Class SampleSets

java.lang.Object
  |
  +--SampleSets

class SampleSets

extends java.lang.Object

The SampleSets class maintains the set of all HP samples, the HP-X set, HP-Y set and the HP-E list.

 List of sets of MaHybridSample sample instances in this class  
   msList[1:nHP]     is the set of all samples currently loaded in the database     
   msListX[1:nHP_X]  is the HP-X set samples  
   msListY[1:nHP_Y]  is the HP-Y set samples  
   msListE[1:nHP_E]  is the HP-E set samples 

The HPxyData class is used for computing means, stdDev, CVs for the HP-X and HP-Y sets.

The PopupHPChooser and PopupHPmenuGuesser classes create user GUI popup windows that are used to change these data structures.

The HP-E list is used for defining expression profiles (@see ExprProfile) that is used in expression profile plots and for computing cluster distances used in clustering methods.

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: 2003/02/18 18:02:35 $ $Revision: $

Author:

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

See Also:

MAExplorer Home, ExprProfile, HPxyData, MaHybridSample, PopupHPChooser, PopupHPmenuGuesser

Field Summary

(package private) int	idxRatioHP 1/msRatioHP for ratio EP calcs.
private MAExplorer	mae link to global MAExplorer instance
(package private) static MaHybridSample[]	msList total HP list [1:nHP] for all active samples
(package private) static MaHybridSample[]	msListE Expression Profile [1:nHP_E]
(package private) static MaHybridSample[]	msListX X-axis [1:nHP_X]
(package private) static MaHybridSample[]	msListY Y-axis [1:nHP_Y]
private java.lang.String[]	nameList Names of samples for Cy5/Cy3 swap
(package private) static int	nHP number of Samples in msList[]
(package private) static int	nHP_E list H.P.
(package private) static int	nHP_X list (set) Samples for X-axis msListX[]
(package private) static int	nHP_Y list (set) Samples for Y-Axis msListY[]
(package private) int	nTopSubMenus number of top level menus
private boolean[]	oldValueList originbal list for Cy5/Cy3 swap if cancel
(package private) java.lang.String	sCy35 "Cy3/Cy5" based on mae.cfg.fluoresLbl[12]
(package private) java.lang.String	sCy53 "Cy5/Cy3" based on mae.cfg.fluoresLbl[12]
(package private) java.lang.String	sHPsetCy53 may have " some HPs ("+sCy53+") swapped"
(package private) java.lang.String	sMod prefix title "" or " 'set'"
(package private) java.lang.String	sModX HP-X epilog "", sHPsetCy53, sCy35, sCy53
(package private) java.lang.String	sModXY either sModX or sModY depending on mode
(package private) java.lang.String	sModY HP-Y epilog "", sHPsetCy53, sCy35, sCy53
(package private) java.lang.String[]	topSubMenuNames The following are the order of the top level menus in the menu tree.
private boolean[]	valueList list for Cy5/Cy3 swap

Constructor Summary

(package private)

SampleSets(MAExplorer mae) SampleSets() - constructor to create the sample lists.

Method Summary

(package private) boolean	addHPtoDB(MaHybridSample ms, int i) addHPtoDB() - set HP sample to active database entry i
(package private) boolean	addHPtoElist(MaHybridSample ms) addHPtoElist() - add HP sample to end of HP-E list
(package private) boolean	addHPtoXset(MaHybridSample ms) addHPtoXset() - add HP sample to HP-X set
(package private) boolean	addHPtoYset(MaHybridSample ms) addHPtoYset() - add HP sample to HP-Y set
(package private) boolean	addNewHPtoDB(MaHybridSample ms) addNewHPtoDB() - add new HP sample to end of active database list
private void	assignHPtoAxis(int n, int axis, MaHybridSample ms) assignHPtoAxis() - assign sample to current HP-X or HP-Y sample This is the default.
(package private) void	changeHPswapCy5Cy3Samples() changeHPswapCy5Cy3Samples() - popup scrollable GUI array of checkbox to change cy3/Cy5 swap flags msList[0:nHP-1].swapCy5Cy3DataFlags
(package private) boolean	chkSwapCy5Cy3(java.lang.String msListToCheck) chkSwapCy5Cy3() - test if HP-X, HP-Y or HP-E list have Cy3/Cy5 swap flag set.
(package private) void	copyValuesToMlistCy3Cy5Flags() copyValuesToMlistCy3Cy5Flags() - copy nameListCB[] state to valueList[]
(package private) static int	lookupHPsampleNbr(MaHybridSample ms) lookupHPsampleNbr() - lookup MaHybidSample's sampleNbr.
(package private) boolean	rmvHPfromElist(MaHybridSample ms) rmvHPfromElist() - remove HP sample from HP-E list
(package private) boolean	rmvHPfromXset(MaHybridSample ms) rmvHPfromXset() - remove HP sample from HP-X set
(package private) boolean	rmvHPfromYset(MaHybridSample ms) rmvHPfromYset() - remove HP sample from HP-Y set
(package private) boolean	setHPlistsFromPARAM() setHPlistsFromPARAM() - set msList{X|Y|E}[] from PARAM cfg.{X|Y|E}list.
(package private) void	setHPxyModStrings() setHPxyModStrings() - set up (sMod, sModX, sModY, sModXY) state strings.
(package private) void	showHP_E_assignmentsPopup() showHP_E_assignmentsPopup() - make popup display of HP_E list of samples.
(package private) void	showHP_XY_assignmentsPopup() showHP_XY_assignmentsPopup() - make popup display of HP_X and HP-Y sample lists

Methods inherited from class java.lang.Object

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

Field Detail

mae

private MAExplorer mae

link to global MAExplorer instance

topSubMenuNames

java.lang.String[] topSubMenuNames

The following are the order of the top level menus in the menu tree. NOTE that the key words are in the Samples Table "Source" or "Probe" fields.

nTopSubMenus

int nTopSubMenus

number of top level menus

msListX

static MaHybridSample[] msListX

X-axis [1:nHP_X]

msListY

static MaHybridSample[] msListY

Y-axis [1:nHP_Y]

msListE

static MaHybridSample[] msListE

Expression Profile [1:nHP_E]

msList

static MaHybridSample[] msList

total HP list [1:nHP] for all active samples

nHP_X

static int nHP_X

list (set) Samples for X-axis msListX[]

nHP_Y

static int nHP_Y

list (set) Samples for Y-Axis msListY[]

nHP_E

static int nHP_E

list H.P. Samples for expr.profiles msListE[]

nHP

static int nHP

number of Samples in msList[]

idxRatioHP

int idxRatioHP

1/msRatioHP for ratio EP calcs.

sMod

java.lang.String sMod

prefix title "" or " 'set'"

sModX

java.lang.String sModX

HP-X epilog "", sHPsetCy53, sCy35, sCy53

sModY

java.lang.String sModY

HP-Y epilog "", sHPsetCy53, sCy35, sCy53

sModXY

java.lang.String sModXY

either sModX or sModY depending on mode

sCy35

java.lang.String sCy35

"Cy3/Cy5" based on mae.cfg.fluoresLbl[12]

sCy53

java.lang.String sCy53

"Cy5/Cy3" based on mae.cfg.fluoresLbl[12]

sHPsetCy53

java.lang.String sHPsetCy53

may have " some HPs ("+sCy53+") swapped"

nameList

private java.lang.String[] nameList

Names of samples for Cy5/Cy3 swap

valueList

private boolean[] valueList

list for Cy5/Cy3 swap

oldValueList

private boolean[] oldValueList

originbal list for Cy5/Cy3 swap if cancel

Constructor Detail

SampleSets

SampleSets(MAExplorer mae)

SampleSets() - constructor to create the sample lists.

Parameters:

mae - is MAExplorer instance

See Also:

MaHybridSample

Method Detail

lookupHPsampleNbr

static int lookupHPsampleNbr(MaHybridSample ms)

lookupHPsampleNbr() - lookup MaHybidSample's sampleNbr. Make sure it is legal return sampleNbr.

Parameters:

ms - is MaHybridSample. If null, return current HP

Returns:

corresponding sampleNbr else -1 if not found.

addHPtoDB

boolean addHPtoDB(MaHybridSample ms,
                  int i)

addHPtoDB() - set HP sample to active database entry i

Parameters:

ms - is sample to replace at entry i

i - is position of sample list to replace

Returns:

true if succeed.

addNewHPtoDB

boolean addNewHPtoDB(MaHybridSample ms)

addNewHPtoDB() - add new HP sample to end of active database list

Parameters:

ms - is sample to add

Returns:

true if succeed.

addHPtoXset

boolean addHPtoXset(MaHybridSample ms)

addHPtoXset() - add HP sample to HP-X set

Parameters:

ms - is sample to add to HP-X set

Returns:

true if succeed.

See Also:

MenuBarFrame.setHP_XYlabels(), Util.showMsg(java.lang.String), assignHPtoAxis(int, int, MaHybridSample)

addHPtoYset

boolean addHPtoYset(MaHybridSample ms)

addHPtoYset() - add HP sample to HP-Y set

Parameters:

ms - is sample to add to HP-Y set

Returns:

true if succeed.

See Also:

MenuBarFrame.setHP_XYlabels(), Util.showMsg(java.lang.String), assignHPtoAxis(int, int, MaHybridSample)

addHPtoElist

boolean addHPtoElist(MaHybridSample ms)

addHPtoElist() - add HP sample to end of HP-E list

Parameters:

ms - is sample to add to HP-E list

Returns:

true if succeed.

See Also:

Util.showMsg(java.lang.String)

rmvHPfromXset

boolean rmvHPfromXset(MaHybridSample ms)

rmvHPfromXset() - remove HP sample from HP-X set

Parameters:

ms - is sample to remove from HP-X set

Returns:

true if succeed.

See Also:

Util.showMsg(java.lang.String)

rmvHPfromYset

boolean rmvHPfromYset(MaHybridSample ms)

rmvHPfromYset() - remove HP sample from HP-Y set

Parameters:

ms - is sample to remove from HP-Y set

Returns:

true if succeed.

See Also:

Util.showMsg(java.lang.String)

rmvHPfromElist

boolean rmvHPfromElist(MaHybridSample ms)

rmvHPfromElist() - remove HP sample from HP-E list

Parameters:

ms - is sample to remove from HP-E list

Returns:

true if succeed.

See Also:

Util.showMsg(java.lang.String)

assignHPtoAxis

private void assignHPtoAxis(int n,
                            int axis,
                            MaHybridSample ms)

assignHPtoAxis() - assign sample to current HP-X or HP-Y sample This is the default.

Parameters:

n - is the sampleNbr to set to mae.curHP

axis - is either mae.X_AXIS or mae.Y_AXIS

ms - is HP sample to assign

setHPlistsFromPARAM

boolean setHPlistsFromPARAM()

setHPlistsFromPARAM() - set msList{X|Y|E}[] from PARAM cfg.{X|Y|E}list. Also sets limits for msListX[1:nHP_X], msListY[1:nHP_Y] and msListE[1:nHP_X]. Set the default current HP-X and HP-Y to the first entries on the Xlist and Ylist PARAM lists (if any) using the map entries idxListX[0] for curHP_X and idxListY[0] for curHP_Y. Handles case where there is NO intial data!

Returns:

true if succeed

showHP_XY_assignmentsPopup

void showHP_XY_assignmentsPopup()

showHP_XY_assignmentsPopup() - make popup display of HP_X and HP-Y sample lists

See Also:

ShowStringPopup, Util.showFeatures(java.lang.String, java.lang.String), Util.showMsg(java.lang.String)

showHP_E_assignmentsPopup

void showHP_E_assignmentsPopup()

showHP_E_assignmentsPopup() - make popup display of HP_E list of samples.

See Also:

ShowStringPopup, Util.showFeatures(java.lang.String, java.lang.String), Util.showMsg(java.lang.String)

chkSwapCy5Cy3

boolean chkSwapCy5Cy3(java.lang.String msListToCheck)

chkSwapCy5Cy3() - test if HP-X, HP-Y or HP-E list have Cy3/Cy5 swap flag set. If in ratio density mode, check to see if any HPs in the specified list have the ms.swapCy5Cy3DataFlag set.

Returns:

true if this is true, else false.

setHPxyModStrings

void setHPxyModStrings()

setHPxyModStrings() - set up (sMod, sModX, sModY, sModXY) state strings. The string reflects the ratio or intensity mode state as well as whether swapCy5Cy3DataFlags is in effect.

See Also:

chkSwapCy5Cy3(java.lang.String)

changeHPswapCy5Cy3Samples

void changeHPswapCy5Cy3Samples()

changeHPswapCy5Cy3Samples() - popup scrollable GUI array of checkbox to change cy3/Cy5 swap flags msList[0:nHP-1].swapCy5Cy3DataFlags

See Also:

Component.repaint(), Filter.computeWorkingGeneList(), Component.repaint(), MaHybridSample.swapCy5Cy3AndReCalcStats(), PopupRegistry.updateCurGene(int, int, java.lang.Object), PopupScrollableSelector, setHPxyModStrings()

copyValuesToMlistCy3Cy5Flags

void copyValuesToMlistCy3Cy5Flags()

copyValuesToMlistCy3Cy5Flags() - copy nameListCB[] state to valueList[]