Package bacnet.genomeBrowser.tracksGUI

Class TrackCanvasData

java.lang.Object
org.eclipse.swt.widgets.Widget
org.eclipse.swt.widgets.Control
org.eclipse.swt.widgets.Scrollable
org.eclipse.swt.widgets.Composite
org.eclipse.swt.widgets.Canvas
bacnet.genomeBrowser.tracksGUI.TrackCanvasData
All Implemented Interfaces:
Serializable, EventListener, org.eclipse.rap.rwt.Adaptable, org.eclipse.swt.events.MouseMoveListener, org.eclipse.swt.graphics.Drawable, org.eclipse.swt.internal.SerializableCompatibility, org.eclipse.swt.internal.SWTEventListener
public class TrackCanvasData extends org.eclipse.swt.widgets.Canvas implements org.eclipse.swt.events.MouseMoveListener
A TrackCanvasData is the Canvas in which will be displayed datasets
Author:
christophebecavin
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static int
    HEIGHT_SEQUENCE
    Height of the sequence track (when displayed)
    int
    MINIMUM_DATA_SIZE
    Minimal height of a data track

  • Constructor Summary

    Constructors
    Constructor
    Description
    TrackCanvasData(org.eclipse.swt.widgets.Composite parent, int style, org.eclipse.swt.widgets.Composite trackComposite)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    clickedElement(org.eclipse.swt.events.MouseEvent e)
    Get base-pair position of the clicked element
    int
    convertXtoBP(int x)
    Convert position in the display to a position in the genome
    (inverse function of basepairToXimage(int bpIndex))
    If MassSpec data has not been register do it
    Annotation
    getAnnotation()
     
    double
    getBpSizeH()
     
    String
    getCanvasName()
     
    String
    getChromoID()
     
    int
    getDataWindowSize()
     
    int
    getDecaySliderVBar()
     
    String
    getGenomeName()
     
    int
    getHeightPix()
     
    NTermData
    getMassSpecData()
     
    int
    getMouseXPosition()
     
    int
    getMouseYPosition()
     
    NTerm
    getnTermHighlight()
     
    String
    getnTermTypeOverlap()
     
    Track
    getTrack()
     
    org.eclipse.swt.widgets.Composite
    getTrackComposite()
     
    int
    getWidthBP()
     
    double
    getZoomVertical()
     
    boolean
    isDisplayMouseLine()
     
    boolean
    isTestData()
     
    void
    mouseMove(org.eclipse.swt.events.MouseEvent e)
    If the mouse is over the genome viewer, detect it is on the annotation, and display the corresponding gene, sRNA, asRNA
    void
    moveVertically(int sliderVBarIncrement)
    From the position of the vertical bar draw the corresponding part of the data
    void
    setAnnotation(Annotation annotation)
     
    void
    setBpSizeH(double bpSizeH)
     
    void
    setChromoID(String chromoID)
     
    void
    setDataWindowSize(int dataWindowSize)
     
    void
    setDecaySliderVBar(int decaySliderVBar)
     
    void
    setDisplayMouseLine(boolean displayMouseLine)
     
    void
    setGenomeName(String genomeName)
     
    void
    setHeightPix(int heightPix)
     
    void
    setMassSpecData(NTermData massSpecData)
     
    void
    setMouseXPosition(int mouseXPosition)
     
    void
    setMouseYPosition(int mouseYPosition)
     
    void
    setName(String name)
     
    void
    setnTermHighlight(NTerm nTermHighlight)
     
    void
    setnTermTypeOverlap(String nTermTypeOverlap)
     
    void
    setTestData(boolean testData)
     
    void
    setTrack(Track track)
    Set the data of the Canvas, and implement the PaintListener Execute different tasks:
    Fix the number of pixel for one base pair Set width and height parameters for data and annotation track Display in order:
    different line and ticks for the base pair position, every display needed in the background display all the data display sequence if needed display annotation different genome name and mouse line in foreground
    void
    setTrackComposite(org.eclipse.swt.widgets.Composite trackComposite)
     
    void
    setWidthBP(int widthBP)
     
    void
    setZoomVertical(double zoomVertical)
     

    Methods inherited from class org.eclipse.swt.widgets.Canvas

    addPaintListener, getAdapter, removePaintListener

    Methods inherited from class org.eclipse.swt.widgets.Composite

    changed, computeSize, getBackgroundMode, getChildren, getLayout, getLayoutDeferred, getTabList, isLayoutDeferred, layout, layout, layout, layout, layout, setBackgroundMode, setFocus, setLayout, setLayoutDeferred, setTabList

    Methods inherited from class org.eclipse.swt.widgets.Scrollable

    computeTrim, getClientArea, getHorizontalBar, getVerticalBar

    Methods inherited from class org.eclipse.swt.widgets.Control

    addControlListener, addDragDetectListener, addFocusListener, addGestureListener, addHelpListener, addKeyListener, addMenuDetectListener, addMouseListener, addTouchListener, addTraverseListener, computeSize, forceFocus, getAccessible, getBackground, getBackgroundImage, getBorderWidth, getBounds, getCursor, getEnabled, getFont, getForeground, getLayoutData, getLocation, getMenu, getMonitor, getOrientation, getParent, getShell, getSize, getToolTipText, getTouchEnabled, getVisible, isEnabled, isFocusControl, isReparentable, isVisible, moveAbove, moveBelow, pack, pack, redraw, redraw, removeControlListener, removeDragDetectListener, removeFocusListener, removeGestureListener, removeHelpListener, removeKeyListener, removeMenuDetectListener, removeMouseListener, removeTouchListener, removeTraverseListener, requestLayout, setBackground, setBackgroundImage, setBounds, setBounds, setCursor, setData, setEnabled, setFont, setForeground, setLayoutData, setLocation, setLocation, setMenu, setOrientation, setParent, setRedraw, setSize, setSize, setToolTipText, setTouchEnabled, setVisible, toControl, toControl, toDisplay, toDisplay, update

    Methods inherited from class org.eclipse.swt.widgets.Widget

    addDisposeListener, addListener, dispose, getData, getData, getDisplay, getListeners, getStyle, isDisposed, isListening, notifyListeners, removeDisposeListener, removeListener, reskin, setData, toString

    Methods inherited from class java.lang.Object

    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Field Details

    • MINIMUM_DATA_SIZE

      public int MINIMUM_DATA_SIZE
      Minimal height of a data track

    • HEIGHT_SEQUENCE

      public static int HEIGHT_SEQUENCE
      Height of the sequence track (when displayed)

  • Constructor Details

    • TrackCanvasData

      public TrackCanvasData(org.eclipse.swt.widgets.Composite parent, int style, org.eclipse.swt.widgets.Composite trackComposite)

  • Method Details

    • setTrack

      public void setTrack(Track track)
      Set the data of the Canvas, and implement the PaintListener Execute different tasks:
    • Fix the number of pixel for one base pair
    • Set width and height parameters for data and annotation track Display in order:
    • different line and ticks for the base pair position, every display needed in the background
    • display all the data
    • display sequence if needed
    • display annotation
    • different genome name and mouse line in foreground
      • Parameters:
      tracks - Track
      data - TrackData

    • convertXtoBP

      public int convertXtoBP(int x)
      Convert position in the display to a position in the genome
      (inverse function of basepairToXimage(int bpIndex))
      If MassSpec data has not been register do it
      Parameters:
      x - position in the view
      Returns:
      bpIndex in the genome

    • mouseMove

      public void mouseMove(org.eclipse.swt.events.MouseEvent e)
      If the mouse is over the genome viewer, detect it is on the annotation, and display the corresponding gene, sRNA, asRNA
      Specified by:
      mouseMove in interface org.eclipse.swt.events.MouseMoveListener
      Parameters:
      e -

    • moveVertically

      public void moveVertically(int sliderVBarIncrement)
      From the position of the vertical bar draw the corresponding part of the data
      Parameters:
      sliderVBarPosition -

    • clickedElement

      public int clickedElement(org.eclipse.swt.events.MouseEvent e)
      Get base-pair position of the clicked element
      Parameters:
      e -
      Returns:

    • getnTermTypeOverlap

      public String getnTermTypeOverlap()

    • setnTermTypeOverlap

      public void setnTermTypeOverlap(String nTermTypeOverlap)

    • getnTermHighlight

      public NTerm getnTermHighlight()

    • setnTermHighlight

      public void setnTermHighlight(NTerm nTermHighlight)

    • getMouseXPosition

      public int getMouseXPosition()

    • setMouseXPosition

      public void setMouseXPosition(int mouseXPosition)

    • getMouseYPosition

      public int getMouseYPosition()

    • setMouseYPosition

      public void setMouseYPosition(int mouseYPosition)

    • isDisplayMouseLine

      public boolean isDisplayMouseLine()

    • setDisplayMouseLine

      public void setDisplayMouseLine(boolean displayMouseLine)

    • getMassSpecData

      public NTermData getMassSpecData()

    • setMassSpecData

      public void setMassSpecData(NTermData massSpecData)

    • getTrack

      public Track getTrack()

    • getAnnotation

      public Annotation getAnnotation()

    • setAnnotation

      public void setAnnotation(Annotation annotation)

    • getHeightPix

      public int getHeightPix()

    • setHeightPix

      public void setHeightPix(int heightPix)

    • getWidthBP

      public int getWidthBP()

    • setWidthBP

      public void setWidthBP(int widthBP)

    • getDecaySliderVBar

      public int getDecaySliderVBar()

    • setDecaySliderVBar

      public void setDecaySliderVBar(int decaySliderVBar)

    • getDataWindowSize

      public int getDataWindowSize()

    • setDataWindowSize

      public void setDataWindowSize(int dataWindowSize)

    • getBpSizeH

      public double getBpSizeH()

    • setBpSizeH

      public void setBpSizeH(double bpSizeH)

    • getTrackComposite

      public org.eclipse.swt.widgets.Composite getTrackComposite()

    • setTrackComposite

      public void setTrackComposite(org.eclipse.swt.widgets.Composite trackComposite)

    • getZoomVertical

      public double getZoomVertical()

    • setZoomVertical

      public void setZoomVertical(double zoomVertical)

    • isTestData

      public boolean isTestData()

    • setTestData

      public void setTestData(boolean testData)

    • getCanvasName

      public String getCanvasName()

    • setName

      public void setName(String name)

    • getGenomeName

      public String getGenomeName()

    • setGenomeName

      public void setGenomeName(String genomeName)

    • getChromoID

      public String getChromoID()

    • setChromoID

      public void setChromoID(String chromoID)