All Packages  Class Hierarchy

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Index of all Fields and Methods

A

actionPerformed(ActionEvent). Method in class PairwiseComparativeMap.MapResizeDialog
actionPerformed(ActionEvent). Method in class PairwiseComparativeMap.MultiPCM: Deals with the action when a click occurs on any of the maps.
actionPerformed(ActionEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap
addActionListener(ActionListener). Method in class PairwiseComparativeMap.PairwiseCanvas: Add an action listener.
addActionListener(ActionListener). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Add an action listener.
addData(PairwiseComparativeMapData, Array). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Add data to the component by passing in the preformed datastructure.
addData(String, int). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Add data to component via a PCM file.
addData(String[], boolean). Method in class PairwiseComparativeMap.MultiPCM: Allows you to add data to the component.
addLocusToHomologyGroup(int, LocusNoAndMap). Method in class PairwiseComparativeMap.PairwiseHomologys: Adds a locus to a homology group.
adjustmentValueChanged(AdjustmentEvent). Method in class PairwiseComparativeMap.MapResizeDialog: Scrollbar uses this.
adjustmentValueChanged(AdjustmentEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap: This method is called when the user moves the scrollbar.

C

calculateLociPsns(boolean, boolean, int, int, FontMetrics). Method in class PairwiseComparativeMap.PairwiseMap: This method calculates where all the ticks corresponding to the loci positions should be drawn and where the locus labels should also be drawn.
calculateScaleBarData(int). Method in class PairwiseComparativeMap.PairwiseMap: This method determines how often to draw a tick on the map and by how much to increment the scalebar label.
clickInAdjacentMap(String). Method in class PairwiseComparativeMap.PairwiseCanvas: This method is called when there is a click in a pairwise map that is sitting adjacent to this one and there has been a click in it.
clickInAdjacentMap(String). Method in class PairwiseComparativeMap.PairwiseComparativeMap: This is used by MultiPCM when there's been a click in an adjacent map to highlight any loci in this map of the same name.
colour. Variable in class PairwiseComparativeMap.Line: The colour of the line 1=black, 2=red, 3=lightGray.
componentAdded(ContainerEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Not used.
componentHidden(ComponentEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Not used.
componentMoved(ComponentEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Not used.
componentRemoved(ContainerEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Not used.
componentResized(ComponentEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Used when the user resizes the component.
componentShown(ComponentEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Not used.
createNewHomologyGroup(LocusNoAndMap, LocusNoAndMap). Method in class PairwiseComparativeMap.PairwiseHomologys: Adds a new homology group to the data structure.

D

doesLocusMatch(LocusNoAndMap). Method in class PairwiseComparativeMap.LocusNoAndMap: Returns true if the input LocusNoAndMap object matches the LocusNoAndMap object.
drawHomologys(Array, PairwiseMap, PairwiseMap, int, int). Method in class PairwiseComparativeMap.PairwiseHomologys: This method called by the PairwiseCanvas class and creates a set of Line objects in an Array that represent the lines between the two maps in the PCM.

F

FILE_PATH_TYPE_FILE. Static variable in class PairwiseComparativeMap.PairwiseComparativeMap: File path to parse is a local file.
FILE_PATH_TYPE_URL. Static variable in class PairwiseComparativeMap.PairwiseComparativeMap: File path to parse corresponds to a URL.

G

getCompleteMapSize(). Method in class PairwiseComparativeMap.PairwiseCanvas: Returns the complete size of the pairwise comparative map, not just the viewport size.
getDatabaseColour_1(). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Returns the colour that the sausages from the first database encountered in the data will be painted.
getDatabaseColour_2(). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Returns the colour that the sausage from the second database encountered in the data will be painted.
getDatabaseName(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the database name.
getDatabaseURL(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the database URL.
getHighlightedHomologyGroup(LocusNoAndMap). Method in class PairwiseComparativeMap.PairwiseHomologys: Checks the LocusNoAndMap object passed in to the method to see if this is contained within any homology groups.
getHomologyGroupNumber(LocusNoAndMap). Method in class PairwiseComparativeMap.PairwiseHomologys: Takes in a LocusNoAndMap object and see if it already exists in one of the homology groups that this class holds.
getIcon(int). Method in class PairwiseComparativeMap.MultiPCMBeanInfo
getIcon(int). Method in class PairwiseComparativeMap.PairwiseComparativeMapBeanInfo: Returns the images for PairwiseComparativeMap, a 32x32 pixel and a 16x16 pixel image are available.
getLabelScreenPsn(). Method in class PairwiseComparativeMap.PairwiseLocus: Gets the area of the label on screen.
getLHS_map(). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: Returns the map on the left-hand side.
getLocus(int). Method in class PairwiseComparativeMap.PairwiseMap: The index of a locus in the locus array is fed in.
getLocusArray(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the array of PairwiseLocus objects.
getLocusDatabaseClass(). Method in class PairwiseComparativeMap.PairwiseLocus: Return the database class of the locus.
getLocusLocationInArray(String). Method in class PairwiseComparativeMap.PairwiseMap: Tests to see if there's is a locus within the map with the same name as passed in to the method.
getLocusName(). Method in class PairwiseComparativeMap.PairwiseLocus: Returns the name of the locus.
getLocusNo(). Method in class PairwiseComparativeMap.LocusNoAndMap: Returns the locus index in the loci array.
getLocusPosition(). Method in class PairwiseComparativeMap.PairwiseLocus: Returns the position of the locus on the map.
getLocusTickScreenPsn(). Method in class PairwiseComparativeMap.PairwiseLocus: Gets the screen position of the tick on the map sausage.
getLowestLabel_y_position(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the y position of the lowest locus label in the map.
getMapExtentFrom(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the lower level of the map scale extent.
getMapExtentTo(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the upper level of the map scale extent.
getMapSausageColour(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the colour of the map sausage.
getMapScreenLength(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the screen length of the map.
getMapTitle(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the map title.
getMapTitleScreenPsn(). Method in class PairwiseComparativeMap.PairwiseMap: Sets the on-screen co-ordinates of the title label.
getMapUnits(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the map units.
getMax_ScaleBarLabel_Length(FontMetrics). Method in class PairwiseComparativeMap.PairwiseMap: Returns the maximum pixel length of the labels that appear on the scale bar.
getPairwiseHomologys(). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: Returns the PairwiseHomologys object.
getPCM_File(). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Returns the file path or URL to the file that the component is to parse.
getPCMDataObject(). Method in class PairwiseComparativeMap.PairwiseComparativeMap
getPosition_AsString(). Method in class PairwiseComparativeMap.PairwiseLocus: Returns a string representation of the locus position.
getPropertyDescriptors(). Method in class PairwiseComparativeMap.MultiPCMBeanInfo
getPropertyDescriptors(). Method in class PairwiseComparativeMap.PairwiseComparativeMapBeanInfo: Returns the properties for PairwiseComparativeMap.
getRHS_map(). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: Returns the map on the right-hand side.
getSausageLength_LHS(). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Returns the length of the chromosome on the default left-hand side of the map in units of pixels.
getSausageLength_RHS(). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Returns the length of the chromosome on the default right-hand side of the map in units of pixels.
getScaleBar_LabelIncrement(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the increment in each label along the scale bar.
getScaleBar_PixelIncrement(). Method in class PairwiseComparativeMap.PairwiseMap: Returns the distance in pixels between each scalebar tick.
getUnitsScreenPsn(). Method in class PairwiseComparativeMap.PairwiseMap: Sets the on-screen co-ordinates of the units label.
getURL(int). Method in class PairwiseComparativeMap.PairwiseMap: Returns the URL to a webACE database to a particular locus.
getValue(). Method in class PairwiseComparativeMap.MapResizeDialog: Returns the new value.

H

height. Variable in class PairwiseComparativeMap.PairwiseRectangle: Coordinate.
highlighted. Variable in class PairwiseComparativeMap.ScreenString: Whether the string is to be highlighted.
highlightLocus(int). Method in class PairwiseComparativeMap.PairwiseMap: The index of a locus in the locus array is fed in.

I

invertMap(boolean). Method in class PairwiseComparativeMap.PairwiseCanvas: Inverts a map- draws it upside down.
isCrossLinkToDatabase(). Method in class PairwiseComparativeMap.PairwiseComparativeMap: When set to true, a double-click on a locus will fire off an action event to component listeners containing the URL to the database..
isHighlighted(). Method in class PairwiseComparativeMap.PairwiseLocus: Returns whether the locus is highlighted or not.
isLocusNameInAMap(String). Method in class PairwiseComparativeMap.PairwiseMap: Checks out whether a locus name is in a map.
isMouseInALocus(int, int). Method in class PairwiseComparativeMap.PairwiseMap: Finds out whether the mouse co-ordinates are within a PairwiseLocus object that is held within the map object.
isMouseInLocus(int, int). Method in class PairwiseComparativeMap.PairwiseLocus: Returns true if the x and y co-ordinates are within the rectangular area in which the label is found.
isOnLHS(). Method in class PairwiseComparativeMap.LocusNoAndMap: Returns whether the locus is on the left-hand side map.
isSingleMap(). Method in class PairwiseComparativeMap.PairwiseCanvas: Returns true if there is only one chromosomal map and false if there are two.

J

jbInit(). Method in class PairwiseComparativeMap.PairwiseComparativeMap: This is a residual JBuilder class that sets up things like buttons etc.

L

Line(int, int, int, int, byte). Constructor for class PairwiseComparativeMap.Line: Default constructor.
locusFont. Variable in class PairwiseComparativeMap.ScreenString: Whether the same font is used to draw the string as is for the loci labels
LocusNoAndMap(int, boolean). Constructor for class PairwiseComparativeMap.LocusNoAndMap: Default constructor.
longestLabelInMap(FontMetrics). Method in class PairwiseComparativeMap.PairwiseMap: Goes through all the PairwiseLocus objects in the map and returns a value corresponding to the longest locus label that is encountered.

M

MapResizeDialog(Frame, String, int). Constructor for class PairwiseComparativeMap.MapResizeDialog: Default constructor
mergeHomologyGroups(int, int). Method in class PairwiseComparativeMap.PairwiseHomologys: This method merges the two homology groups in the data structure at the homologyGroup_LHS and homologyGroup_RHS indexes
mouseClicked(MouseEvent). Method in class PairwiseComparativeMap.PairwiseCanvas: Called when there's a mouse click on the canvas.
mouseEntered(MouseEvent). Method in class PairwiseComparativeMap.PairwiseCanvas: Not used.
mouseExited(MouseEvent). Method in class PairwiseComparativeMap.PairwiseCanvas: Not used.
mousePressed(MouseEvent). Method in class PairwiseComparativeMap.PairwiseCanvas: Not used.
mouseReleased(MouseEvent). Method in class PairwiseComparativeMap.PairwiseCanvas: Not used.
MultiPCM(). Constructor for class PairwiseComparativeMap.MultiPCM
MultiPCM(String[], boolean). Constructor for class PairwiseComparativeMap.MultiPCM: Constructor that creates the maps.
MultiPCMBeanInfo(). Constructor for class PairwiseComparativeMap.MultiPCMBeanInfo

O

onLHS. Variable in class PairwiseComparativeMap.PairwiseRectangle: Whether the rectanlgle is on the LHS map.

P

paint(Graphics). Method in class PairwiseComparativeMap.PairwiseCanvas
PairwiseCanvas(Dimension). Constructor for class PairwiseComparativeMap.PairwiseCanvas: Default constructor.
PairwiseCanvas(PairwiseComparativeMapData, Dimension). Constructor for class PairwiseComparativeMap.PairwiseCanvas: Pass in the PairwiseComparativeMapData object to process.
pairwiseCanvasResized(Dimension). Method in class PairwiseComparativeMap.PairwiseCanvas: Called when the viewport window size is changed.
PairwiseComparativeMap(). Constructor for class PairwiseComparativeMap.PairwiseComparativeMap: Default constructor.
PairwiseComparativeMap(String, int). Constructor for class PairwiseComparativeMap.PairwiseComparativeMap: This constructor accepts a reference to a .pcm file and processes the data within to create the PCM.
PairwiseComparativeMapBeanInfo(). Constructor for class PairwiseComparativeMap.PairwiseComparativeMapBeanInfo
PairwiseComparativeMapData(PairwiseMap, PairwiseMap). Constructor for class PairwiseComparativeMap.PairwiseComparativeMapData: Default constructor.
PairwiseComparativeMapData(PairwiseMap, PairwiseMap, PairwiseHomologys). Constructor for class PairwiseComparativeMap.PairwiseComparativeMapData: This constructor allows you to enter the PairwiseHomologys object yourself.
PairwiseHomologys(). Constructor for class PairwiseComparativeMap.PairwiseHomologys: Default constructor
PairwiseLocus(String, float). Constructor for class PairwiseComparativeMap.PairwiseLocus: Default constructor describing the minimum amount of data needed to create class
PairwiseLocus(String, float, String). Constructor for class PairwiseComparativeMap.PairwiseLocus: This constructor takes in a bit more information.
PairwiseMap(Array, String, String, int, int). Constructor for class PairwiseComparativeMap.PairwiseMap: Default constructor that takes in the minimum amount of information to create a PairwiseMap.
PairwiseMap(Array, String, String, int, int, String, String). Constructor for class PairwiseComparativeMap.PairwiseMap: This constructor takes in a bit more information that is not mandatory but adds more functionality.
PairwiseRectangle(boolean, int, int, int, int). Constructor for class PairwiseComparativeMap.PairwiseRectangle: Default constructor.
parseFile(). Method in class PairwiseComparativeMap.PCM_FileParser: Call this method to parse a file.
PCM_FileParser(BufferedReader). Constructor for class PairwiseComparativeMap.PCM_FileParser: Default constructor.
PCMFileParsingException(). Constructor for class PairwiseComparativeMap.PCMFileParsingException: Default constructor.
PCMFileParsingException(String). Constructor for class PairwiseComparativeMap.PCMFileParsingException: Constructor takes in a string containing the exception message.
processActionEvent(ActionEvent). Method in class PairwiseComparativeMap.PairwiseCanvas
processActionEvent(ActionEvent). Method in class PairwiseComparativeMap.PairwiseComparativeMap
processData(PairwiseComparativeMapData). Method in class PairwiseComparativeMap.PairwiseCanvas: Processes data for presentation on screen.
processHomologys(Array). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: This method creates the data necessary to describe the homologys between the two maps.

R

removeActionListener(ActionListener). Method in class PairwiseComparativeMap.PairwiseCanvas: Remove an action listener.
removeActionListener(ActionListener). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Remove an action listener.
resizeSausage(boolean, int). Method in class PairwiseComparativeMap.PairwiseCanvas: Sets the size of a map sausage.

S

ScreenString(String, int, int, boolean, boolean). Constructor for class PairwiseComparativeMap.ScreenString: Default constructor.
scrollMap(int). Method in class PairwiseComparativeMap.PairwiseCanvas: When the user wants to scroll down the map this method is called.
setCrossLinkToDatabase(boolean). Method in class PairwiseComparativeMap.PairwiseComparativeMap: When set to true, a double-click on a locus will fire off an action event to component listeners containing the URL to the database..
setDatabaseColour_1(Color). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Sets the colour that the sausages from the first database encountered in the data will be painted.
setDatabaseColour_2(Color). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Returns the colour that the sausage from the second database encountered in the data will be painted.
setHighlighted(boolean). Method in class PairwiseComparativeMap.PairwiseLocus: Sets whether the locus is highlighted or not.
setLabelScreenPsn(Rectangle). Method in class PairwiseComparativeMap.PairwiseLocus: Sets the area of the label on screen.
setLHS_Map(PairwiseMap). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: Sets the map on the left-hand side.
setLocusTickScreenPsn(int). Method in class PairwiseComparativeMap.PairwiseLocus: Sets the screen position of the tick on the map sausage.
setMapSausageColour(Color). Method in class PairwiseComparativeMap.PairwiseMap: Sets the colour of the map sausage.
setMapScreenLength(int). Method in class PairwiseComparativeMap.PairwiseMap: Sets the screen length of the map.
setMapTitleScreenPsn(Rectangle). Method in class PairwiseComparativeMap.PairwiseMap: Gets the on-screen co-ordinates of the title label.
setPCM_File(String). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Sets the file path or URL to the file that the component is to parse.
setRHS_Map(PairwiseMap). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: Sets the map on the left-hand side.
setSausageColour1(Color). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: Sets the colour of the sausages of the first database to be encountered in the data
setSausageColour2(Color). Method in class PairwiseComparativeMap.PairwiseComparativeMapData: Sets the colour of the sausages of the second database to be encountered in the data
setSausageColourToDatabase(String, Color). Method in class PairwiseComparativeMap.PairwiseComparativeMap: This method can be called if you have a number of Pairwise maps linked together and you want to standardise the colours of the sausages for a particular database.
setSausageLength_LHS(int). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Sets the length of the chromosome on the default left-hand side of the map in units of pixels.
setSausageLength_RHS(int). Method in class PairwiseComparativeMap.PairwiseComparativeMap: Sets the length of the chromosome on the default left-hand side of the map in units of pixels.
setScaleBar_LabelIncrement(int). Method in class PairwiseComparativeMap.PairwiseMap: Sets the increment in each label along the scale bar.
setScaleBar_PixelIncrement(int). Method in class PairwiseComparativeMap.PairwiseMap: Sets the distance in pixels between each scalebar tick.
setUnitsScreenPsn(Rectangle). Method in class PairwiseComparativeMap.PairwiseMap: Gets the on-screen co-ordinates of the units label.
string. Variable in class PairwiseComparativeMap.ScreenString: The string
swapMaps(). Method in class PairwiseComparativeMap.PairwiseCanvas: Swaps the maps.

T

trimArrays(). Method in class PairwiseComparativeMap.PairwiseHomologys: Trims the array data structure so to minimize on the space it uses.

U

unhighlightLocus(int). Method in class PairwiseComparativeMap.PairwiseMap: The index of a locus in the locus array is fed in.
update(Graphics). Method in class PairwiseComparativeMap.PairwiseCanvas

V

verifyMapData(). Method in class PairwiseComparativeMap.PairwiseMap: This method is used when the programmer feeds in the actual data objects themselves rather than using the standard file parser.

W

width. Variable in class PairwiseComparativeMap.PairwiseRectangle: Coordinate.
windowActivated(WindowEvent). Method in class PairwiseComparativeMap.MapResizeDialog
windowClosed(WindowEvent). Method in class PairwiseComparativeMap.MapResizeDialog
windowClosing(WindowEvent). Method in class PairwiseComparativeMap.MapResizeDialog
windowDeactivated(WindowEvent). Method in class PairwiseComparativeMap.MapResizeDialog
windowDeiconified(WindowEvent). Method in class PairwiseComparativeMap.MapResizeDialog
windowIconified(WindowEvent). Method in class PairwiseComparativeMap.MapResizeDialog
windowOpened(WindowEvent). Method in class PairwiseComparativeMap.MapResizeDialog

X

x. Variable in class PairwiseComparativeMap.PairwiseRectangle: Coordinate.
x. Variable in class PairwiseComparativeMap.ScreenString: The x coordinates
x1. Variable in class PairwiseComparativeMap.Line: Coordinate.
x2. Variable in class PairwiseComparativeMap.Line: Coordinate.

Y

y. Variable in class PairwiseComparativeMap.PairwiseRectangle: Coordinate.
y. Variable in class PairwiseComparativeMap.ScreenString: The y coordinate.
y1. Variable in class PairwiseComparativeMap.Line: Coordinate.
y2. Variable in class PairwiseComparativeMap.Line: Coordinate.