schrodinger.ui.sequencealignment.viewer module

This class implements a sequence viewer main window, all menus, toolbars and associated actions.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.ui.sequencealignment.viewer.AlignmentWindow(filename=None)

Bases: schrodinger.ui.qt.appframework.AppFramework

AlignmentWindow class implements a main window of the sequence viewer.

__init__(filename=None)

See class docstring.

project_name

Current project name.

closeEvent(event)

Called when the main window is about to be closed.

showEvent(event)

Synchronize with Maestro whenever the MSV window is opened and the sequence group is empty.

setBuildModel()

Called in multiseqviewer.py

newFile()

Creates a new project. Deletes all contents and sets a default window title.

open()

Opens a sequence file. Currently supported formats are FASTA, PDB and SwissProt.

Return type

bool

Returns

True if operation succeeded, False otherwise

processCommandLine(cmdline)

This processes the command line.

loadFiles(file_list)

loadProject()

Loads a MSV project.

saveAs()

Opens “Export Sequences” file dialog.

saveProject()

Saves the project.

saveProjectAs()

Saves MSV project.

backToKnime()

Sends the alignment back to a specified output file for KNIME.

saveImageAs()

Export image file dialog.

nameMenuCB(position, seq=None)

sequenceMenuCB(position, res=None)

treeMenuCB(position, tree=None)

createActionsAndMenu(list)

Creates all menus and their actions. Sets their slots, short cuts, tool tips, and checkable. Also creates self.actions = {labels: QActions} All base components of MENU_LIST are strings.

Parameters

list (list of never ending lists with strings inside) – MENU_LIST of all the menus, actions, and slots.

createAction(action_list, menu_name, menu)

Creates actions from sublists of msv_menu

Parameters

• action_list – [‘action label’, ‘slot method name’, ‘tool tip’, ‘shortcut’, ‘set checkable’, ‘icon’] or [SEPARATOR]

• menu_name – string name of Menu label

• menu – menu item to add action to

Returns

(key_value, action) for self.actions

setUpActionsDisabled()

Disables desired actions for setup.

setUpMenuActionsChecked()

Sets up desired checked status at initialization

fixShortCuts()

Sets shortcuts that were not set by createActionsAndMenu

addColorIconsToMenu()

Adds the color icons to the color menu after setup

createActions()

Create Qt actions.

createMenus()

Creates main window menus.

connectFontActions()

viewerSetFontSize(action)

Set font size action callback.

Parameters

action (QAction) – Qt action

createToolBars()

Create main window toolbars.

createStatusBar()

Creates a status bar.

statusBarMessageChanged(message)

readSettings(settings)

Reads sequence viewer user settings.

writeSettings(settings)

Writes sequence viewer user settings.

viewerModeChanged(value)

Mode changed action callback.

Parameters

value (int) – Sequence viewer mode, same as Mode combo box item index.

viewerTranslate()

Translates DNA / RNA sequence to amino acids.

viewerWrapSequences()

Toggle wrap sequences action callback.

viewerToggleMouseAcross()

Toggle mouse across rows action callback.

viewerToggleIdentityInColumns()

Toggle mouse across rows action callback.

viewerToggleColors()

Toggle mouse across rows action callback.

viewerPadAlignment()

Pad alignment action callback.

viewerHideEmptyLines()

Hide empty lines action callback.

viewerHideSelected()

Hide selected sequences action callback.

viewerDeleteSelected()

Delete selected sequences action callback.

viewerShowAll()

Show all sequences action callback.

viewerFillGaps()

Fill gaps action callback.

viewerRemoveGaps()

Remove gaps action callback.

viewerDeleteSelectedResidues()

Delete selected residues action callback.

viewerMinimizeAlignment()

Minimize alignment action callback.

viewerToggleTooltips()

Toggle tooltips action callback.

viewerToggleHeaderRow()

Toggle header row action callback.

viewerToggleRuler()

Toggle ruler action callback.

viewerToggleDisplayIdentity()

Toggle display percentage identity action callback.

viewerToggleDisplaySimilarity()

Toggle display percentage similarity action callback.

viewerToggleDisplayScore()

Toggle display score action callback.

viewerToggleDisplayHomology()

Toggle display homology action callback.

viewerToggleDisplayBoundaries()

Toggle display score action callback.

viewerLockGaps()

Lock gaps action callback.

viewerExpandAll()

Expand all action callback.

viewerCollapseAll()

Collapse all action callback.

viewerAddAllColorBlocks()

Adds all color block annotations.

viewerRemoveAllColorBlocks()

Adds all color block annotations.

viewerUnlockGaps()

Unlock gaps action callback.

viewerSelectBlocks()

Select blocks action callback.

viewerSelectStructure()

Select structure action callback.

viewerSelectIdentities()

Select identities action callback.

viewerSelectLigandContacts()

Select ligand contacts action callback.

viewerToggleLockDownstream()

Toggle lock downstream action callback.

viewerRunClustal()

Run Clustal action callback.

viewerRunPfam()

Run Pfam action callback.

viewerRunSSP()

Run SSP action callback.

viewerRunBlast()

Run Blast action callback.

viewerShowBlast()

Show Blast action callback.

viewerZoomIn()

Zoom in action callback.

viewerZoomOut()

Zoom out action callback.

viewerHelp()

Invokes MSV help.

viewerAddConsensus()

Add conesensus action callback.

viewerAddSymbols()

Add symbols action callback.

viewerAddGlobal()

Add global annotations action callback.

viewerRemoveGlobal()

Add global annotations action callback.

viewerAddHistory()

Add history action callback.

viewerSetAlwaysAsk()

viewerResetHistory()

Reset history action callback.

viewerAddMeanHydrophobicity()

Add mean hydrophobicity action callback.

viewerAddMeanPI()

Add mean isoelectric point action callback.

viewerAddSequenceLogo()

Add sequence logo action callback.

viewerDeleteAnnotations()

Delete annotations action callback.

viewerDeletePredictions()

Delete predictions action callback.

viewerGroupAnnotations()

Group annotations action callback.

viewerAverageColumns()

Average columns action callback.

viewerWeightColors()

Weight colors action callback.

viewerWeightColorsSettings()

viewerWeightColorsIdentity()

Weight colors by identity action callback.

viewerWeightColorsDifference()

Weight colors by difference action callback.

findTextChanged()

Called whenever text in “Find pattern” widget has changed.

Parameters

string (str) – pattern string

clearPattern()

Called whenever user clicks on ‘Clear Pattern’ button.

Parameters

string (str) – pattern string

viewerFindPrevious()

Find previous action callback.

viewerFindNext()

Find next action callback.

viewerRenumberResidues()

Renumber residues action callback.

viewerUndo()

Undo action callback.

viewerRedo()

Redo action callback.

viewerAddSimilarityAnnotation()

Add similarity action callback.

viewerAddResnumAnnotation()

Add residue number annotation.

viewerAddIdentityAnnotation()

Add identity annotation action callback.

viewerAddHydrophobicityAnnotation()

Add helix propensity action callback.

viewerAddPIAnnotation()

Add helix propensity action callback.

viewerAddBFactorAnnotation()

Add helix propensity action callback.

viewerAddSSBondAnnotation()

Add helix propensity action callback.

viewerAddHelixPropensityAnnotation()

Add helix propensity action callback.

viewerAddStrandPropensityAnnotation()

Add strand propensity action annotation callback.

viewerAddTurnPropensityAnnotation()

Add strand propensity annotation action callback.

viewerAddStericGroupAnnotation()

Add steric group action annotation callback.

viewerAddExposureTendencyAnnotation()

Add steric group action annotation callback.

viewerAddHelixTerminatorsAnnotation()

Add helix terminators annotation action callback.

viewerAddSidechainChemistryAnnotation()

Add sidechain chemistry annotation action callback.

viewerColorHelixPropensity()

Add helix propensity action callback.

viewerColorStrandPropensity()

Add strand propensity action annotation callback.

viewerColorTurnPropensity()

Add strand propensity annotation action callback.

viewerColorStericGroup()

Add steric group action annotation callback.

viewerColorExposureTendency()

Add steric group action annotation callback.

viewerColorHelixTerminators()

Add helix terminators annotation action callback.

viewerColorSidechainChemistry()

Add sidechain chemistry annotation action callback.

viewerAnchorSelection()

viewerClearAnchors()

sortByName()

Sort by name action callback.

sortByChain()

Sort by chain ID action callback.

sortByLength()

Sort by length action callback.

sortByGaps()

Sort by gaps action callback.

sortByIdentity()

Sort by identity action callback.

sortBySimilarity()

Sort by similarity action callback.

sortByHomology()

Sort by similarity action callback.

sortByScore()

Sort by score action callback.

sortByNameReverse()

Reverse sort by name action callback.

sortByChainReverse()

Reverse sort by name action callback.

sortByLengthReverse()

Reverse sort by length action callback.

sortByGapsReverse()

Reverse sort by gaps action callback.

sortByIdentityReverse()

Reverse sort by identity action callback.

sortBySimilarityReverse()

Reverse sort by identity action callback.

sortByHomologyReverse()

Reverse sort by identity action callback.

sortByScoreReverse()

Reverse sort by identity action callback.

treeSwapBranches()

Swap tree branches action callback.

treeHideBranches()

Hide tree branches action callback.

treeSelectSequences()

Select tree branches action callback.

sortByTreeOrder()

Sort by tree order action callback.

viewerSplitterMoved(pos, index)

Splitter moved action callback.

Parameters

• pos (int) – new splitter position

• index (int) – splitter index

viewerFetchSequence()

Fetch sequence action callback.

viewerEditSequence()

Edits a sequence as a text.

viewerCreateSequence()

Creates a new sequence.

viewerMoveUp()

Move sequences up action callback.

viewerMoveDown()

Move sequences down action callback.

viewerMoveTop()

Move sequences up action callback.

viewerMoveBottom()

Move sequences down action callback.

viewerInvertSelection()

Invert residue selection range action callback.

viewerSelectAll()

Select all residues action callback.

viewerDeselectAll()

Deselect all residues action callback.

viewerSynchronizeWithMaestro()

Synchronize with Maestro action callback.

viewerPassSelectionToMaestro()

viewerAutoSynchronizeWithMaestro()

Synchronize with Maestro action callback.

viewerComputeSequenceProfile()

Synchronize with Maestro action callback.

viewerAutoComputeSequenceProfile()

Synchronize with Maestro action callback.

viewerMutateWhileTyping()

Mutate sequence while typing action callback.

viewerRemoveRedundancy()

viewerDuplicate()

Duplicates currently selected sequences.

viewerPairwiseAlignment()

viewerAlignMerge()

viewerAlignByResidueNumbers()

viewerRenumberToAntibody()

viewerSelectAntibodyRegions()

viewerSetAsReference()

viewerSelectAllSequences()

viewerUnselectAllSequences()

viewerInvertSequenceSelection()

viewerPasteFasta()

viewerColorResidueType()

viewerColorSecondary()

viewerColorBfactor()

viewerColorPosition()

viewerToggleUseDots()

viewerToggleAutoColor()

viewerColorSimilarity()

viewerColorKyteDoolittle()

viewerColorHoppWoods()

viewerColorGrayscale()

viewerColorWhite()

viewerColorTaylor()

viewerColorMaestro()

viewerPropagateColors()

Propagates colors to Maestro workspace.

viewerConsiderGaps()

viewerClearConstraints()

viewerSetConstraints()

viewerAddSSA()

viewerRunACCpro()

Run solvent accessibility prediction.

viewerRunDOMpro()

Run domain arrangement prediction.

viewerRunDISpro()

Run disordered region prediction.

viewerRunDIpro()

Run disulfide bridges prediction.

viewerRunBETApro()

Run beta sheet prediction.

viewerRunAllPredictions()

viewerExpandSelection()

viewerHideColumns()

viewerHideUnselectedColumns()

viewerShowColumns()

viewerExpandSelectionRef()

viewerMarkColorCustom()

viewerBackgroundColorCustom()

viewerConstantColorCustom()

viewerMaestroSuperposition()

Superposes structures in Maestro workspace according to the current alignment.

viewerAlignmentSettings()

Displays alignment setting dialog.

viewerDownloadPDB()

Downloads a corresponding PDB structure.

viewerMarkResidues()

viewerBackgroundColor()

viewerColorResidues()

viewerClearMarkedResidues()

viewerShowJobLog()

Shows job log window.

viewerShowJobSettings()

Shows job settings window.

viewerBuildModel()

Builds a 3D model of the reference sequence.

connectNoSlot()

Hacker fix to not connecting “Include Incorporated Entries in Workspace” to anything

viewerColorEntrySurface()

viewerAssociateMaestroEntries()

viewerAlignStructures()

Aligns 3D protein structures.

viewerGetStructureAlignment()

Aligns 3D protein structures.

viewerCropSelectedResidues()

Crops the residues in the selected area.

viewerShowLigands()

Displays Maestro ligand interaction fingerprints.

viewerFindPattern()

Switch focus to Find Pattern input box.

viewerNewSet()

viewerDuplicateSet()

addNewQueryTab(open_file=True)

Adds a new query tab.

queryTabChanged(index)

queryDelete()

queryTabClose(index)

queryContextMenu(position)

Displays a query context menu.

queryDuplicate()

Duplicates the picked query.

queryRename()

Renames the picked query.

viewerSetSequenceColor()

viewerIncorporateSelected()

viewerIncorporateIncluded()

viewerRenameSequence()

viewerAnalyzeBindingSite()

viewerCompareSequences()

Open ‘Compare sequences’ dialog.

viewerUserAddRectangle()

viewerUserAddAlignmentRegion()

viewerUserAddCustomAnnotation()

viewerUserRemoveAll()

viewerResetSettings()

Resets all user settings to default.

AllowNestedDocks = 2

AllowTabbedDocks = 4

AnimatedDocks = 1

class DockOption

Bases: int

class DockOptions

class DockOptions(Union[QMainWindow.DockOptions, QMainWindow.DockOption]) → None

class DockOptions(QMainWindow.DockOptions) → None

Bases: sip.simplewrapper

__init__(*args, **kwargs)

DrawChildren = 2

DrawWindowBackground = 1

ForceTabbedDocks = 8

GroupedDragging = 32

IgnoreMask = 4

class PaintDeviceMetric

Bases: int

PdmDepth = 6

PdmDevicePixelRatio = 11

PdmDevicePixelRatioScaled = 12

PdmDpiX = 7

PdmDpiY = 8

PdmHeight = 2

PdmHeightMM = 4

PdmNumColors = 5

PdmPhysicalDpiX = 9

PdmPhysicalDpiY = 10

PdmWidth = 1

PdmWidthMM = 3

class RenderFlag

Bases: int

class RenderFlags

class RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) → None

class RenderFlags(QWidget.RenderFlags) → None

Bases: sip.simplewrapper

__init__(*args, **kwargs)

VerticalTabs = 16

acceptDrops(self) → bool

accessibleDescription(self) → str

accessibleName(self) → str

actionEvent(self, QActionEvent)

actions(self) → List[QAction]

activateWindow(self)

addAction(self, QAction)

addActions(self, Iterable[QAction])

addButtonToBottomLayout(text, command)

Adds a button to the bottom bar, to go to the right of Job Start buttons. Useful when you need a button on the bottom which is not standard job launching.

Buttons are added from left to right in the order that this function is called..

:param text text that goes on the button :type text str

:param command the slot that the button will run :param callable

Return type

str

Returns

name of button, to be used in setButtonEnabled

addCentralWidget(w)

Add a widget to the central area of the AppFramework dialog

addDockWidget(self, Qt.DockWidgetArea, QDockWidget)

addDockWidget(self, Qt.DockWidgetArea, QDockWidget, Qt.Orientation) → None

addToolBar(self, Qt.ToolBarArea, QToolBar)

addToolBar(self, QToolBar) → None

addToolBar(self, str) → QToolBar

addToolBarBreak(self, area: Qt.ToolBarArea = Qt.TopToolBarArea)

adjustSize(self)

askOverwrite(files=None, parent=None)

Display a dialog asking the user whether to overwrite existing files. Returns True if user chose to overwrite, False otherwise.

Optionally specify a list of files that will be overwritten if the user presses the Overwrite button.

askOverwriteIfNecessary(files)

If any of the files in the <files> list exists, will bring up a dialog box asking the user whether they want to overwrite them. Returns True if the user chose to overwrite or if specified files do not exist. Returns False if the user cancelled.

autoFillBackground(self) → bool

backgroundRole(self) → QPalette.ColorRole

baseSize(self) → QSize

blockSignals(self, bool) → bool

centralWidget(self) → QWidget

changeEvent(self, QEvent)

childAt(self, QPoint) → QWidget

AlignmentWindow.childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)

children(self) → List[QObject]

childrenRect(self) → QRect

childrenRegion(self) → QRegion

clearFocus(self)

clearMask(self)

close(self) → bool

closePanel()

Hide panel, if in Maestro. Otherwise close it.

colorCount(self) → int

connectNotify(self, QMetaMethod)

contentsMargins(self) → QMargins

contentsRect(self) → QRect

contextMenuEvent(self, QContextMenuEvent)

contextMenuPolicy(self) → Qt.ContextMenuPolicy

corner(self, Qt.Corner) → Qt.DockWidgetArea

create(self, window: PyQt5.sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)

createPopupMenu(self) → QMenu

createWindowContainer(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget

cursor(self) → QCursor

customContextMenuRequested

customContextMenuRequested(self, QPoint) [signal]

customEvent(self, QEvent)

deleteLater(self)

depth(self) → int

destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)

destroyed

destroyed(self, object: QObject = None) [signal]

devType(self) → int

devicePixelRatio(self) → int

devicePixelRatioF(self) → float

devicePixelRatioFScale() → float

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dockOptions(self) → QMainWindow.DockOptions

dockWidgetArea(self, QDockWidget) → Qt.DockWidgetArea

documentMode(self) → bool

dragEnterEvent(self, QDragEnterEvent)

dragLeaveEvent(self, QDragLeaveEvent)

dragMoveEvent(self, QDragMoveEvent)

dropEvent(self, QDropEvent)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

effectiveWinId(self) → PyQt5.sip.voidptr

ensurePolished(self)

enterEvent(self, QEvent)

error(text, preferences=None, key=None)

Display an error dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters

• text (str) – The information to display in the dialog

• preferences – obsolete; ignored.

• key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

exec_()

Calls exec_() method of the application.

find(PyQt5.sip.voidptr) → QWidget

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

focusInEvent(self, QFocusEvent)

focusNextChild(self) → bool

focusNextPrevChild(self, bool) → bool

focusOutEvent(self, QFocusEvent)

focusPolicy(self) → Qt.FocusPolicy

focusPreviousChild(self) → bool

focusProxy(self) → QWidget

focusWidget(self) → QWidget

font(self) → QFont

fontInfo(self) → QFontInfo

fontMetrics(self) → QFontMetrics

foregroundRole(self) → QPalette.ColorRole

frameGeometry(self) → QRect

frameSize(self) → QSize

geometry(self) → QRect

getApp()

Return QApplication instance which this panel is running under. If in Maestro, returns Maestro’s global QApplication instance.

getContentsMargins(self) → Tuple[int, int, int, int]

getInputFile()

Return the selected input file path (Python string).

If the panel has no input frame, raises RuntimeError. If FILE source is not allowed, raises RuntimeError.

getInputSource()

Return the selected input source. Available values (module constants):

• WORKSPACE

• SELECTED_ENTRIES

• INCLUDED_ENTRIES

• INCLUDED_ENTRY

• FILE

If the panel has no input frame, raises RuntimeError.

getOpenFileName(caption='Select a file', initial_dir=None, support_mae=True, support_sd=True, support_pdb=True)

Brings up an open file dialog box for selecting structure files. By default reads Maestro, SD, and PDB formats. Returns file path that is readable by StructureReader. Is user pressed cancel, empty string is returned.

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap

grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())

grabKeyboard(self)

grabMouse(self)

grabMouse(self, Union[QCursor, Qt.CursorShape]) → None

grabShortcut(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int

graphicsEffect(self) → QGraphicsEffect

graphicsProxyWidget(self) → QGraphicsProxyWidget

hasFocus(self) → bool

hasHeightForWidth(self) → bool

hasMouseTracking(self) → bool

hasTabletTracking(self) → bool

height(self) → int

heightForWidth(self, int) → int

heightMM(self) → int

help()

Display the help dialog (or a warning dialog if no help can be found). This function requires help_topic to have been given when the class was initialized.

hide(self)

hideEvent(self, QHideEvent)

iconSize(self) → QSize

iconSizeChanged

iconSizeChanged(self, QSize) [signal]

info(text, preferences=None, key=None)

Display an information dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters

• text (str) – The information to display in the dialog

• preferences – obsolete; ignored.

• key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

inherits(self, str) → bool

initPainter(self, QPainter)

inputMethodEvent(self, QInputMethodEvent)

inputMethodHints(self) → Qt.InputMethodHints

inputMethodQuery(self, Qt.InputMethodQuery) → Any

AlignmentWindow.insertAction(self, QAction, QAction)

insertActions(self, QAction, Iterable[QAction])

AlignmentWindow.insertToolBar(self, QToolBar, QToolBar)

insertToolBarBreak(self, QToolBar)

installEventFilter(self, QObject)

interior()

Return the interior frame where client widgets should be parented from

isActiveWindow(self) → bool

isAncestorOf(self, QWidget) → bool

isAnimated(self) → bool

isDockNestingEnabled(self) → bool

isDockableInMaestro()

Returns True if the PyQt panel can be docked into Maestro mainwindow. Otherwise returns false. This function should be called only after parsing the ‘dockable’ argument inside the constructor.

isEnabled(self) → bool

isEnabledTo(self, QWidget) → bool

isFullScreen(self) → bool

isHidden(self) → bool

isLeftToRight(self) → bool

isMaximized(self) → bool

isMinimized(self) → bool

isModal(self) → bool

isRightToLeft(self) → bool

isSeparator(self, QPoint) → bool

isSignalConnected(self, QMetaMethod) → bool

isVisible(self) → bool

isVisibleTo(self, QWidget) → bool

isWidgetType(self) → bool

isWindow(self) → bool

isWindowModified(self) → bool

isWindowType(self) → bool

jobCompleted

keyPressEvent(self, QKeyEvent)

keyReleaseEvent(self, QKeyEvent)

keyboardGrabber() → QWidget

killTimer(self, int)

launchJobCmd(cmd)

Launches job control command. Automatically tracked by the job status button (no need to call monitorJob method afterwards). NOTE: Unlike similar method in AF2, this method does not add -HOST etc options.

layout(self) → QLayout

layoutDirection(self) → Qt.LayoutDirection

leaveEvent(self, QEvent)

locale(self) → QLocale

logicalDpiX(self) → int

logicalDpiY(self) → int

lower(self)

mapFrom(self, QWidget, QPoint) → QPoint

mapFromGlobal(self, QPoint) → QPoint

mapFromParent(self, QPoint) → QPoint

mapTo(self, QWidget, QPoint) → QPoint

mapToGlobal(self, QPoint) → QPoint

mapToParent(self, QPoint) → QPoint

mask(self) → QRegion

maximumHeight(self) → int

maximumSize(self) → QSize

maximumWidth(self) → int

menuBar(self) → QMenuBar

menuWidget(self) → QWidget

metaObject(self) → QMetaObject

metric(self, QPaintDevice.PaintDeviceMetric) → int

minimumHeight(self) → int

minimumSize(self) → QSize

minimumSizeHint(self) → QSize

minimumWidth(self) → int

monitorJob(jobid, showpanel=False)

Monitor the given jobid and show the monitor panel; if in maestro.

Parameters

• jobid – jobid of the job to monitor

• showpanel – whether to bring up the Monitor panel. By default, the panel will open if the “Open Monitor panel” preference is set.

Example, after launching the job, use the jobid to issue the command:

<AppFramework_instance>.monitorJob(<jobid>)

mouseDoubleClickEvent(self, QMouseEvent)

mouseGrabber() → QWidget

mouseMoveEvent(self, QMouseEvent)

mousePressEvent(self, QMouseEvent)

mouseReleaseEvent(self, QMouseEvent)

move(self, QPoint)

AlignmentWindow.move(self, int, int) -> None

moveEvent(self, QMoveEvent)

moveToThread(self, QThread)

nativeEvent(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]

nativeParentWidget(self) → QWidget

nextInFocusChain(self) → QWidget

normalGeometry(self) → QRect

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

overrideWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])

overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])

paintEngine(self) → QPaintEngine

paintEvent(self, QPaintEvent)

paintingActive(self) → bool

palette(self) → QPalette

parent(self) → QObject

parentWidget(self) → QWidget

physicalDpiX(self) → int

physicalDpiY(self) → int

pos(self) → QPoint

previousInFocusChain(self) → QWidget

processEvents()

Allow the QApplication’s or Maestro’s main event loop to process pending events.

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

question(msg, button1='OK', button2='Cancel', title='Question')

Display a prompt dialog window with specified text. Returns True if first button (default OK) is pressed, False otherwise.

quitPanel()

Quit the panel (even if in Maestro)

Note that the calling script needs to unset the variable that holds this panel instance in order to truly delete the panel. For example, this method should be subclassed as follows:

def quitPanel(self):

global mypanel # Where mypanel is the variable holding this object appframework.AppFramework.quitPanel(self) mypanel = None

raise_(self)

receivers(self, PYQT_SIGNAL) → int

rect(self) → QRect

releaseKeyboard(self)

releaseMouse(self)

releaseShortcut(self, int)

removeAction(self, QAction)

removeDockWidget(self, QDockWidget)

removeEventFilter(self, QObject)

removeToolBar(self, QToolBar)

removeToolBarBreak(self, QToolBar)

render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren))

render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.RenderFlag.DrawWindowBackground | QWidget.RenderFlag.DrawChildren)) → None

repaint(self)

AlignmentWindow.repaint(self, int, int, int, int) -> None

repaint(self, QRect) → None

repaint(self, QRegion) → None

resize(self, QSize)

AlignmentWindow.resize(self, int, int) -> None

resizeDocks(self, Iterable[QDockWidget], Iterable[int], Qt.Orientation)

resizeEvent(self, QResizeEvent)

restoreCursor(app_wide=True)

Restore the application level cursor to the default. If ‘app_wide’ is True then if will be restored for the entire application, if it’s False, it will be just for this panel.

restoreDockWidget(self, QDockWidget) → bool

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool

restoreState(self, Union[QByteArray, bytes, bytearray], version: int = 0) → bool

saveGeometry(self) → QByteArray

saveState(self, version: int = 0) → QByteArray

AlignmentWindow.scroll(self, int, int)

AlignmentWindow.scroll(self, int, int, QRect) -> None

sender(self) → QObject

senderSignalIndex(self) → int

setAcceptDrops(self, bool)

setAccessibleDescription(self, str)

setAccessibleName(self, str)

setAnimated(self, bool)

setAttribute(self, Qt.WidgetAttribute, on: bool = True)

setAutoFillBackground(self, bool)

setBackgroundRole(self, QPalette.ColorRole)

AlignmentWindow.setBaseSize(self, int, int)

setBaseSize(self, QSize) → None

setButtonEnabled(button, enabled)

Enable / disable the specified button, e.g.,

self.setButtonEnabled(‘start’, False)

Raises a RuntimeError if the button doesn’t exist.

setButtonState(button, state)

Set the state of the specified button, e.g.,

self.setButtonState(‘start’, ‘disabled’)

The standard state is ‘normal’. Raises a RuntimeError if the button doesn’t exist or if the requested state can’t be set.

Obsolete. Please use setButtonEnabled() method instead.

setCentralWidget(self, QWidget)

AlignmentWindow.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins) → None

setContextMenuPolicy(self, Qt.ContextMenuPolicy)

setCorner(self, Qt.Corner, Qt.DockWidgetArea)

setCursor(self, Union[QCursor, Qt.CursorShape])

setDisabled(self, bool)

setDockNestingEnabled(self, bool)

setDockOptions(self, Union[QMainWindow.DockOptions, QMainWindow.DockOption])

setDocumentMode(self, bool)

setEnabled(self, bool)

setFixedHeight(self, int)

setFixedSize(self, QSize)

AlignmentWindow.setFixedSize(self, int, int) -> None

setFixedWidth(self, int)

setFocus(self)

setFocus(self, Qt.FocusReason) → None

setFocusPolicy(self, Qt.FocusPolicy)

setFocusProxy(self, QWidget)

setFont(self, QFont)

setForegroundRole(self, QPalette.ColorRole)

setGeometry(self, QRect)

AlignmentWindow.setGeometry(self, int, int, int, int) -> None

setGraphicsEffect(self, QGraphicsEffect)

setHidden(self, bool)

setIconSize(self, QSize)

setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])

setJobname(jobname)

setLayout(self, QLayout)

setLayoutDirection(self, Qt.LayoutDirection)

setLocale(self, QLocale)

setMask(self, QBitmap)

setMask(self, QRegion) → None

setMaximumHeight(self, int)

AlignmentWindow.setMaximumSize(self, int, int)

setMaximumSize(self, QSize) → None

setMaximumWidth(self, int)

setMenuBar(self, QMenuBar)

setMenuWidget(self, QWidget)

setMinimumHeight(self, int)

AlignmentWindow.setMinimumSize(self, int, int)

setMinimumSize(self, QSize) → None

setMinimumWidth(self, int)

setMouseTracking(self, bool)

setObjectName(self, str)

setPalette(self, QPalette)

setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType]) → None

setProgress(step, total_steps)

Set the progress bar value (bottom of the panel) to <step> out of <total_steps>

Set both to 0 to hide the progress bar.

setProgressError(error)

Set the color of the progress bar to red (error=True) or normal color (error=False).

setProperty(self, str, Any) → bool

setShortcutAutoRepeat(self, int, enabled: bool = True)

setShortcutEnabled(self, int, enabled: bool = True)

AlignmentWindow.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize) → None

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy) → None

setStatusBar(self, QStatusBar)

setStatusTip(self, str)

setStyle(self, QStyle)

setStyleSheet(self, str)

AlignmentWindow.setTabOrder(QWidget, QWidget)

setTabPosition(self, Union[Qt.DockWidgetAreas, Qt.DockWidgetArea], QTabWidget.TabPosition)

setTabShape(self, QTabWidget.TabShape)

setTabletTracking(self, bool)

setToolButtonStyle(self, Qt.ToolButtonStyle)

setToolTip(self, str)

setToolTipDuration(self, int)

setUnifiedTitleAndToolBarOnMac(self, bool)

setUpdatesEnabled(self, bool)

setVisible(self, bool)

setWaitCursor(app_wide=True)

Set the cursor to the wait cursor. This will be an hourglass, clock or similar. Call restoreCursor() to return to the default cursor. If ‘app_wide’ is True then it will apply to the entire application (including Maestro if running there). If it’s False then it will apply only to this panel.

setWhatsThis(self, str)

setWindowFilePath(self, str)

setWindowFlag(self, Qt.WindowType, on: bool = True)

setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])

setWindowIcon(self, QIcon)

setWindowIconText(self, str)

setWindowModality(self, Qt.WindowModality)

setWindowModified(self, bool)

setWindowOpacity(self, float)

setWindowRole(self, str)

setWindowState(self, Union[Qt.WindowStates, Qt.WindowState])

setWindowTitle(self, str)

setupJobParameters()

Setups up the job parameters from the state of the input frame. Do not call directly from your script.

Returns True if success, False on error (after displaying an error message).

sharedPainter(self) → QPainter

show(also_raise=True, also_activate=True)

Redefine the show() method to deiconize if necessary and also raise_() the panel if ‘also_raise’ is specified as True.

Parameters

• also_raise (bool) – If True (default), the raise_ method will also be called on the window. If False it is not. This is important on some Window managers to ensure the window is placed on top of other windows.

• also_activate (bool) – If True (default), the activateWindow method will also be called on the window. If False it is not. This is important on some Window managers to ensure the window is placed on top of other windows.

showFullScreen(self)

showMaximized(self)

showMinimized(self)

showNormal(self)

signalsBlocked(self) → bool

size(self) → QSize

sizeHint(self) → QSize

sizeIncrement(self) → QSize

sizePolicy(self) → QSizePolicy

splitDockWidget(self, QDockWidget, QDockWidget, Qt.Orientation)

stackUnder(self, QWidget)

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

start_wrapper_timeout = 3000

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

statusBar(self) → QStatusBar

statusTip(self) → str

style(self) → QStyle

styleSheet(self) → str

tabPosition(self, Qt.DockWidgetArea) → QTabWidget.TabPosition

tabShape(self) → QTabWidget.TabShape

tabifiedDockWidgetActivated

tabifiedDockWidgetActivated(self, QDockWidget) [signal]

tabifiedDockWidgets(self, QDockWidget) → List[QDockWidget]

AlignmentWindow.tabifyDockWidget(self, QDockWidget, QDockWidget)

tabletEvent(self, QTabletEvent)

takeCentralWidget(self) → QWidget

testAttribute(self, Qt.WidgetAttribute) → bool

thread(self) → QThread

timerEvent(self, QTimerEvent)

toolBarArea(self, QToolBar) → Qt.ToolBarArea

toolBarBreak(self, QToolBar) → bool

toolButtonStyle(self) → Qt.ToolButtonStyle

toolButtonStyleChanged

toolButtonStyleChanged(self, Qt.ToolButtonStyle) [signal]

toolTip(self) → str

toolTipDuration(self) → int

tr(self, str, disambiguation: str = None, n: int = - 1) → str

trackJobProgress(job)

Display a progress dialog showing the progress of this job. (Any previously tracked job will no longer be tracked)

job - a jobcontrol.Job object.

underMouse(self) → bool

ungrabGesture(self, Qt.GestureType)

unifiedTitleAndToolBarOnMac(self) → bool

unsetCursor(self)

unsetLayoutDirection(self)

unsetLocale(self)

update(self)

update(self, QRect) → None

update(self, QRegion) → None

AlignmentWindow.update(self, int, int, int, int) -> None

updateGeometry(self)

updateJobname()

Update jobname in parameters from main window.

updateMicroFocus(self)

updateStatusBar()

Updates the status bar.

updatesEnabled(self) → bool

visibleRegion(self) → QRegion

warning(text, preferences=None, key=None)

Display a warning dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters

• text (str) – The information to display in the dialog

• preferences – obsolete; ignored.

• key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

whatsThis(self) → str

wheelEvent(self, QWheelEvent)

width(self) → int

widthMM(self) → int

winId(self) → PyQt5.sip.voidptr

window(self) → QWidget

windowFilePath(self) → str

windowFlags(self) → Qt.WindowFlags

windowHandle(self) → QWindow

windowIcon(self) → QIcon

windowIconChanged

windowIconChanged(self, QIcon) [signal]

windowIconText(self) → str

windowIconTextChanged

windowIconTextChanged(self, str) [signal]

windowModality(self) → Qt.WindowModality

windowOpacity(self) → float

windowRole(self) → str

windowState(self) → Qt.WindowStates

windowTitle(self) → str

windowTitleChanged

windowTitleChanged(self, str) [signal]

windowType(self) → Qt.WindowType

x(self) → int

y(self) → int