schrodinger.ui.sequencealignment.sequence_area module¶

This class implements a sequence area widget that performs actual display and manipulation of the sequences and annotation data.

class schrodinger.ui.sequencealignment.sequence_area.SequenceArea(parent=None)[source]¶

Bases: PyQt5.QtWidgets.QWidget

The sequence area displays sequence rows and associated annotations. It is a scrollable widget. The presence of horizontal and vertical scrollbars depends on current sequence viewer mode (wrapped or not wrapped).

__init__(parent=None)[source]¶

min_row¶: Used for Shift-click selection

focusInEvent(self, QFocusEvent)[source]¶

horizontalScrollBarChanged(value)[source]¶

Horizontal scrollbar callback.

Parameters: value (int) – new scrollbar value

verticalScrollBarChanged(value)[source]¶

Vertical scrollbar callback.

Parameters: value (int) – new scrollbar value

mouseToCoords(x, y)[source]¶

Translates mouse coordinates in global space to sequence area discrete coordinates (row, position).

Parameters

x (int) – x coordinate
y (int) – y coordinate

Return type

(int, int)

Returns

(row, position) coordinates

rowPosToCoords(row, pos, visible_only=True)[source]¶

Translates (row, position) coordinates to widget coordinates. This method is used for drawing auxiliary objects such as text edit cursor.

Parameters

row ((Sequence, int, int, int)) – row
pos (int) – row position

Return type

(int, int)

Returns

pair of widget coordinates, or (None, None) if the conversion fails.

mouseToRowPosition(x, y)[source]¶

Converts mouse coordinates to (row, position, residue) tuple.

Parameters

x (int) – x coordinate
y (int) – y coordinate

Return type

(row, int, Residue)

Returns

row, position pair or (None, None, None) if the conversion fails.

mouseDoubleClickEvent(event)[source]¶: Handles Qt double click event.

selectExtent(row, pos, reset=False)[source]¶: Select minimum residue extent between previous selection and current position.

mousePressEvent(event)[source]¶

Handles Qt mouse press event.

Parameters: event (QMouseEvent) – Qt mouse event.

startDraggingRect(row, pos)[source]¶

Begins rectangle dragging. Determines boundaries of the area that needs to be dragged and calculates coordinates of the auxiliary rectangle. The initial coordinates (row and position) should be inside the area that needs to be dragged. This method assumes the area is rectangular. Otherwise, results are non-predictable - usually a rectangular superset of irregular area will be dragged.

Parameters

row ((Sequence, int, int ,int)) – sequence viewer row in the dragged area
pos (int) – row position

mouseReleaseEvent(event)[source]¶

Handles Qt mouse release event.

Parameters: event (QMouseEvent) – Qt mouse event.

keyReleaseEvent(event)[source]¶

Handles Qt key release events.

Parameters: event (QKeyEvent) – Qt key release event

keyPressEvent(event)[source]¶

Handles Qt key press events.

Parameters: event (QKeyEvent) – Qt key press event

showToolTip(mouse_pos, seq_pos, res, sequence)[source]¶

Displays mouse move tooltip depending on the viewer mode and underlying object.

Parameters

mouse_pos (QPoint) – Global position of the mouse cursor.
seq_pos (int) – Sequence position where the mouse cursor is.
res (Residue) – Residue beneath the mouse cursor.
sequence (Sequence) – Sequence beneath the mouse cursor.

wheelEvent(event)[source]¶

Handles Qt mouse wheel event.

Parameters: event (QWheelEvent) – Qt mouse wheel event.

autoScroll()[source]¶

mouseMoveEvent(event)[source]¶

Handles mouse move event for the sequence viewer widget.

Parameters: event (QMouseEvent) – Qt mouse move event.

setViewer(viewer)[source]¶: Sets a parent sequence viewer widget for this sequence area.

resizeEvent(event)[source]¶

Qt resize event handler. When the widget is resized, the sequence viewer has to re-generate rows and update itself.

Parameters: event (QResizeEvent) – Qt resize event

paintAuxRectangle(painter)[source]¶

Paints the auxiliary rectangle on a specified painter. The aux rectangle is used to mark a sequence area in “select and slide” sequence viewer mode.

Parameters: painter (QPainter) – target Qt painter

paintUserAnnotations(painter)[source]¶: Renders user-defined annotations.

paintCursor(painter)[source]¶

Draw edit mode cursor at present cursor position.

Parameters: painter (QPainter) – painter used to draw the cursor

paintEvent(event)[source]¶

Qt paint event handler. Calls self.paintSequenceArea to paint the widget contents.

Parameters: event (QPaintEvent) – Qt paint event

paintRowBackground(painter, row, x_pos, y_pos, draw_text, selection_only=False, use_parent=False)[source]¶: Paints a row background.

paintRowText(painter, row, row_position, x_pos, y_pos, x_offset)[source]¶: Paints the row text contents.

paintRowLogo(painter, row, row_position)[source]¶: Paints the row text contents.

paintRowSSA(painter, row, row_position)[source]¶

paintRowSSBond(painter, row, row_position)[source]¶: Paints disulfide bond row (both assignment and prediction).

paintRowConstraints(painter, row, row_position)[source]¶: Paints constraints row (both alignment and Prime).

paintRowAnnotationPlot(painter, row, row_position)[source]¶: Paints annotation plot.

cacheSSAImages()[source]¶: Paints a secondary structure annotation row.

paintSequenceArea(painter, event, clip=True, custom_width=None, custom_height=None)[source]¶

Actually paints the sequence area widget.

Note

This code should be re-factored. Each component of the sequence area should have its own painting method.

Parameters

painter (QPainter) – target Qt painter
event (QPaintEvent) – Qt paint event

updateColumns(start, end)[source]¶

DrawChildren = 2¶

DrawWindowBackground = 1¶

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)¶

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])¶

adjustSize(self)¶

autoFillBackground(self) → bool¶

backgroundRole(self) → QPalette.ColorRole¶

baseSize(self) → QSize¶

blockSignals(self, bool) → bool¶

changeEvent(self, QEvent)¶

childAt(self, QPoint) → QWidget¶
SequenceArea.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¶

closeEvent(self, QCloseEvent)¶

colorCount(self) → int¶

connectNotify(self, QMetaMethod)¶

contentsMargins(self) → QMargins¶

contentsRect(self) → QRect¶

contextMenuEvent(self, QContextMenuEvent)¶

contextMenuPolicy(self) → Qt.ContextMenuPolicy¶

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

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)¶

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)¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

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]

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¶

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

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¶

hide(self)¶

hideEvent(self, QHideEvent)¶

inherits(self, str) → bool¶

initPainter(self, QPainter)¶

inputMethodEvent(self, QInputMethodEvent)¶

inputMethodHints(self) → Qt.InputMethodHints¶

inputMethodQuery(self, Qt.InputMethodQuery) → Any¶

SequenceArea.insertAction(self, QAction, QAction)

insertActions(self, QAction, Iterable[QAction])¶

installEventFilter(self, QObject)¶

isActiveWindow(self) → bool¶

isAncestorOf(self, QWidget) → bool¶

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¶

isSignalConnected(self, QMetaMethod) → bool¶

isVisible(self) → bool¶

isVisibleTo(self, QWidget) → bool¶

isWidgetType(self) → bool¶

isWindow(self) → bool¶

isWindowModified(self) → bool¶

isWindowType(self) → bool¶

keyboardGrabber() → QWidget¶

killTimer(self, int)¶

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¶

metaObject(self) → QMetaObject¶

metric(self, QPaintDevice.PaintDeviceMetric) → int¶

minimumHeight(self) → int¶

minimumSize(self) → QSize¶

minimumSizeHint(self) → QSize¶

minimumWidth(self) → int¶

mouseGrabber() → QWidget¶

move(self, QPoint)¶
SequenceArea.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¶

paintingActive(self) → bool¶

palette(self) → QPalette¶

parent(self) → QObject¶

parentWidget(self) → QWidget¶

physicalDpiX(self) → int¶

physicalDpiY(self) → int¶

pos(self) → QPoint¶

previousInFocusChain(self) → QWidget¶

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.

raise_(self)¶

receivers(self, PYQT_SIGNAL) → int¶

rect(self) → QRect¶

releaseKeyboard(self)¶

releaseMouse(self)¶

releaseShortcut(self, int)¶

removeAction(self, QAction)¶

removeEventFilter(self, QObject)¶

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)¶
SequenceArea.repaint(self, int, int, int, int) -> None
repaint(self, QRect) → None
repaint(self, QRegion) → None

resize(self, QSize)¶
SequenceArea.resize(self, int, int) -> None

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

saveGeometry(self) → QByteArray¶

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setAcceptDrops(self, bool)¶

setAccessibleDescription(self, str)¶

setAccessibleName(self, str)¶

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

setAutoFillBackground(self, bool)¶

setBackgroundRole(self, QPalette.ColorRole)¶

SequenceArea.setBaseSize(self, int, int)
setBaseSize(self, QSize) → None¶

SequenceArea.setContentsMargins(self, int, int, int, int)
setContentsMargins(self, QMargins) → None¶

setContextMenuPolicy(self, Qt.ContextMenuPolicy)¶

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

setDisabled(self, bool)¶

setEnabled(self, bool)¶

setFixedHeight(self, int)¶

setFixedSize(self, QSize)¶
SequenceArea.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)¶
SequenceArea.setGeometry(self, int, int, int, int) -> None

setGraphicsEffect(self, QGraphicsEffect)¶

setHidden(self, bool)¶

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

setLayout(self, QLayout)¶

setLayoutDirection(self, Qt.LayoutDirection)¶

setLocale(self, QLocale)¶

setMask(self, QBitmap)¶
setMask(self, QRegion) → None

setMaximumHeight(self, int)¶

SequenceArea.setMaximumSize(self, int, int)
setMaximumSize(self, QSize) → None¶

setMaximumWidth(self, int)¶

setMinimumHeight(self, int)¶

SequenceArea.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

setProperty(self, str, Any) → bool¶

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

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

SequenceArea.setSizeIncrement(self, int, int)
setSizeIncrement(self, QSize) → None¶

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

setStatusTip(self, str)¶

setStyle(self, QStyle)¶

setStyleSheet(self, str)¶

SequenceArea.setTabOrder(QWidget, QWidget)

setTabletTracking(self, bool)¶

setToolTip(self, str)¶

setToolTipDuration(self, int)¶

setUpdatesEnabled(self, bool)¶

setVisible(self, bool)¶

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)¶

sharedPainter(self) → QPainter¶

show(self)¶

showEvent(self, QShowEvent)¶

showFullScreen(self)¶

showMaximized(self)¶

showMinimized(self)¶

showNormal(self)¶

signalsBlocked(self) → bool¶

size(self) → QSize¶

sizeHint(self) → QSize¶

sizeIncrement(self) → QSize¶

sizePolicy(self) → QSizePolicy¶

stackUnder(self, QWidget)¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

statusTip(self) → str¶

style(self) → QStyle¶

styleSheet(self) → str¶

tabletEvent(self, QTabletEvent)¶

testAttribute(self, Qt.WidgetAttribute) → bool¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toolTip(self) → str¶

toolTipDuration(self) → int¶

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

underMouse(self) → bool¶

ungrabGesture(self, Qt.GestureType)¶

unsetCursor(self)¶

unsetLayoutDirection(self)¶

unsetLocale(self)¶

update(self)¶
update(self, QRect) → None
update(self, QRegion) → None
SequenceArea.update(self, int, int, int, int) -> None

updateGeometry(self)¶

updateMicroFocus(self)¶

updatesEnabled(self) → bool¶

visibleRegion(self) → QRegion¶

whatsThis(self) → str¶

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¶