Package schrodinger :: Package application :: Package msv :: Package gui :: Module msv_gui :: Class MSVPanel

Class MSVPanel

                                                       object --+            
                                                                |            
ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin --+        
                                                                    |        
            ui.qt.appframework2.maestro_callback.MaestroCallbackMixin --+    
                                                                        |    
                                                           object --+   |    
                                                                    |   |    
                              ui.qt.appframework2.markers.MarkerMixin --+    
                                                                        |    
                                                       object --+       |    
                                                                |       |    
                       ui.qt.appframework2.settings.SettingsMixin --+   |    
                                                                    |   |    
                      ui.qt.appframework2.settings.SettingsPanelMixin --+    
                                                                        |    
                                       object --+                       |    
                                                |                       |    
                                sip.simplewrapper --+                   |    
                                                    |                   |    
                                          sip.wrapper --+               |    
                                                        |               |    
                                     PyQt5.QtCore.QObject --+           |    
                                                            |           |    
                                           object --+       |           |    
                                                    |       |           |    
                                    sip.simplewrapper --+   |           |    
                                                        |   |           |    
                                 PyQt5.QtGui.QPaintDevice --+           |    
                                                            |           |    
                                      PyQt5.QtWidgets.QWidget --+       |    
                                                                |       |    
                            ui.qt.appframework2.baseapp.BasePanel --+   |    
                                                                    |   |    
                                                       object --+   |   |    
                                                                |   |   |    
                   ui.qt.appframework2.validation.ValidationMixin --+   |    
                                                                    |   |    
                           ui.qt.appframework2.baseapp.ValidatedPanel --+    
                                                                        |    
                                              ui.qt.appframework2.af2.App --+
                                                                            |
                                                                           MSVPanel

Nested Classes

[hide private]

Inherited from PyQt5.QtWidgets.QWidget: RenderFlag, RenderFlags

Inherited from PyQt5.QtGui.QPaintDevice: PaintDeviceMetric

Instance Methods

[hide private]

colorSchemeChanged(...)

show(self)
We call raise here so that the panel comes to the front on all platforms when running in standalone mode.

setup(self)

updateOptions(self)
Update shared ui elements to fit the current widget

addTab(self, title='Query', make_active=True)
Add a tab to the query tabs

duplicateTab(self, index)
Duplicate the tab at the given index

schrodinger.application.msv.gui.menu.MsvMenuBar

_makeMenu(self)
Return a menu of the appropriate kind

toggleAllColorBlocks(self, checked)
slot for the "All color blocks" toggle

dict

_makeMenuMap(self)
Returns: A mapping of menu actions to callbacks

_setUpMenu(self)
Set up the application menu, wiring up all signals

_setUpViewStyleDialog(self)
Set up the view dialog, wiring up all the signals

_setUpQuickAnnotationsDialog(self)
Set up the Quick Annotations dialog, wiring up all the signals

_setUpColorDialog(self)
Set up the Color dialog, wiring up all the signals.

callable

_makeCurrentWidgetCallback(self, meth_name)
Return a callback that calls the specified method on the current widget

callable

_makeToggleAnnotationCallbackForAction(self, ann)
Return a callback that toggles the specified annotation on the top widget

callable

_makeTopWidgetCallbackForAction(self, meth_name)
Returns a callback that executes the specified method on the top level widget

callable

_makeTopWidgetCallbackForSort(self, sort_by, order)
Returns a callback that sets the specified sorting on the top level widget

setPanelOptions(self)
Configure the panel by setting instance variables here.

setDefaults(self)

layOut(self)

schrodinger.application.msv.gui.msv_widget.AbstractMsvWidget or None

currentWidget(self)
Return the widget belonging to the currently active tab, or None if all tabs are closed

updateNumSeqsLabel(self, num_seqs)
Update the label to the current alignment length.

updateNumSelectedSeqsLabel(self, num_selected)
Update the label to the current number of selected sequences.

setQuerySeq(self)
Set the currently selected sequence as the query sequence

removeSelectedSeqs(self)
Delete the selected sequences.

updateVizLabel(self, num_shown, num_hidden)
Update the label to the current number of sequences in the Workspace that are shown and hidden.

updateAllStatusLabels(self)
Get the status from the current widget and update status labels accordingly.

showDebugGui(self)

showColorSchemeEditor(self)

updateColorScheme(self, info)

updateSeqRowColorScheme(self, color_scheme)
Convenience function for changing Sequence row color schemes.

removeColorScheme(self)
Remove the current color scheme.

updateColorByAln(self, mode)
Update the color by alignment mode

canUndoChanged(self, can_undo)
Update widget states to reflect availability of undo

canRedoChanged(self, can_redo)
Update widget states to reflect availability of redo

undo(self)

redo(self)
Redo the last undone operation

syncMaestro(self)

Inherited from ui.qt.appframework2.af2.App: __init__, addMainTaskRunner, cleanup, closeEvent, createBottomBar, createInputSelector, currentTaskRunner, getWorkspaceStructure, processSettings, processTaskMessage, resetAllRunners, resizeEvent, setCurrentTask, setupTaskRunner, showEvent, showProgressBarForJob

Inherited from ui.qt.appframework2.af2.App (private): _applySettingsFromGroup, _close, _getSettingsForGroup, _help, _prestart, _prewrite, _read, _reset, _start, _statusShrunk, _updateProgressBar

Inherited from ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin: buildCallbackDicts, ignoreMaestroCallbacks

Inherited from ui.qt.appframework2.maestro_callback.AbstractMaestroCallbackMixin (private): _addCallbacks, _closeEvent, _delayedCallbacks, _removeCallbacks, _showEvent

Inherited from ui.qt.appframework2.markers.MarkerMixin: addJaguarMarker, addMarker, addMarkerFromAsl, getAllJaguarMarkers, getAllMarkers, getJaguarMarker, hideAllJaguarMarkers, hideAllMarkers, hideEvent, removeAllJaguarMarkers, removeAllJaguarMarkersForEntry, removeAllMarkers, removeJaguarMarker, removeJaguarMarkerForAtoms, removeMarker, showAllJaguarMarkers, showAllMarkers

Inherited from ui.qt.appframework2.markers.MarkerMixin (private): _calcEntryAtomTotal, _canonicalizeAtomOrder, _clearInvalidatedJaguarMarkers, _createAtomAsl, _createJaguarMarker, _createMarker, _eidsFromHashable, _genMarkerHash, _hideAll, _setMarkerHash, _showAll, _updateMarkers

Inherited from ui.qt.appframework2.settings.SettingsPanelMixin: definePanelSettings, getPanelState, loadPanelState, setPanelState, writePanelState

Inherited from ui.qt.appframework2.settings.SettingsPanelMixin (private): _configurePanelSettings

Inherited from ui.qt.appframework2.settings.SettingsMixin: __getitem__, __setitem__, applyAliasedSettings, applySettings, getAliasedSettings, getAliasedValue, getObjValue, getPersistenceKey, getSettings, loadPersistentOptions, savePersistentOptions, setAlias, setAliasedValue, setAliases, setObjValue, setPersistent

Inherited from ui.qt.appframework2.baseapp.ValidatedPanel: reportValidation

Inherited from ui.qt.appframework2.baseapp.BasePanel: __str__, error, gui_closed, info, keyPressEvent, parent, question, restoreCursor, run, runCanvas, runMaestro, runMode, runStandalone, runSubpanel, setWaitCursor, startUp, warning

Inherited from ui.qt.appframework2.baseapp.BasePanel (private): _dockPrefChanged, _layOutDockWidget

Inherited from PyQt5.QtWidgets.QWidget: acceptDrops, accessibleDescription, accessibleName, actionEvent, actions, activateWindow, addAction, addActions, adjustSize, autoFillBackground, backgroundRole, baseSize, changeEvent, childAt, childrenRect, childrenRegion, clearFocus, clearMask, close, contentsMargins, contentsRect, contextMenuEvent, contextMenuPolicy, create, createWindowContainer, cursor, customContextMenuRequested, destroy, devType, dragEnterEvent, dragLeaveEvent, dragMoveEvent, dropEvent, effectiveWinId, ensurePolished, enterEvent, event, find, focusInEvent, focusNextChild, focusNextPrevChild, focusOutEvent, focusPolicy, focusPreviousChild, focusProxy, focusWidget, font, fontInfo, fontMetrics, foregroundRole, frameGeometry, frameSize, geometry, getContentsMargins, grab, grabGesture, grabKeyboard, grabMouse, grabShortcut, graphicsEffect, graphicsProxyWidget, hasFocus, hasHeightForWidth, hasMouseTracking, height, heightForWidth, hide, initPainter, inputMethodEvent, inputMethodHints, inputMethodQuery, insertAction, insertActions, isActiveWindow, isAncestorOf, isEnabled, isEnabledTo, isFullScreen, isHidden, isLeftToRight, isMaximized, isMinimized, isModal, isRightToLeft, isVisible, isVisibleTo, isWindow, isWindowModified, keyReleaseEvent, keyboardGrabber, 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, nativeEvent, nativeParentWidget, nextInFocusChain, normalGeometry, overrideWindowFlags, overrideWindowState, paintEngine, paintEvent, palette, parentWidget, pos, previousInFocusChain, raise_, rect, releaseKeyboard, releaseMouse, releaseShortcut, removeAction, render, repaint, resize, 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, setInputMethodHints, setLayout, setLayoutDirection, setLocale, setMask, setMaximumHeight, setMaximumSize, setMaximumWidth, setMinimumHeight, setMinimumSize, setMinimumWidth, setMouseTracking, setPalette, setParent, setShortcutAutoRepeat, setShortcutEnabled, setSizeIncrement, setSizePolicy, setStatusTip, setStyle, setStyleSheet, setTabOrder, setToolTip, setToolTipDuration, setUpdatesEnabled, setVisible, setWhatsThis, setWindowFilePath, setWindowFlags, setWindowIcon, setWindowIconText, setWindowModality, setWindowModified, setWindowOpacity, setWindowRole, setWindowState, setWindowTitle, sharedPainter, showFullScreen, showMaximized, showMinimized, showNormal, size, sizeHint, sizeIncrement, sizePolicy, stackUnder, statusTip, style, styleSheet, tabletEvent, testAttribute, toolTip, toolTipDuration, underMouse, ungrabGesture, unsetCursor, unsetLayoutDirection, unsetLocale, update, updateGeometry, updateMicroFocus, updatesEnabled, visibleRegion, whatsThis, wheelEvent, width, winId, window, windowFilePath, windowFlags, windowHandle, windowIcon, windowIconChanged, windowIconText, windowIconTextChanged, windowModality, windowOpacity, windowRole, windowState, windowTitle, windowTitleChanged, windowType, x, y

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

Inherited from PyQt5.QtGui.QPaintDevice: colorCount, depth, devicePixelRatio, devicePixelRatioF, devicePixelRatioFScale, heightMM, logicalDpiX, logicalDpiY, paintingActive, physicalDpiX, physicalDpiY, widthMM

Inherited from sip.simplewrapper: __new__

Inherited from ui.qt.appframework2.validation.ValidationMixin: runValidation

Inherited from ui.qt.appframework2.validation.ValidationMixin (private): _validate, _validateChildren

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

Class Methods

[hide private]

Inherited from ui.qt.appframework2.af2.App: panel

Class Variables

[hide private]

Inherited from ui.qt.appframework2.af2.App (private): _singleton

Inherited from PyQt5.QtWidgets.QWidget: DrawChildren, DrawWindowBackground, IgnoreMask

Inherited from PyQt5.QtCore.QObject: staticMetaObject

Inherited from PyQt5.QtGui.QPaintDevice: PdmDepth, PdmDevicePixelRatio, PdmDevicePixelRatioScaled, PdmDpiX, PdmDpiY, PdmHeight, PdmHeightMM, PdmNumColors, PdmPhysicalDpiX, PdmPhysicalDpiY, PdmWidth, PdmWidthMM

Instance Variables

[hide private]

Inherited from ui.qt.appframework2.markers.MarkerMixin: MARKER_ICONS

Inherited from ui.qt.appframework2.markers.MarkerMixin (private): _marked_eid_lengths, _markers, _multi_atom_markers

Properties

[hide private]

Inherited from ui.qt.appframework2.baseapp.BasePanel: title

Inherited from object: __class__

Method Details

[hide private]

show(self)

We call raise here so that the panel comes to the front on all platforms when running in standalone mode.

Overrides: PyQt5.QtWidgets.QWidget.show

setup(self)

Overrides: ui.qt.appframework2.baseapp.BasePanel.setup

duplicateTab(self, index)

Duplicate the tab at the given index

Parameters:

index (int) - The index of the tab to rename

_makeMenu(self)

Return a menu of the appropriate kind

Returns: schrodinger.application.msv.gui.menu.MsvMenuBar: A menu bar

toggleAllColorBlocks(self, checked)

slot for the "All color blocks" toggle

Parameters:

checked (bool) - check state of the toggle

_makeMenuMap(self)

Returns: dict: A mapping of menu actions to callbacks

_makeCurrentWidgetCallback(self, meth_name)

Return a callback that calls the specified method on the current widget

Parameters:

meth_name (str) - The name of the method to call on the top level widget

Returns: callable

The requested callback

_makeToggleAnnotationCallbackForAction(self, ann)

Return a callback that toggles the specified annotation on the top widget

Parameters:

ann (annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES or annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES) - The annotation to toggle

Returns: callable

A function that takes a bool indicating check state and sets the visibility of the annotation accordingly

_makeTopWidgetCallbackForAction(self, meth_name)

Returns a callback that executes the specified method on the top level widget

Parameters:

meth_name (str) - The name of the method to call on the top level widget

Returns: callable

The requested callback

_makeTopWidgetCallbackForSort(self, sort_by, order)

Returns a callback that sets the specified sorting on the top level widget

Parameters:

sort_by (viewmodel.SortBy) - The criterion to sort on.
order (int) - Whether the data should be sorted in ascending (Qt.AscendingOrder) or descending (Qt.DescendingOrder) order.

Returns: callable

The requested callback

setPanelOptions(self)


Configure the panel by setting instance variables here. Always call the
parent method. Panel options:

self.maestro_dockable - whether this panel should be dockable in the
    Maestro main window. Setting to false will prevent the panel from
    docking regardless of Maestro preference. When setting it to true, if
    Maestro Preference allows docking of panels, it will dock the panel
    on the right-hand side of the main window if "Location" is set to
    "Main window", or a floating window if "Location" is set to
    "Floating window". Default is False.

self.title - string to display in the window title bar

self.ui - a Ui_Form instance defining the main ui, default None

self.allowed_run_modes - subset of [MODE_MAESTRO, MODE_STANDALONE,
    MODE_SUBPANEL, MODE_CANVAS] defining how the panel may be run.
    Default is all.

self.help_topic - string defining the help topic. Default ''

self.input_selector_options - dict of options for the common input
    selector widget. Default is an empty dict, meaning do not add an
    input selector

self.add_main_layout_stretch - bool of whether to add a stretch to the
    main layout under the main ui (if self.ui exists). Default is True

self.save_resize - bool indicating whether a panel should
retain any custom resizing done by the user when it is hidden and
shown again. Default is True.

Overrides: ui.qt.appframework2.baseapp.BasePanel.setPanelOptions

setDefaults(self)

Overrides: ui.qt.appframework2.baseapp.BasePanel.setDefaults

layOut(self)

Overrides: ui.qt.appframework2.baseapp.BasePanel.layOut

currentWidget(self)

Return the widget belonging to the currently active tab, or None if all tabs are closed

Returns: schrodinger.application.msv.gui.msv_widget.AbstractMsvWidget or None: The current msv widget or None

updateNumSeqsLabel(self, num_seqs)

Update the label to the current alignment length.

Parameters:

num_seqs (int) - Number of sequences in the alignment.

updateNumSelectedSeqsLabel(self, num_selected)

Update the label to the current number of selected sequences.

Parameters:

num_selected (int) - Number of selected sequences.

updateVizLabel(self, num_shown, num_hidden)

Update the label to the current number of sequences in the Workspace that are shown and hidden.

Parameters:

num_shown (int) - Number of sequences in the Workspace that are visible.
num_hidden (int) - Number of sequences in the Workspace that are hidden.

updateSeqRowColorScheme(self, color_scheme)

Convenience function for changing Sequence row color schemes.

Parameters:

color_scheme (color.updateSeqRowColorScheme) - New color scheme to use

updateColorByAln(self, mode)

Update the color by alignment mode

Parameters:

color_by_aln (viewconstants.ColorByAln)