the query sequence will be unset.

Parameters:

seq - Sequence to set as query sequence or None
reordering - An optional reordering of sequences to apply to the alignment

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.setQuerySeq

(inherited documentation)

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: domain.alignment.BaseAlignment.addSeqs

(inherited documentation)

addSeqsByIndices(self, seq_map)

Insert a sequences at the specified indices in the alignment. The sequences will be added from lowest to highest to allow for specification of indexes that may be out of range of the current alignment until lower-indexed sequences have been added. Note that indexes that remain out of range will result in their corresponding sequence simply being appended to the end of the alignment.

Parameters:

seq_index_map - Map of insertion indices to sequences to be added. @type seq_index_map dict of {int: sequence.Sequence}

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.addSeqsByIndices

(inherited documentation)

removeSeq(self, seq)

See _removeSeq for documentation.

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.removeSeq

(inherited documentation)

removeSeqByIndex(self, index)

See _removeSeqByIndex for documentation.

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.removeSeqByIndex

(inherited documentation)

removeSeqs(self, seqs)

Remove multiple sequences from the alignment

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.removeSeqs

(inherited documentation)

replaceSeq(self, seq, index)

Replace the sequence at the specified index with the elements in the specified sequence

Note that this leaves the original sequence itself intact so that it continues to be monitored

Parameters:

seq - The sequence whose elements we use
index - The index of the sequence to replace

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.replaceSeq

(inherited documentation)

addOrReplaceSeqs(self, seqs, identifier_func)

Given seqs and an identifier_func, replaces seqs in the alignment matching the identifier_func and appends any additional seqs to the alignment

Parameters:

seqs - The sequences to add to the alignment
identifier_func - A key function to uniquely identify sequences

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.addOrReplaceSeqs

(inherited documentation)

removeAllSeqs(self)

Clears the entire alignment of sequences

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.removeAllSeqs

(inherited documentation)

removeResidues(self, residues)

Removes the specified residues from the alignment and emits the residuesRemoved signal with the selection

Parameters:

residues - The residues to remove

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.removeResidues

(inherited documentation)

mutateResidues(self, mutations)

Mutate the residues at the specified locations in the alignment

Note that the individual sequences will emit a signal announcing the mutation

Parameters:

mutations

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.mutateResidues

(inherited documentation)

addResidues(self, selection)

Adds the specified residues to the alignment

Parameters:

selection - A selection of residues

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.addResidues

(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: domain.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: domain.alignment.BaseAlignment.setGaps

(inherited documentation)

removeGaps(self, gap_indices)

Parameters:

gap_indices - Indices of gaps to remove

Decorators:

@command.do_command

Overrides: domain.alignment.BaseAlignment.removeGaps

(inherited documentation)

removeTerminalGaps(self)

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

Decorators:

@command.do_command

Overrides: domain.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: domain.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: domain.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: domain.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: domain.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: domain.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: domain.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: domain.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: domain.alignment.BaseAlignment.minimizeAlignment

(inherited documentation)