Class GenomeView
Defined in: GenomeView.js.
Constructor Attributes | Constructor Name and Description |
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GenomeView(elem, stripeWidth, refseq, zoomLevel, browserRoot)
Main view class, shows a scrollable, horizontal view of annotation
tracks.
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Method Attributes | Method Name and Description |
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absXtoBp(pixels)
Convert absolute pixels X position to base pair position on the
current reference sequence.
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addOverviewTrack(track)
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addTrack(track)
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bpToPx(bp)
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calculatePositionLabelHeight(containerElement)
Conduct a DOM test to calculate the height of div.pos-label
elements with a line of text in them.
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calculateSequenceCharacterSize(containerElement)
Conducts a test with DOM elements to measure sequence text width
and height.
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centerAtBase(base, instantly)
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checkDragOut(event)
stop the drag if we mouse out of the view
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checkY(y)
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clampX(x)
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clampY(y)
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doubleClickZoom(event)
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dragEnd(event)
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dragMove(event)
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getWidth()
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getX()
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getY()
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hideRubberHighlight(start, end)
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onCoarseMove(startbp, endbp)
Hook for other components to dojo.connect to.
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onFineMove(startbp, endbp)
Hook for other components to dojo.connect to.
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onResize()
Hook to be called on a window resize.
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Convert absolute X pixel position to base pair position on the
overview track.
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overviewClicked(evt)
Event handler fired when the overview bar is single-clicked.
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overviewTrackIterate(callback)
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pxToBp(pixels)
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rawSetPosition(pos)
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rawSetX(x)
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rawSetY(y)
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rubberCancel(event)
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rubberExecute(event)
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rubberMove(event)
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scaleClicked(evt)
Event handler fired when the track scale bar is single-clicked.
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setLocation(refseq, startbp, endbp)
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setPosition(pos)
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setRubberHighlight(start, end)
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setX(x)
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setY(y)
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showDone()
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showFine()
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showVisibleBlocks(updateHeight, pos, startX, endX)
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showWait()
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sizeInit()
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slide(distance)
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startMouseDragScroll(event)
Event fired when a user's mouse button goes down inside the main
element of the genomeview.
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startRubberZoom(absToBp, container, event)
Start a rubber-band dynamic zoom.
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stripeWidthForZoom(zoomLevel)
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thumbMoved(mover)
Event handler fired when the region thumbnail in the overview bar
is dragged.
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trackHeightUpdate(trackName, height)
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trackIterate(callback)
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trimVertical(y)
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updateOverviewHeight(trackName, height)
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Given a new X and Y pixels position for the main track container,
reposition static elements that "float" over it, like track labels,
Y axis labels, the main track ruler, and so on.
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wheelScroll(e)
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zoomIn(e, zoomLoc, steps)
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zoomOut(e, zoomLoc, steps)
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zoomUpdate(zoomLoc, fixedBp)
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Class Detail
GenomeView(elem, stripeWidth, refseq, zoomLevel, browserRoot)
Main view class, shows a scrollable, horizontal view of annotation
tracks. NOTE: All coordinates are interbase.
- Parameters:
- elem
- stripeWidth
- refseq
- zoomLevel
- browserRoot
Method Detail
{Number}
absXtoBp(pixels)
Convert absolute pixels X position to base pair position on the
current reference sequence.
- Parameters:
- {Number} pixels
- Returns:
- {Number}
addOverviewTrack(track)
- Parameters:
- track
addTrack(track)
- Parameters:
- track
afterSlide()
bpToPx(bp)
- Parameters:
- bp
calculatePositionLabelHeight(containerElement)
Conduct a DOM test to calculate the height of div.pos-label
elements with a line of text in them.
- Parameters:
- containerElement
calculateSequenceCharacterSize(containerElement)
Conducts a test with DOM elements to measure sequence text width
and height.
- Parameters:
- containerElement
centerAtBase(base, instantly)
- Parameters:
- base
- instantly
checkDragOut(event)
stop the drag if we mouse out of the view
- Parameters:
- event
checkY(y)
- Parameters:
- y
clampX(x)
- Parameters:
- x
clampY(y)
- Parameters:
- y
doubleClickZoom(event)
- Parameters:
- event
dragEnd(event)
- Parameters:
- event
dragMove(event)
- Parameters:
- event
getHeight()
getPosition()
getWidth()
getX()
getY()
hideRubberHighlight(start, end)
- Parameters:
- start
- end
instantZoomUpdate()
{Number}
maxVisible()
- Returns:
- {Number} maximum basepair coordinate of the current reference sequence visible in the genome view
{Number}
minVisible()
- Returns:
- {Number} minimum basepair coordinate of the current reference sequence visible in the genome view
onCoarseMove(startbp, endbp)
Hook for other components to dojo.connect to.
- Parameters:
- startbp
- endbp
onFineMove(startbp, endbp)
Hook for other components to dojo.connect to.
- Parameters:
- startbp
- endbp
onResize()
Hook to be called on a window resize.
overview_absXtoBp(x)
Convert absolute X pixel position to base pair position on the
overview track. This needs refactoring; a scale bar should
itself know how to convert an absolute X position to base pairs.
- Parameters:
- {Number} x
- absolute pixel X position (for example, from a click event's clientX property)
overviewClicked(evt)
Event handler fired when the overview bar is single-clicked.
- Parameters:
- evt
overviewTrackIterate(callback)
- Parameters:
- callback
pxToBp(pixels)
- Parameters:
- pixels
rawSetPosition(pos)
- Parameters:
- pos
rawSetX(x)
- Parameters:
- x
rawSetY(y)
- Parameters:
- y
rubberCancel(event)
- Parameters:
- event
rubberExecute(event)
- Parameters:
- event
rubberMove(event)
- Parameters:
- event
scaleClicked(evt)
Event handler fired when the track scale bar is single-clicked.
- Parameters:
- evt
scrollUpdate()
setLocation(refseq, startbp, endbp)
- Parameters:
- refseq
- startbp
- endbp
setPosition(pos)
- Parameters:
- pos
setRubberHighlight(start, end)
- Parameters:
- start
- end
setX(x)
- Parameters:
- x
setY(y)
- Parameters:
- y
showCoarse()
showDone()
showFine()
showVisibleBlocks(updateHeight, pos, startX, endX)
- Parameters:
- updateHeight
- pos
- startX
- endX
showWait()
sizeInit()
slide(distance)
- Parameters:
- distance
startMouseDragScroll(event)
Event fired when a user's mouse button goes down inside the main
element of the genomeview.
- Parameters:
- event
startRubberZoom(absToBp, container, event)
Start a rubber-band dynamic zoom.
- Parameters:
- {Function} absToBp
- function to convert page X coordinates to base pair positions on the reference sequence. Called in the context of the GenomeView object.
- {HTMLElement} container
- element in which to draw the rubberbanding highlight
- {Event} event
- the mouse event that's starting the zoom
stripeWidthForZoom(zoomLevel)
- Parameters:
- zoomLevel
thumbMoved(mover)
Event handler fired when the region thumbnail in the overview bar
is dragged.
- Parameters:
- mover
trackHeightUpdate(trackName, height)
- Parameters:
- trackName
- height
trackIterate(callback)
- Parameters:
- callback
trimVertical(y)
- Parameters:
- y
updateOverviewHeight(trackName, height)
- Parameters:
- trackName
- height
updateTrackList()
updateViewDimensions()
Given a new X and Y pixels position for the main track container,
reposition static elements that "float" over it, like track labels,
Y axis labels, the main track ruler, and so on.
- Parameters:
- args.x Optional
- the new X coordinate. if not provided, elements that only need updates on the X position are not updated.
- args.y Optional
- the new Y coordinate. if not provided, elements that only need updates on the Y position are not updated.
wheelScroll(e)
- Parameters:
- e
zoomCallback()
zoomIn(e, zoomLoc, steps)
- Parameters:
- e
- zoomLoc
- steps
zoomOut(e, zoomLoc, steps)
- Parameters:
- e
- zoomLoc
- steps
zoomUpdate(zoomLoc, fixedBp)
- Parameters:
- zoomLoc
- fixedBp