Class StageNames

java.lang.Object
  |
  +--StageNames

class StageNames

extends java.lang.Object

The class sets up staging names for building menus and sample labels. These sample labels are used in variousplots and reports. The stage names reflects the structure of SamplesDB.txt:Menu_Stage_Name entries which are saved in menuNames[] and are used later to build the Samples menu trees. We build the mae.hps.topSubMenuNames[] list from these entries if any. The staging data is contained in the SamplesDB.txt Table and the snXXXX[sample#] results are in the mae.snXXX[] arrays.

The use of the PopupHPChooser is the preferred method as it is easier to navigate than the menus.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2002/12/11 17:23:27 $ $Revision: $

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home

Field Summary

(package private) StageNames[]	HPmnuEntry list of menus that the entry belongs to
(package private) int	hpNbr idx of mae.snHPNames[]
(package private) int	menuJ index for menuNames[]
(package private) java.lang.String[]	menuNames List unique menu name entries for various entities in Samples tbl
(package private) int	nHPmnuEntries # of menu entries
(package private) int	nmenuNames # unique menu name entries in Samples tbl
(package private) int	nprobeNames # unique probe name entries in Samples tbl
(package private) int	nsourceNames # unique source name entries in Samples tbl
(package private) int	nstageNames # unique stage name entries in Samples tbl
(package private) int	nstrainNames # unique strain name entries in Samples tbl
(package private) int	probeJ index for probeNames[]
(package private) java.lang.String[]	probeNames List unique probe name entries for various entities in Samples tbl
(package private) int	sampleDBrow row of membrane table
(package private) int	sourceJ index for sourceNames[]
(package private) java.lang.String[]	sourceNames List unique source name entries for various entities in Samples tbl
(package private) int	stageJ index for stageNames[]
(package private) java.lang.String	stageLabel itemLabel to be used in menu
(package private) java.lang.String[]	stageNames List unique stage name entries for various entities in Samples tbl
(package private) int	strainJ index for strainNames[]
(package private) java.lang.String[]	strainNames List unique strain name entries for various entities in Samples tbl
(package private) int	subMenuNbr submenu # correspndg to Source

Constructor Summary

(package private)	StageNames(int subMenuNbr, int hpNbr, int sampleDBrow, int menuJ, int sourceJ, int strainJ, int stageJ, int probeJ, java.lang.String stageLabel) StageNames() - constructor with data
(package private)	StageNames(MAExplorer mae) StageNames() - initial global constructor with no data

Method Summary

(package private) boolean	getMenuTreeFromSamplesTable(MAExplorer mae) getMenuTreeFromSamplesTable() - build tree from Samples.txt Table
private void	sortMenuEntriesByStage(StageNames[] data, int lth) sortMenuEntriesByStage() - sort HPmnuEntry[] by Stage.

Methods inherited from class java.lang.Object

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

Field Detail

menuNames

java.lang.String[] menuNames

List unique menu name entries for various entities in Samples tbl

sourceNames

java.lang.String[] sourceNames

List unique source name entries for various entities in Samples tbl

strainNames

java.lang.String[] strainNames

List unique strain name entries for various entities in Samples tbl

stageNames

java.lang.String[] stageNames

List unique stage name entries for various entities in Samples tbl

probeNames

java.lang.String[] probeNames

List unique probe name entries for various entities in Samples tbl

nmenuNames

int nmenuNames

# unique menu name entries in Samples tbl

nsourceNames

int nsourceNames

# unique source name entries in Samples tbl

nstrainNames

int nstrainNames

# unique strain name entries in Samples tbl

nstageNames

int nstageNames

# unique stage name entries in Samples tbl

nprobeNames

int nprobeNames

# unique probe name entries in Samples tbl

HPmnuEntry

StageNames[] HPmnuEntry

list of menus that the entry belongs to

nHPmnuEntries

int nHPmnuEntries

# of menu entries

subMenuNbr

int subMenuNbr

submenu # correspndg to Source

hpNbr

int hpNbr

idx of mae.snHPNames[]

sampleDBrow

int sampleDBrow

row of membrane table

menuJ

int menuJ

index for menuNames[]

sourceJ

int sourceJ

index for sourceNames[]

strainJ

int strainJ

index for strainNames[]

stageJ

int stageJ

index for stageNames[]

probeJ

int probeJ

index for probeNames[]

stageLabel

java.lang.String stageLabel

itemLabel to be used in menu

Constructor Detail

StageNames

StageNames(MAExplorer mae)

StageNames() - initial global constructor with no data

Parameters:

mae - is MAExplorer instance

StageNames

StageNames(int subMenuNbr,
           int hpNbr,
           int sampleDBrow,
           int menuJ,
           int sourceJ,
           int strainJ,
           int stageJ,
           int probeJ,
           java.lang.String stageLabel)

StageNames() - constructor with data

Parameters:

subMenuNbr - is the submenu # correspndg to Source

hpNbris - the idx of mae.snHPNames[]

sampleDBrow - is the row of sample DB table

menuJ - is the index for menuNames[]

sourceJ - is the index for sourceNames[]

strainJ - is the index for strainNames[]

stageJ - is the index for stageNames[]

probeJ - is the index for probeNames[]

stageLabel - is the item label for menu

Method Detail

getMenuTreeFromSamplesTable

boolean getMenuTreeFromSamplesTable(MAExplorer mae)

getMenuTreeFromSamplesTable() - build tree from Samples.txt Table

 The Pull-down menus should look like:
  Menu_Stage_Name
    Source
      Strain
        Stage

Parameters:

mae - is MAExplorer instance

Returns:

true if succeed

See Also:

SamplesTable.getUniqueTableFieldData(int), StageNames, Util.findIndexForKey(java.lang.String[], java.lang.String), sortMenuEntriesByStage(StageNames[], int)

sortMenuEntriesByStage

private void sortMenuEntriesByStage(StageNames[] data,
                                    int lth)

sortMenuEntriesByStage() - sort HPmnuEntry[] by Stage.

Parameters:

data - is list of stagenames