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Class PairwiseComparativeMap.PairwiseComparativeMap

java.lang.Object
   |
   +----java.awt.Component
           |
           +----java.awt.Container
                   |
                   +----java.awt.Panel
                           |
                           +----PairwiseComparativeMap.PairwiseComparativeMap

public class PairwiseComparativeMap

extends Panel

implements ActionListener, AdjustmentListener, ComponentListener

You can either create a PCM with a blank constructor and feed in the data later, or do them both at the same time. A BeanInfo class is available for this class so you can use it in a Java IDE.

Version:

1.0

Author:

Written by Jeremy Dickson for the UK Crop Plant Bioinformatics Network, October 1998.

See Also:

PCM_FileParser, MultiPCM

FILE_PATH_TYPE_FILE

File path to parse is a local file.

FILE_PATH_TYPE_URL

File path to parse corresponds to a URL.

PairwiseComparativeMap()

Default constructor.

PairwiseComparativeMap(String, int)

This constructor accepts a reference to a .pcm file and processes the data within to create the PCM.

actionPerformed(ActionEvent)

addActionListener(ActionListener)

Add an action listener.

addData(PairwiseComparativeMapData, Array)

Add data to the component by passing in the preformed datastructure.

addData(String, int)

Add data to component via a PCM file.

adjustmentValueChanged(AdjustmentEvent)

This method is called when the user moves the scrollbar.

clickInAdjacentMap(String)

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.

componentAdded(ContainerEvent)

Not used.

componentHidden(ComponentEvent)

Not used.

componentMoved(ComponentEvent)

Not used.

componentRemoved(ContainerEvent)

Not used.

componentResized(ComponentEvent)

Used when the user resizes the component.

componentShown(ComponentEvent)

Not used.

getDatabaseColour_1()

Returns the colour that the sausages from the first database encountered in the data will be painted.

getDatabaseColour_2()

Returns the colour that the sausage from the second database encountered in the data will be painted.

getPCM_File()

Returns the file path or URL to the file that the component is to parse.

getPCMDataObject()

getSausageLength_LHS()

Returns the length of the chromosome on the default left-hand side of the map in units of pixels.

getSausageLength_RHS()

Returns the length of the chromosome on the default right-hand side of the map in units of pixels.

isCrossLinkToDatabase()

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..

jbInit()

This is a residual JBuilder class that sets up things like buttons etc.

processActionEvent(ActionEvent)

removeActionListener(ActionListener)

Remove an action listener.

setCrossLinkToDatabase(boolean)

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)

Sets the colour that the sausages from the first database encountered in the data will be painted.

setDatabaseColour_2(Color)

Returns the colour that the sausage from the second database encountered in the data will be painted.

setPCM_File(String)

Sets the file path or URL to the file that the component is to parse.

setSausageColourToDatabase(String, Color)

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)

Sets the length of the chromosome on the default left-hand side of the map in units of pixels.

setSausageLength_RHS(int)

Sets the length of the chromosome on the default left-hand side of the map in units of pixels.

 public static final int FILE_PATH_TYPE_FILE

File path to parse is a local file.

 public static final int FILE_PATH_TYPE_URL

File path to parse corresponds to a URL.

 public PairwiseComparativeMap()

Default constructor.

 public PairwiseComparativeMap(String filePath,
                               int filePathType)

This constructor accepts a reference to a .pcm file and processes the data within to create the PCM.

Parameters:

filePath - A file path or URL to the .pcm file which you wish to use as a data source.

filePathType - This is an int that describes whether you wish to parse a file from a URL (1) or a file path from a local drive (0). You can use the variables FILE_PATH_TYPE_FILE and FILE_PATH_TYPE_URL for this purpose.

 public void addData(String filePath,
                     int FilePathType)

Add data to component via a PCM file.

Parameters:

filePath - A file path or URL to the .pcm file which you wish to use as a data source.

filePathType - This is an int that describes whether you wish to parse a file from a URL (1) or a file path from a local drive (0). You can use the variables FILE_PATH_TYPE_FILE and FILE_PATH_TYPE_URL for this purpose.

 public void addData(PairwiseComparativeMapData data,
                     Array homologys) throws PCMFileParsingException

Add data to the component by passing in the preformed datastructure. It is preferable to use a pcm file and the PCM_FileParser instead.

Parameters:

data - The data structure that the map uses.

homologys - An array of String[2] arrays describing the pairwise relationships. The string arrays should contain the names of a locus on either side of the map you wish to make a relationship between. Omit from the array any loci with no homolog on the other side.

 public void setSausageColourToDatabase(String databaseName,
                                        Color color)

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. Get a list of all the database names across the maps and then call this method in each map for every database name feeding in a different colour each time.

 public void clickInAdjacentMap(String locusName)

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.

Parameters:

locusName - The name of the locus.

 public void jbInit() throws Exception

This is a residual JBuilder class that sets up things like buttons etc. when the class is created. Who am I to delete it?!

 public void actionPerformed(ActionEvent e)

 public void adjustmentValueChanged(AdjustmentEvent parm1)

This method is called when the user moves the scrollbar.

 public void componentAdded(ContainerEvent parm1)

Not used.

 public void componentRemoved(ContainerEvent parm1)

Not used.

 public void componentResized(ComponentEvent parm1)

Used when the user resizes the component.

 public void componentMoved(ComponentEvent parm1)

Not used.

 public void componentShown(ComponentEvent parm1)

Not used.

 public void componentHidden(ComponentEvent parm1)

Not used.

 public PairwiseComparativeMapData getPCMDataObject()

 public Color getDatabaseColour_1()

Returns the colour that the sausages from the first database encountered in the data will be painted.

 public void setDatabaseColour_1(Color databaseColour_1)

Sets the colour that the sausages from the first database encountered in the data will be painted.

 public Color getDatabaseColour_2()

Returns the colour that the sausage from the second database encountered in the data will be painted.

 public void setDatabaseColour_2(Color databaseColour_2)

Returns the colour that the sausage from the second database encountered in the data will be painted.

 public String getPCM_File()

Returns the file path or URL to the file that the component is to parse.

 public void setPCM_File(String PCM_File)

Sets the file path or URL to the file that the component is to parse.

 public boolean isCrossLinkToDatabase()

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..

 public void setCrossLinkToDatabase(boolean crossLinkToDatabase)

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..

 public int getSausageLength_LHS()

Returns the length of the chromosome on the default left-hand side of the map in units of pixels.

 public void setSausageLength_LHS(int sausageLength_LHS)

Sets the length of the chromosome on the default left-hand side of the map in units of pixels.

 public int getSausageLength_RHS()

Returns the length of the chromosome on the default right-hand side of the map in units of pixels.

 public void setSausageLength_RHS(int sausageLength_RHS)

Sets the length of the chromosome on the default left-hand side of the map in units of pixels.

 public synchronized void addActionListener(ActionListener l)

Add an action listener.

 public synchronized void removeActionListener(ActionListener l)

Remove an action listener.

 protected void processActionEvent(ActionEvent e)

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