org.systemsbiology.gaggle.geese.mev
Class GaggledMev

java.lang.Object
  MultipleArrayViewer
      org.systemsbiology.gaggle.geese.mev.GaggledMev

All Implemented Interfaces:

java.rmi.Remote, Goose

public class GaggledMev
extends MultipleArrayViewer
implements Goose

Constructor Summary

GaggledMev()

GaggledMev(MultipleArrayData data)

GaggledMev(MultipleArrayData data, MultipleArrayMenubar origMenubar)

Method Summary

void	clearSelections()
void	connectToGaggle()
void	doBroadcastList()
void	doExit() Tells the goose to exit (terminate).
void	doHide() Tells the goose to hide itself
void	doShow() Tells the goose to show itself
java.lang.String	getName() Returns the name of the goose.
int	getSelectionCount()
void	handleCluster(java.lang.String source, Cluster cluster) Called when the goose receives a Cluster object
void	handleCluster(java.lang.String species, java.lang.String[] geneNames, java.lang.String[] conditionNames)
void	handleMatrix(java.lang.String source, DataMatrix matrix) this, the GaggledMev implementation of Goose.handleMatrix () is inspired by the org/tigr/microarray/mev/file/StanfordFileLoader class.
void	handleNameList(java.lang.String source, Namelist nameList) Called when the goose receives a NameList object
void	handleNetwork(java.lang.String source, Network network) Called when the goose receives a Network object
void	handleTuple(java.lang.String source, GaggleTuple gaggleTuple) Called when the goose receives a GaggleTuple object
protected void	init()
static void	main(java.lang.String[] args)
void	setGeometry(int x, int y, int width, int height)
void	setName(java.lang.String newName) Sets the name of (renames) the goose.
protected void	showHelp()
void	storeOperationCluster(java.lang.String source, java.lang.String clusterID, int[] indices, boolean geneCluster) I hijack this standard MultipleArrayViewer method, called (perhaps among other places) from the 'broadcast' button listener I added to org/tigr/microarray/mev/SearchResultDialog.java.
void	update(java.lang.String[] gooseNames) Provides the goose with an updated list of the names of active geese.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GaggledMev

public GaggledMev()

GaggledMev

public GaggledMev(MultipleArrayData data)

GaggledMev

public GaggledMev(MultipleArrayData data,
                  MultipleArrayMenubar origMenubar)

Method Detail

storeOperationCluster

public void storeOperationCluster(java.lang.String source,
                                  java.lang.String clusterID,
                                  int[] indices,
                                  boolean geneCluster)

I hijack this standard MultipleArrayViewer method, called (perhaps among other places) from the 'broadcast' button listener I added to org/tigr/microarray/mev/SearchResultDialog.java.

init

protected void init()

connectToGaggle

public void connectToGaggle()

handleNameList

public void handleNameList(java.lang.String source,
                           Namelist nameList)

Description copied from interface: Goose

Called when the goose receives a NameList object

Specified by:

handleNameList in interface Goose

Parameters:

source - Optional string indicating name of source goose

nameList - The NameList object

handleNetwork

public void handleNetwork(java.lang.String source,
                          Network network)

Description copied from interface: Goose

Called when the goose receives a Network object

Specified by:

handleNetwork in interface Goose

Parameters:

source - Optional string indicating name of source goose

network - The Network object

handleCluster

public void handleCluster(java.lang.String source,
                          Cluster cluster)

Description copied from interface: Goose

Called when the goose receives a Cluster object

Specified by:

handleCluster in interface Goose

Parameters:

source - Optional string indicating name of source goose

cluster - The Cluster object

handleMatrix

public void handleMatrix(java.lang.String source,
                         DataMatrix matrix)

this, the GaggledMev implementation of Goose.handleMatrix () is inspired by the org/tigr/microarray/mev/file/StanfordFileLoader class. it reads a file of (typically) log10 ratio values, and returns a vector version of an array it constructs out of SlideData objects, one for each column found in the incoming data.

---- ISlideData [] slideDataArray = new ISlideData [experimentCount] slideDataArray [0] = new SlideData (rRows == spotCount == # of genes, rColumn=1); for (int i=1; i < slideDataArray.length; i++) { slideDataArray[i] = new FloatSlideData (slideDataArray[0].getSlideMetaData(), spotCount);

the above suggests that the 0th slideDataArray element is metadata and that 1-n+1 elements are the actual data

int experimentCount = ss.countTokens () + 1 - preExperimentColumns; // numerical columns + 1 slideDataArray = new ISlideData [experimentCount];

upon reading first row of file -- the title line -- these things occur, creating & initializing a structure to hold a column's worth (a condition) of data

slideDataArray = new ISlideData [experimentCount]; slideDataArray [0] = new SlideData (rRows == spotCount == # of genes, rColumn=1); slideDataArray [0].setSlideFileName (f.getPath()); for (int i=1; i < slideDataArray.length; i++) { slideDataArray[i] = new FloatSlideData (slideDataArray[0].getSlideMetaData(), spotCount); slideDataArray[i].setSlideFileName (f.getPath()); }

then, looping through all rows in the input matrix (or file) these things occur: a SlideDataElement 'sde' is created, and added to SlideDataArray [0] i am not sure what this accomplishes

then looping through the columns, slideDataArray [columnNumber].setIntensities (rowNumber, cy3=0, cy5=ration)

SlideDataElement sde: constructed with these arguments: String UID int [] rows int [] columns float [] intensities String [] values)

Vector slideDataList: a vector form of the slideDataArray

Specified by:

handleMatrix in interface Goose

Parameters:

source -

matrix -

handleTuple

public void handleTuple(java.lang.String source,
                        GaggleTuple gaggleTuple)

Description copied from interface: Goose

Called when the goose receives a GaggleTuple object

Specified by:

handleTuple in interface Goose

Parameters:

source - Optional string indicating name of source goose

gaggleTuple - The GaggleTuple object

handleCluster

public void handleCluster(java.lang.String species,
                          java.lang.String[] geneNames,
                          java.lang.String[] conditionNames)

getName

public java.lang.String getName()

Description copied from interface: Goose

Returns the name of the goose.

Specified by:

getName in interface Goose

Returns:

the name of the goose

setName

public void setName(java.lang.String newName)

Description copied from interface: Goose

Sets the name of (renames) the goose.

Specified by:

setName in interface Goose

Parameters:

newName - The new name of the goose

doHide

public void doHide()

Description copied from interface: Goose

Tells the goose to hide itself

Specified by:

doHide in interface Goose

doShow

public void doShow()

Description copied from interface: Goose

Tells the goose to show itself

Specified by:

doShow in interface Goose

clearSelections

public void clearSelections()

setGeometry

public void setGeometry(int x,
                        int y,
                        int width,
                        int height)

getSelectionCount

public int getSelectionCount()

doBroadcastList

public void doBroadcastList()

Specified by:

doBroadcastList in interface Goose

doExit

public void doExit()

Description copied from interface: Goose

Tells the goose to exit (terminate).

Specified by:

doExit in interface Goose

showHelp

protected void showHelp()

update

public void update(java.lang.String[] gooseNames)

Description copied from interface: Goose

Provides the goose with an updated list of the names of active geese. This list includes the name of the goose receiving the list.

Specified by:

update in interface Goose

Parameters:

gooseNames - the names of the currently active geese

See Also:

MiscUtil.updateGooseChooser(javax.swing.JComboBox gooseChooser, String callingGoose, String[] allGeese);

main

public static void main(java.lang.String[] args)