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2016-4 Schrodinger Python API
Package schrodinger :: Package application :: Package msv :: Package gui :: Module msv_widget :: Class AbstractMsvWidget
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Class AbstractMsvWidget

       object --+                
                |                
sip.simplewrapper --+            
                    |            
          sip.wrapper --+        
                        |        
     PyQt4.QtCore.QObject --+    
                            |    
           object --+       |    
                    |       |    
    sip.simplewrapper --+   |    
                        |   |    
 PyQt4.QtGui.QPaintDevice --+    
                            |    
          PyQt4.QtGui.QWidget --+
                                |
                               AbstractMsvWidget
Known Subclasses:
Nested Classes [hide private]

Inherited from PyQt4.QtGui.QWidget: RenderFlag, RenderFlags

Inherited from PyQt4.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods [hide private]
 
optionsChanged(...)
A signal emitted when the widget options have changed and the GUI ui (e.g.
 
alignmentLengthChanged(...)
A signal emitted when the widget's alignment length is changed.
 
seqWSVisibilityChanged(...)
Signal emitted when sequences are shown or hidden in the Worksapce.
 
selectedSeqsChanged(...)
 
__init__(self, parent=None, undo_stack=None, options=())
x.__init__(...) initializes x; see help(type(x)) for signature
AbstractMsvWidget
__deepcopy__(self, memo)
Returns: Another instance of the AbstractMsvWidget with the same data
 
applyOptions(self)
Updates the widgets from its own options
 
_setupStructureModel(self)
Sets up structure model-related signals and attributes
list of int
getSeqsFromResidues(self, residues)
Given a list of residues, return a set of the sequences taht contain these residues.
 
onResidueSelection(self, selection_info)
Set selection information on the alignment.
 
onResidueDeletionRequested(self, residues)
Takes residues to delete and removes them from the alignment
4-tuple of (int, int, int, int)
getSequenceStatusInfo(self)
Return info about the status of the current alignment, including number of sequences in the alignment, number of sequences with selected residues, number of sequences visible in the Worksapce, and number of sequences hidden in theWorkspace.
 
_getNewAlignment(self)
Return an alignment appropriate for the widget (ProteinAlignment, etc.) with a reference to the widget's undo stack set on it.
 
_getAlignmentView(self)
Return an alignment view appropriate for the widget.
 
_getNoScrollBarView(self)
Return an alignment view without scroll bars
 
_getAlignmentInfoView(self)
Return an alignment view for the "frozen" metrics columns on the right side
 
_getAlignmentViewModel(self)
Return an alignment viewmodel appropriate for the widget.
 
_onStructureViewInclusionChanged(self, seqs)
TODO: Update icon inclusion status for all sequences in viewer
 
undo(self)
Call undo on the undo stack
 
redo(self)
Call redo on the undo stack
 
resetUndoStack(self)
Reset the undo stack
 
syncFromStructureModel(self)
Request a synchronization with the structure model, which will emit a signal with the new alignment.
schrodinger.application.msv.domain.alignment.BaseAlignment
getAlignment(self)
Returns the widget's alignment instance
 
addSeq(self, seq)
Adds a given sequence to the widget's alignment
 
addSeqs(self, seqs)
Add a list of seqs to the widget's alignment
 
removeSeq(self, seq)
Remove a given sequence from the widget's alignment
 
getColorScheme(self)
list
getShownRowTypes(self)
Returns a list of enums representing the shown row types
bool
rowWrap(self)
Indicates whether rows are currently wrapped
bool
groupedByType(self)
Indicates whether rows are grouped by type
bool
replaceIDsWithDots(self)
Retrun whether or not dots should be drawn for columns of the same residue.
schrodinger.application.msv.gui.viewconstants.ResidueDisplay
getResidueFormat(self)
Returns: An enum representing the residue display format in current use in the widget
 
setResidueFormat(self, residue_format)
 
setReplaceIDsWithDots(self, disp_mode)
Set the identities to be displayed as dots or not.
 
changeTextSize(self, plus_minus)
bool
getAlnByIdentity(self)
Returns: Whether align by identity is turned on
 
setAlnByIdentity(self, by_identity)
bool
getAlnBySimilarity(self)
Returns: Whether align by similarity is turned on
 
setAlnBySimilarity(self, by_similarity)
bool
getAlnByHomology(self)
Returns: Whether align by homology is turned on
 
setAlnByHomology(self, by_homology)
bool
getAlnByScore(self)
Returns: Whether align by score is turned on
 
setAlnByScore(self, by_score)
 
setIncludeGaps(self, include)
 
_getSetAlignmentCommand(self, aln, desc='Set sequences')
 
setAlignment(self, aln)
 
_onAlignmentLengthChanged(self)
Called when the widget's alignment length changes.
 
_onWSVisibilityChanged(self)
Respond to changes in visibility of sequences initiated by MSV or via the Workspace and notify listeners of the changes.
 
clear(self)
 
deleteSelection(self)
 
runAlignment(self, aligner)
 
applyColorScheme(self, row_type, scheme)
Sets the color scheme for a given row type.
 
setGroupAnnotationsByType(self, by_annotation=True)
Set the grouping option for annotations and sequences
 
setShownRowTypes(self, row_types)
Set all the specified row types to visible and hide the rest
 
_setAllColorBlockVisible(self, show)
 
setAllColorBlocksVisible(self, show)
Set the visibility of all color blocks annotations
 
setAnnotationVisible(self, ann, show=True)
Set the visibility of an annotation
 
setRowWrap(self, wrap=False)
Set the row wrapping on the widget
 
sortBy(self, sort_by, order)
Sort the table by the specified criteria.
 
sortingChanged(self, menu_update_required=True)
When the table sorting has been changed, update the WidgetOptions and notify the panel of the change if the menus need to be updated.
 
_applyColorScheme(self, row_type, scheme)
 
_setGroupAnnotationsByType(self, by_annotation=True)
 
_setRowWrap(self, wrap)
 
_setShownRowTypes(self, row_types)
 
_doSetAlignment(self, aln)
Set the alignment on the widget
 
saveImage(self)
Saves multiple sequence alignment as an image file, by default, exports image of the entire alignment.

Inherited from PyQt4.QtGui.QWidget: acceptDrops, accessibleDescription, accessibleName, actionEvent, actions, activateWindow, addAction, addActions, adjustSize, autoFillBackground, backgroundRole, baseSize, changeEvent, childAt, childrenRect, childrenRegion, clearFocus, clearMask, close, closeEvent, contentsMargins, contentsRect, contextMenuEvent, contextMenuPolicy, create, cursor, customContextMenuRequested, destroy, devType, dragEnterEvent, dragLeaveEvent, dragMoveEvent, dropEvent, effectiveWinId, enabledChange, ensurePolished, enterEvent, event, find, focusInEvent, focusNextChild, focusNextPrevChild, focusOutEvent, focusPolicy, focusPreviousChild, focusProxy, focusWidget, font, fontChange, fontInfo, fontMetrics, foregroundRole, frameGeometry, frameSize, geometry, getContentsMargins, grabGesture, grabKeyboard, grabMouse, grabShortcut, graphicsEffect, graphicsProxyWidget, handle, hasFocus, hasMouseTracking, height, heightForWidth, hide, hideEvent, inputContext, inputMethodEvent, inputMethodHints, inputMethodQuery, insertAction, insertActions, isActiveWindow, isAncestorOf, isEnabled, isEnabledTo, isEnabledToTLW, isFullScreen, isHidden, isLeftToRight, isMaximized, isMinimized, isModal, isRightToLeft, isTopLevel, isVisible, isVisibleTo, isWindow, isWindowModified, keyPressEvent, keyReleaseEvent, keyboardGrabber, languageChange, layout, layoutDirection, leaveEvent, locale, lower, mapFrom, mapFromGlobal, mapFromParent, mapTo, mapToGlobal, mapToParent, mask, maximumHeight, maximumSize, maximumWidth, metric, minimumHeight, minimumSize, minimumSizeHint, minimumWidth, mouseDoubleClickEvent, mouseGrabber, mouseMoveEvent, mousePressEvent, mouseReleaseEvent, move, moveEvent, nativeParentWidget, nextInFocusChain, normalGeometry, overrideWindowFlags, overrideWindowState, paintEngine, paintEvent, palette, paletteChange, parentWidget, pos, previousInFocusChain, raise_, rect, releaseKeyboard, releaseMouse, releaseShortcut, removeAction, render, repaint, resetInputContext, resize, resizeEvent, restoreGeometry, saveGeometry, scroll, setAcceptDrops, setAccessibleDescription, setAccessibleName, setAttribute, setAutoFillBackground, setBackgroundRole, setBaseSize, setContentsMargins, setContextMenuPolicy, setCursor, setDisabled, setEnabled, setFixedHeight, setFixedSize, setFixedWidth, setFocus, setFocusPolicy, setFocusProxy, setFont, setForegroundRole, setGeometry, setGraphicsEffect, setHidden, setInputContext, setInputMethodHints, setLayout, setLayoutDirection, setLocale, setMask, setMaximumHeight, setMaximumSize, setMaximumWidth, setMinimumHeight, setMinimumSize, setMinimumWidth, setMouseTracking, setPalette, setParent, setShortcutAutoRepeat, setShortcutEnabled, setShown, setSizeIncrement, setSizePolicy, setStatusTip, setStyle, setStyleSheet, setTabOrder, setToolTip, setUpdatesEnabled, setVisible, setWhatsThis, setWindowFilePath, setWindowFlags, setWindowIcon, setWindowIconText, setWindowModality, setWindowModified, setWindowOpacity, setWindowRole, setWindowState, setWindowTitle, show, showEvent, showFullScreen, showMaximized, showMinimized, showNormal, size, sizeHint, sizeIncrement, sizePolicy, stackUnder, statusTip, style, styleSheet, tabletEvent, testAttribute, toolTip, topLevelWidget, underMouse, ungrabGesture, unsetCursor, unsetLayoutDirection, unsetLocale, update, updateGeometry, updateMicroFocus, updatesEnabled, visibleRegion, whatsThis, wheelEvent, width, winId, window, windowActivationChange, windowFilePath, windowFlags, windowIcon, windowIconText, windowModality, windowOpacity, windowRole, windowState, windowTitle, windowType, x, x11Info, x11PictureHandle, y

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

Inherited from PyQt4.QtGui.QPaintDevice: colorCount, depth, heightMM, logicalDpiX, logicalDpiY, numColors, paintingActive, physicalDpiX, physicalDpiY, widthMM

Inherited from sip.simplewrapper: __new__

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

Class Variables [hide private]

Inherited from PyQt4.QtGui.QWidget: DrawChildren, DrawWindowBackground, IgnoreMask

Inherited from PyQt4.QtCore.QObject: staticMetaObject

Inherited from PyQt4.QtGui.QPaintDevice: PdmDepth, PdmDpiX, PdmDpiY, PdmHeight, PdmHeightMM, PdmNumColors, PdmPhysicalDpiX, PdmPhysicalDpiY, PdmWidth, PdmWidthMM

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

optionsChanged(...)

 
A signal emitted when the widget options have changed and the GUI ui (e.g. menu, menubars, etc.) should be updated.

alignmentLengthChanged(...)

 
A signal emitted when the widget's alignment length is changed. Emits an int indicating the new number of sequences in the alignment.

seqWSVisibilityChanged(...)

 
Signal emitted when sequences are shown or hidden in the Worksapce. Emits a pair of ints. The first indicates the number of visible sequences in the Workspace, the second the number of hidden sequences in the Workspace.

__init__(self, parent=None, undo_stack=None, options=())
(Constructor)

 

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

Parameters:
  • selectedSeqsChanged (QtCore.pyqtSignal) - Emitted when the number of sequences containing selected residues changes. Emits an int indicating the number of sequences that contain selected residues.
Overrides: object.__init__
(inherited documentation)

__deepcopy__(self, memo)

 
Returns: AbstractMsvWidget
Another instance of the AbstractMsvWidget with the same data

getSeqsFromResidues(self, residues)

 

Given a list of residues, return a set of the sequences taht contain these residues.

Parameters:
  • residues (list of schrodinnger.application.msv.domain.residue.Residue) - Residues to find the parent sequences of.
Returns: list of int
List of sequences indices that contain these residues

onResidueSelection(self, selection_info)

 

Set selection information on the alignment.

Parameters:
  • selection_info (dict) - A dictionary mapping sequences to selected residues

onResidueDeletionRequested(self, residues)

 

Takes residues to delete and removes them from the alignment

Parameters:
  • residues (list) - A list of residues to delete

getSequenceStatusInfo(self)

 

Return info about the status of the current alignment, including number of sequences in the alignment, number of sequences with selected residues, number of sequences visible in the Worksapce, and number of sequences hidden in theWorkspace.

Returns: 4-tuple of (int, int, int, int)
4-tuple of (Number of sequences, number of selected sequences, number of sequences shown in Workspace, number of sequences hidden in Workspace)

_getNewAlignment(self)

 

Return an alignment appropriate for the widget (ProteinAlignment, etc.) with a reference to the widget's undo stack set on it.

Returns:
schrodinger.application.msv.alignment.Alignment

resetUndoStack(self)

 

Reset the undo stack

This needs to be called when we perform an operation that gets tangled up with Maestro's single step undo, so that permitting an undo from msv would result in data corruption.

getAlignment(self)

 

Returns the widget's alignment instance

Returns: schrodinger.application.msv.domain.alignment.BaseAlignment
The widget's alignment

addSeq(self, seq)

 

Adds a given sequence to the widget's alignment

Parameters:

addSeqs(self, seqs)

 

Add a list of seqs to the widget's alignment

Parameters:
  • seqs (list) - An list of seqs

removeSeq(self, seq)

 

Remove a given sequence from the widget's alignment

Parameters:

getShownRowTypes(self)

 

Returns a list of enums representing the shown row types

Returns: list
A list of enums

rowWrap(self)

 

Indicates whether rows are currently wrapped

Returns: bool
Whether the rows are currently wrapped

groupedByType(self)

 

Indicates whether rows are grouped by type

Returns: bool
Whether the rows are currently grouped by type

replaceIDsWithDots(self)

 

Retrun whether or not dots should be drawn for columns of the same residue.

Returns: bool
Whether or not dots should be drawn for columns of the same residue.

getResidueFormat(self)

 
Returns: schrodinger.application.msv.gui.viewconstants.ResidueDisplay
An enum representing the residue display format in current use in the widget

setResidueFormat(self, residue_format)

 
Parameters:
  • residue_format (schrodinger.application.msv.gui.viewconstants. ResidueDisplay) - The format for residues

setReplaceIDsWithDots(self, disp_mode)

 

Set the identities to be displayed as dots or not.

Parameters:

changeTextSize(self, plus_minus)

 
Parameters:

getAlnByIdentity(self)

 
Returns: bool
Whether align by identity is turned on

setAlnByIdentity(self, by_identity)

 
Parameters:
  • by_identity (bool) - Whether to show alignment identity percentage

getAlnBySimilarity(self)

 
Returns: bool
Whether align by similarity is turned on

setAlnBySimilarity(self, by_similarity)

 
Parameters:
  • by_similarity (bool) - Whether to show alignment similarity percentage

getAlnByHomology(self)

 
Returns: bool
Whether align by homology is turned on

setAlnByHomology(self, by_homology)

 
Parameters:
  • by_homology (bool) - Whether to show alignment homology percentage

getAlnByScore(self)

 
Returns: bool
Whether align by score is turned on

setAlnByScore(self, by_score)

 
Parameters:
  • by_score (bool) - Whether to show alignment score based on similarity matrix

setIncludeGaps(self, include)

 
Parameters:
  • include (bool) - Whether to include gaps in calculating alignment metrics

setAlignment(self, aln)

 
Decorators:
  • @command.do_command

clear(self)

 
Decorators:
  • @command.do_command

deleteSelection(self)

 
Decorators:
  • @command.do_command

runAlignment(self, aligner)

 
Decorators:
  • @command.do_command

applyColorScheme(self, row_type, scheme)

 

Sets the color scheme for a given row type.

Parameters:
  • row_type - The type of row whose scheme is to be changed.
  • scheme - The color scheme to be applied.
Decorators:
  • @command.do_command

setGroupAnnotationsByType(self, by_annotation=True)

 

Set the grouping option for annotations and sequences

If the choice is not by_annotation, items will be grouped by sequence

Parameters:
  • by_annotation (bool) - Whether to group by annotation or sequence
Decorators:
  • @command.do_command

setShownRowTypes(self, row_types)

 

Set all the specified row types to visible and hide the rest

Parameters:
  • row_types (list) - A list of row types
Decorators:
  • @command.do_command

_setAllColorBlockVisible(self, show)

 
Decorators:
  • @command.from_command_only

setAllColorBlocksVisible(self, show)

 

Set the visibility of all color blocks annotations

Parameters:
  • show (bool) - Whether to show or hide the annotations
Decorators:
  • @command.do_command

setAnnotationVisible(self, ann, show=True)

 

Set the visibility of an annotation

Parameters:

setRowWrap(self, wrap=False)

 

Set the row wrapping on the widget

Parameters:
  • wrap (bool) - Whether to wrap sequences or not
Decorators:
  • @command.do_command

sortBy(self, sort_by, order)

 

Sort the table by the specified criteria.

Parameters:
  • sort_by (viewconstants.SortBy or NoneType) - The category to use for sorting. If None, the original input order will be used.
  • order (int) - Whether the data should be sorted in ascending (Qt.AscendingOrder) or descending (Qt.DescendingOrder) order.

sortingChanged(self, menu_update_required=True)

 

When the table sorting has been changed, update the WidgetOptions and notify the panel of the change if the menus need to be updated.

Parameters:
  • menu_update_required (bool) - True if the menus need to be updated as a result of the change. False otherwise.

_applyColorScheme(self, row_type, scheme)

 
Decorators:
  • @command.from_command_only

_setGroupAnnotationsByType(self, by_annotation=True)

 
Decorators:
  • @command.from_command_only

_setRowWrap(self, wrap)

 
Decorators:
  • @command.from_command_only

_setShownRowTypes(self, row_types)

 
Decorators:
  • @command.from_command_only

_doSetAlignment(self, aln)

 

Set the alignment on the widget

Parameters:
  • aln (schrodinger.application.msv.alignment.Alignment) - The alignment to set
Decorators:
  • @command.from_command_only

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2016-4 Schrodinger Python API
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