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Index of all Fields and Methods

A

addActionListener(ActionListener). Method in class CPGMap.CPGMap

C

convertString(double, boolean). Method in class CPGMap.CPGMapUtilities: Converts a double in to the appropriate format to be displayed on the scale bar.
CPG_File(String). Method in class CPGMap.FileParser
CPG_Locus(). Constructor for class CPGMap.CPG_Locus: Empty constructor
CPG_Locus(String, double, double, double, double, String, int[]). Constructor for class CPGMap.CPG_Locus: Constructor for loci making up a double map.
CPG_Locus(String, double, double, String, int[]). Constructor for class CPGMap.CPG_Locus: Constructor for loci making up a single map.
CPGMap(). Constructor for class CPGMap.CPGMap: Initialises an instance of the class but does not create any maps or graphical representation; 'HeresSomeData()' has to be called.
CPGMapUtilities(boolean, int). Constructor for class CPGMap.CPGMapUtilities: Creates an instance of the class and itialises the variables passed to it as local
createHomologyData(Vector). Method in class CPGMap.CPGMapUtilities: This method takes the data describing the maps and accesses the homology group data variable of each CPG_Locus.

F

FileParser(). Constructor for class CPGMap.FileParser
findTheMinimumAndRangeOfTheMaps(Vector, FontMetrics). Method in class CPGMap.CPGMapUtilities: Finds the minimum and range in loci positions for each map and stores the results in an array of doubles.
fullNumbersToggle(). Method in class CPGMap.CPGMap

G

getBackgroundColour(). Method in class CPGMap.CPGMap: Returns the background colour of the canvas.
getBoxSize(). Method in class CPGMap.CPGMap: Returns the size of the little boxes drawn beside the loci labels.
getColour(Color). Method in class CPGMap.CPG_Locus
getDoubleMapData(). Method in class CPGMap.FileParser
getError1(). Method in class CPGMap.CPG_Locus: Returns the error of position 1
getError2(). Method in class CPGMap.CPG_Locus: Returns the error of position 2.
getErrorBarsOn(). Method in class CPGMap.CPGMap: Returns whether the error bars are turned on or not
getErrorSausageColour(). Method in class CPGMap.CPGMap: Returns the colour of the error bars drawn over the sausages.
getFullNumbers(). Method in class CPGMap.CPGMap: Returns whether the numbers shown along the scale bar are shown as the complete numbers or as exponents.
getHighlightedLocus(). Method in class CPGMap.CPGMap
getHomologyGroup(). Method in class CPGMap.CPG_Locus: Returns a string representation of the homology group.
getIntCodeOfColour(). Method in class CPGMap.CPG_Locus
getLabelFont(). Method in class CPGMap.CPGMap: Returns the font used on the labels and titles.
getLineAndBoxColour(). Method in class CPGMap.CPGMap: Returns the colour of the lines, little boxes and labels.
getLineDistance(). Method in class CPGMap.CPGMap: Returns the length of the distance between the sausages and the little boxes.
getLocusOwns(). Method in class CPGMap.CPG_Locus: Returns the locusOwns array, the array describing the other loci in the map that the locus is homologous to .
getMapSeparationDistance(). Method in class CPGMap.CPGMap: Returns the value of the distance between adjacent maps.
getMapTitles(). Method in class CPGMap.CPGMap: Returns a list of the map titles.
getMaximumMagnification(int[], int[]). Method in class CPGMap.CPGMapUtilities: Returns the value of the maximum size of a map in the current data set.
getMaxNumbersInLabel(). Method in class CPGMap.CPGMap: Returns the maximum number of digits shown in a label.
getMouseMotionSensitive(). Method in class CPGMap.CPGMap: Returns whether mouseMotionSensitive.
getName(). Method in class CPGMap.CPG_Locus: Returns the name of the locus.
getNoOfMaps(). Method in class CPGMap.CPGMap: Returns the number of maps.
getPosition1(). Method in class CPGMap.CPG_Locus: Returns position 1.
getPosition2(). Method in class CPGMap.CPG_Locus: Returns position 2.
getSausageColour(). Method in class CPGMap.CPGMap: Returns the colour of the map sausages.
getSausageWidth(). Method in class CPGMap.CPGMap: Returns the width of the sausages.
getTextArea(). Method in class CPGMap.CPG_Locus: Returns a rectangle object corresponding to the area on the screen occupied by the locus label.
getTitles(). Method in class CPGMap.FileParser
getUnits(). Method in class CPGMap.FileParser
getUnitsLHS(). Method in class CPGMap.CPGMap: Retuns the units appering at the top of the maps on the left-hand side maps.
getUnitsRHS(). Method in class CPGMap.CPGMap: Returns the units appering at the top of the maps on the right-hand side maps.
getXLabelPosition(). Method in class CPGMap.CPG_Locus: Returns the x co-ordinate of the locus label
getYHeaderToMapDistance(). Method in class CPGMap.CPGMap: Returns the distance from the top of the canvas to where the maps are drawn.
getYLabelPosition(). Method in class CPGMap.CPG_Locus: Returns the y co-ordinate of the locus label

H

heresSomeData(boolean, Vector, String[]). Method in class CPGMap.CPGMap: This is the method that is called to make double/sinlge maps out of a set of data.

I

isDoubleMapData(). Method in class CPGMap.CPGMap: Returns whether the data passed to the component is describes double maps or not.
isFullNumbers(boolean). Method in class CPGMap.CPGMap: Sets whether the numbers shown along the scale bar are shown as the complete numbers or as exponents.
isMouseMotionSensitive(boolean). Method in class CPGMap.CPGMap: Changes the mouse user-interaction mode of the component.
isPointWithinLocus(int, int, int). Method in class CPGMap.CPG_Locus: Returns whether or not the clicked point on the screen was within the bounds of the label area.

M

MapAndLocusNumber(). Constructor for class CPGMap.MapAndLocusNumber
MapAndLocusNumber(int, int). Constructor for class CPGMap.MapAndLocusNumber
MapAndLocusNumber(Point). Constructor for class CPGMap.MapAndLocusNumber
mouseClicked(MouseEvent). Method in class CPGMap.CPGMap: Called when the canvas is activated with the mouse if 'mouseMotionSensitive' is set to false.
mouseDragged(MouseEvent). Method in class CPGMap.CPGMap: Part of interface, not used.
mouseEntered(MouseEvent). Method in class CPGMap.CPGMap: Part of interface, not used.
mouseExited(MouseEvent). Method in class CPGMap.CPGMap: Part of interface, not used.
mouseMoved(MouseEvent). Method in class CPGMap.CPGMap: Called when the canvas is activated with the mouse if 'mouseMotionSensitive' is set to true.
mousePressed(MouseEvent). Method in class CPGMap.CPGMap: Part of interface, not used.
mouseReleased(MouseEvent). Method in class CPGMap.CPGMap: Part of interface, not used.

P

paint(Graphics). Method in class CPGMap.CPGMap: Draws the maps on the Graphics object.
processActionEvent(ActionEvent). Method in class CPGMap.CPGMap

R

removeActionListener(ActionListener). Method in class CPGMap.CPGMap
resetMapAndLocus(int, int). Method in class CPGMap.MapAndLocusNumber

S

setBackgroundColour(Color). Method in class CPGMap.CPGMap: Sets the background colour of the canvas.
setBoxSize(int). Method in class CPGMap.CPGMap: Sets the size of the little boxes drawn beside the loci labels.
setColour(int). Method in class CPGMap.CPG_Locus: Called when the locus is highlight.
setColourCascade(int, Vector, Vector, MapAndLocusNumber). Method in class CPGMap.CPGMapUtilities: This method changes the 'colour' of a particular locus by resetting the colour value of the locus.
setErrorBarsOn(boolean). Method in class CPGMap.CPGMap: Sets whether the error bars are turned on or not.
setErrorSausageColour(Color). Method in class CPGMap.CPGMap: Sets the colour of the error bars drawn over the sausages.
setLabelFont(Font). Method in class CPGMap.CPGMap: Sets the font used on the labels and titles.
setLineAndBoxColour(Color). Method in class CPGMap.CPGMap: Sets the colour of the lines, little boxes and labels.
setLineDistance(int). Method in class CPGMap.CPGMap: Sets the distance between the sausages and the little boxes.
setMagnification(int[]). Method in class CPGMap.CPGMap: This method is called when the user wishes to change the values of the magnification of the maps.
setMapSeparationDistance(int). Method in class CPGMap.CPGMap: Sets the distance between two adjacent maps.
setMapTitles(String[]). Method in class CPGMap.CPGMap: Sets the titles of the maps.
setMaxNumbersInLabel(int). Method in class CPGMap.CPGMap: Sets the maximum number of digits shown in a label.
setRectangularLabelArea(int, int, int, int). Method in class CPGMap.CPG_Locus: Sets a local rectangle object to a value directly corresponding to the area on the screen occupied by the locus label.
setSausageColour(Color). Method in class CPGMap.CPGMap: Sets the colour of the map sausages.
setSausageWidth(int). Method in class CPGMap.CPGMap: Sets the width of the map sausages.
setUnitsLHS(String). Method in class CPGMap.CPGMap: Sets the units appering at the top of the maps on the left-hand side maps.
setUnitsRHS(String). Method in class CPGMap.CPGMap: Sets the units appering at the top of the maps on the right-hand side maps.
setYHeaderToMapDistance(int). Method in class CPGMap.CPGMap: Sets the distance from the top of the canvas to where the maps are drawn.

T

toggleErrorBarsOn(). Method in class CPGMap.CPGMap: Toggles the error bars between being on and off.
toggleMouseMotionSensitive(). Method in class CPGMap.CPGMap

U

undoLastZoom(). Method in class CPGMap.CPGMap: Returns the sizes of the AWT components to the last zoom values.
undoZoomToDefaults(). Method in class CPGMap.CPGMap: Returns the the sizes of the AWT components to the program defaults.
update(Graphics). Method in class CPGMap.CPGMap: Overrides the paint method when making a buffered image.

W

whichLocus(). Method in class CPGMap.MapAndLocusNumber
whichMap(). Method in class CPGMap.MapAndLocusNumber
whoWasClicked(Vector, int, int). Method in class CPGMap.CPGMapUtilities: Finds out from the mouse coordinates which particular locus, if any, was clicked.