Class MJAsampleList

java.lang.Object
  |
  +--MJAbase
        |
        +--MJAsampleList

public class MJAsampleList

extends MJAbase

MAExplorer GatherScatter API class to access MJAsampleList methods and data structures. Access lists of samples top-level data

List of methods available to Plugin-writers

 ----------------- global sample set data and sizes of lists ---
 getNbrHPsamples() - get # of ALL HP samples currently loaded in DB
 getSizeOf_HP_X_set() - get # of HP-X 'set' samples
 getSizeOf_HP_Y_set() - get # of HP-Y 'set' samples
 getSizeOf_HP_E_set() - get # of HP-E 'set' samples
 getCurrent_HP_index() - get Current HP sample index
 getCurrent_HP_X_index() - get Current HP-X sample index
 getCurrent_HP_Y_index() - get Current HP-Y sample index
 getCurrent_HP_name() - get Current HP sample name
 getCurrent_HP_X_name() - get Current HP-X sample name
 getCurrent_HP_Y_name() - get Current HP-Y sample name
 get_HP_SampleName() - get HP sample name for sample number
 getClassXname() - get the current Class X name.
 getClassYname() - get the current Class Y name
 ----------------- Lists of samples description data ----------
 getAllSampleNames()- get list of all active sample names used in DB
 getHP_Xset_SampleNames()- get list of HP-X 'set' sample names used in DB
 getHP_Yset_SampleNames()- get list of HP-Y 'set' sample names used in DB
 getHP_Elist_SampleNames()- get list of HP-E 'set' sample names used in DB
 getHP_Xset_SampleIDs()- get list of HP-X 'set' sample IDs used in DB
 getHP_Yset_SampleIDs()- get list of HP-Y 'set' sample IDs used in DB
 getHP_Elist_SampleIDs()- get list of HP-E 'set' sample IDs used in DB
 getHP_Xset_SampleNbrs()- get list of HP-X 'set' sample numbers used in DB
 getHP_Yset_SampleNbrs()- get list of HP-Y 'set' sample numbers used in DB
 getHP_Elist_SampleNbrs()- get list of HP-E 'list' sample numbers used in DB
 getListOfAllActiveHPsampleIndices() - get list of all active sample indices
 getListOfHPXsampleIndices() - get list of sample indices in HP-X set
 getListOfHPXYampleIndices() - get list of sample indices in HP-Y set
 getListOfHPEsampleIndices() - get list of sample indices in HP-E list
 getHP_XYsetsStatistics() - get HP-X and HP-Y 'set statistics for gene.
 getListOfSampleMenuEntries() - get list of sample menu names in in menu.
 getListOfSampleProjectEntries() - get list of sample project names. 
 getListOfSampleStageNames() - get list of sample full stage text names. 
 getListOfSampleNames() - get list sample database file name (no .quant). 
 getGrandMeanCalDNA() - get compute grand mean of calibration DNA
 getGrandMeanUseGeneSet() - get compute grand mean of 'Use Gene Set'
 getSampleVsSampleCorrelationsTable()- list of Sample Vs Sample corre tbl
 getSampleStatisticsTable() - get list of all Sample statistics table.
 ---------------- Set Sample sets and lists ------------------     
 setListOfXsamples() - set int[] list of sample indices in HP-X 'set'.    
 setListOfYsamples() - set int[] list of sample indices in HP-Y 'set'. 
 setListOfEsamples() - set int[] list of sample indices in HP-E 'list'. 
 ----- Lists of HP, HP-X, HP-Y, HP-X and HP-Y 'sets' intensity data ------
 getRawF1F2DataAndBkgdForSample() - get filtered spot list raw intensity, raw bkgrd, props data
 getAllRawF1F2DataAndBkgdForSample() - get all spot list raw intensity, raw bkgrd, props data
 getF1F2dataForSample() - get filtered (f1,f2,prop) lists of Field (F1,F2) intensity data
 getAllF1F2dataForSample() - get all (f1,f2,prop) lists of Field (F1,F2) intensity data
 getHPdataForSample() - get filtered (data,prop) list single sample's intensity data
 getAllHPdataForSample() - get all normalized (data,prop) list single sample's intensity data
 getAllRawHPdataForSample() - get all raw (data,prop) list single sample's intensity data
 getHP_XandYsamplesData() - get filtered (X,Y,prop) lists of single X and Y samples normalized data
 getAllHP_XandYsamplesData() - get all (X,Y,prop) lists of single X and Y samples normalized data
 getHP_XandYsetDataForSample() - get filtered (X,Y,prop) lists of HP-X/-Y 'sets' mean normalized data
 getAllHP_XandYsetDataForSample() - get filtered (X,Y,prop) lists of HP-X/-Y 'sets' mean normalized data
 getMeanDataGeneListDataForCondition() - get filtered (mn,SD,prop) list Condition samples' normalized data
 getAllMeanDataGeneListDataForCondition() - get all (mn,SD,prop) list Condition samples' normalized data

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: 2003/04/28 18:09:38 $ $Revision: 1.19 $

Author:

P. Lemkin (NCI), J. Evans (CIT), C. Santos (CIT), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home

Fields inherited from class MJAbase

COMPARE_ALL, COMPARE_ANY, COMPARE_AT_LEAST, COMPARE_AT_MOST, COMPARE_PRODUCT, COMPARE_SUM, DATA_F1TOT, DATA_F2TOT, DATA_MEAN_F1F2TOT, DATA_RATIO_F1F2TOT, DRAW_BIN, DRAW_BOX, DRAW_CIRCLE, DRAW_PLUS, EDIT_ADD, EDIT_NOP, EDIT_RMV, GENE_ATCC_ID, GENE_BAD_DATA, GENE_BAD_LOCAL_SPOT_BKGRD, GENE_BAD_MID, GENE_BAD_SPOT, GENE_BAD_SPOT_GEOMETRY, GENE_DUP_SPOT, GENE_GOOD_MID, GENE_IMAGE_ID, GENE_IS_CUR_GENE, GENE_IS_EGL_GENE, GENE_IS_FILTERED, GENE_IS_KMEANS, GENE_IS_NOT_FILTERED, GENE_LOW_SPOT_REF_SIGNAL, GENE_MARGINAL_SPOT, GENE_USE_GBID_FOR_CLONEID, HIER_CLUST_NEXT_MIN_LNKG, HIER_CLUST_PGMA_LNKG, HIER_CLUST_PGMC_LNKG, MARKER_CIRCLE, MARKER_CURRENT, MARKER_GENES, MARKER_KMEANS_CLUSTER, MARKER_NONE, MARKER_PLUS, MARKER_SQUARE, MASTER_CLONE_ID, MASTER_DBEST3, MASTER_DBEST5, MASTER_GENBANK, MASTER_GENBANK3, MASTER_GENBANK5, MASTER_GENE_NAME, MASTER_GENERIC_ID, MASTER_LOCUSLINK, MASTER_SWISS_PROT, MASTER_UG_ID, MASTER_UG_NAME, MAX_COLORS, PLOT_CLUSTER_GENES, PLOT_CLUSTER_HIER, PLOT_CLUSTER_HYBSAMPLES, PLOT_CLUSTERGRAM, PLOT_EXPR_PROFILE, PLOT_F1_F2_INTENS, PLOT_F1_F2_MVSA, PLOT_HIST_F1F2_RATIO, PLOT_HIST_HP_XY_RATIO, PLOT_HIST_HP_XY_SETS_RATIO, PLOT_HP_XY_INTENS, PLOT_INTENS_HIST, PLOT_KMEANS_CLUSTERGRAM, PLOT_PSEUDO_F1F2_IMG, PLOT_PSEUDO_F1F2_RYG_IMG, PLOT_PSEUDO_HP_XY_IMG, PLOT_PSEUDO_HP_XY_RYG_IMG, PLOT_PSEUDOIMG, PRPROP_CUR_GENE, PRPROP_FILTER, PRPROP_LABEL, PRPROP_SLIDER, PRPROP_TIMEOUT, PRPROP_UNIQUE, QUALTYPE_ALPHA, QUALTYPE_PROP_CODE, QUALTYPE_THR, RANGE_INSIDE, RANGE_OUTSIDE, RPT_FMT_DYN, RPT_FMT_TAB_DELIM, RPT_NONE, RPT_TBL_ALL_GENES_CLUSTER, RPT_TBL_CALIB_DNA_STAT, RPT_TBL_CUR_GENE_CLUSTER, RPT_TBL_EDITED_GENE_LIST, RPT_TBL_EXPR_PROFILE, RPT_TBL_FILTERED_GENES, RPT_TBL_GENE_CLASS, RPT_TBL_HIER_CLUSTER, RPT_TBL_HIGH_F1F2, RPT_TBL_HIGH_RATIO, RPT_TBL_HP_DB_INFO, RPT_TBL_HP_HP_CORR, RPT_TBL_HP_MN_VAR_STAT, RPT_TBL_HP_XY_SET_STAT, RPT_TBL_KMEANS_CLUSTER, RPT_TBL_LOW_F1F2, RPT_TBL_LOW_RATIO, RPT_TBL_MAE_PRJ_DB, RPT_TBL_MN_KMEANS_CLUSTER, RPT_TBL_NAMED_GENES, RPT_TBL_NORMALIZATION_GENE_LIST, RPT_TBL_OCL_STAT, RPT_TBL_SAMPLES_DB_INFO, RPT_TBL_SAMPLES_WEB_LINKS, SS_MODE_ELIST, SS_MODE_MS, SS_MODE_XANDY_SETS, SS_MODE_XORY_SETS, SS_MODE_XSET, SS_MODE_XY, SS_MODE_YSET

Method Summary

java.lang.String	get_HP_SampleName(int sampleNbr, boolean getFullNameFlag) get_HP_SampleName() - get HP sample name for sample number
int	getAllF1F2dataForSample(float[] f1List, float[] f2List, int sampleNbr) getAllF1F2dataForSample() - get all (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[]) for ALL gene data.
int	getAllHP_XandYsamplesData(float[] xList, float[] yList, int sampleNbrX, int sampleNbrY) getAllHP_XandYsamplesData() - get all (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[]) for ALL genes.
int	getAllHP_XandYsetDataForSample(float[] xList, float[] yList) getAllHP_XandYsetDataForSample() - get all HP-X, -Y 'sets' (X,Y) normalized data lists for sample in (Xdata[],Ydata[] for ALL genes.
int	getAllHPdataForSample(float[] dataList, int sampleNbr) getAllHPdataForSample() - get all normalized (data,prop) list single sample's data for sample in (dataList[]) for ALL genes.
int	getAllMeanDataForCondition(float[] meanData, float[] stdDevData, java.lang.String condListName) getAllMeanDataGeneListDataForCondition() - get all (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in in (meanData[], stdDevData[]) for data filtered by the specified gene list.
int	getAllRawF1F2DataAndBkgdForSample(float[] rawF1data, float[] rawF2data, float[] rawF1bkgd, float[] rawF2bkgd, int[] properties, int[] midList, int sampleNbr) getAllawF1F2DataAndBkgdForSample() - get all spot list raw intensity and background data for genes and return it in the arrays pre-specified by the user.
java.lang.String[]	getAllSampleNames() getAllSampleNames()- get list of all active sample names used in DB
java.lang.String	getClassXname() getClassXname() - get the current Class X name.
java.lang.String	getClassYname() getClassYname() - get the current Class Y name.
int	getCurrent_HP_index() getCurrent_HP_index() - get Current HP sample index.
java.lang.String	getCurrent_HP_name(boolean getFullNameFlag) getCurrent_HP_name() - get Current HP sample name
int	getCurrent_HP_X_index() getCurrent_HP_X_index() - get Current HP-X sample index.
java.lang.String	getCurrent_HP_X_name(boolean getFullNameFlag) getCurrent_HP_X_name() - get Current HP-X sample name
int	getCurrent_HP_Y_index() getCurrent_HP_Y_index() - get Current HP-Y sample index.
java.lang.String	getCurrent_HP_Y_name(boolean getFullNameFlag) getCurrent_HP_Y_name() - get Current HP-Y sample name
int	getF1F2dataForSample(float[] f1List, float[] f2List, int[] propList, int sampleNbr, java.lang.String geneListName) getF1F2dataForSample() - get filtered (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[], propList[]) for FILTERED data by the specified gene list.
float	getGrandMeanCalDNA(boolean doRecalcCalibFlag) getGrandMeanCalDNA() - get compute grand mean of calibration DNA
float	getGrandMeanUseGeneSet(boolean doRecalcCalibFlag) getGrandMeanUseGeneSet() - get compute grand mean of 'Use Gene Set'
java.lang.String[]	getHP_Elist_SampleIDs() getHP_Elist_SampleIDs()- get list of HP-E 'list' sample IDs used in DB
java.lang.String[]	getHP_Elist_SampleNames() getHP_Elist_SampleNames()- get list of HP-E 'list' sample IDs used in DB
int[]	getHP_Elist_SampleNbrs() getHP_Elist_SampleNbrs()- get list of HP-E 'list' sample numbers used in DB
int	getHP_XandYsamplesData(float[] xList, float[] yList, int[] propList, int sampleNbrX, int sampleNbrY, java.lang.String geneListName) getHP_XandYsamplesData() - get filtered (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data by the specified gene list.
int	getHP_XandYsetDataForSample(float[] xList, float[] yList, int[] propList, java.lang.String geneListName) getHP_XandYsetDataForSample() - get normalized HP-X, -Y 'sets' (X,Y,prop) data lists for sample in (Xdata[],Ydata[], propList[] for FILTERED data by the specified gene list.
java.lang.String[]	getHP_Xset_SampleIDs() getHP_Xset_SampleIDs()- get list of HP-X 'set' sample IDs used in DB
java.lang.String[]	getHP_Xset_SampleNames() getHP_Xset_SampleNames()- get list of HP-X 'set' sample names used in DB
int[]	getHP_Xset_SampleNbrs() getHP_Xset_SampleNbrs()- get list of HP-X 'set' sample numbers used in DB
java.util.Hashtable	getHP_XYsetsStatistics(int mid) getHP_XYsetsStatistics() - get HP-X and HP-Y 'set statistics for gene.
java.lang.String[]	getHP_Yset_SampleIDs() getHP_Yset_SampleIDs()- get list of HP-Y 'set' sample IDs used in DB
java.lang.String[]	getHP_Yset_SampleNames() getHP_Yset_SampleNames()- get list of HP-Y 'set' sample names used in DB
int[]	getHP_Yset_SampleNbrs() getHP_Yset_SampleNbrs()- get list of HP-Y 'set' sample numbers used in DB
int	getHPdataForSample(float[] dataList, int[] propList, int sampleNbr, java.lang.String geneListName) getHPdataForSample() - get normalized filtered (data,prop) list single sample's data for sample in (dataList[], propList[]) for FILTERED data by the specified gene list.
int[]	getListOfAllActiveHPsampleIndices() getListOfAllActiveHPsampleIndices() - get list of all active sample HP indices.
int[]	getListOfHPEsampleIndices() getListOfHPEsampleIndices() - get list of sample indices in HP-E list.
int[]	getListOfHPXsampleIndices() getListOfHPXsampleIndices() - get list of sample indices in HP-X set.
int[]	getListOfHPYsampleIndices() getListOfHPYsampleIndices() - get list of sample indices in HP-Y set.
java.lang.String[]	getListOfSampleMenuEntries() getListOfSampleMenuEntries() - get list of sample menu names as appears in the MAExplorer Samples menu.
java.lang.String[]	getListOfSampleNames() getListOfSampleNames() - get list sample database file name (no .quant).
java.lang.String[]	getListOfSampleProjectEntries() getListOfSampleProjectEntries() - get list of sample project names.
java.lang.String[]	getListOfSampleStageNames() getListOfSampleStageNames() - get list of sample full stage text names.
int	getMeanDataForCondition(float[] meanData, float[] stdDevData, int[] propList, java.lang.String condListName, java.lang.String geneListName) getMeanDataGeneListDataForCondition() - get filtered (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in (meanData[], stdDevData[], propList[]) for data filtered by the specified gene list.
int	getNbrHPsamples() getNbrHPsamples() - get # of ALL HP samples currently loaded in DB
int	getRawF1F2DataAndBkgdForSample(float[] rawF1data, float[] rawF2data, float[] rawF1bkgd, float[] rawF2bkgd, int[] properties, int[] midList, int sampleNbr, java.lang.String geneListName) getRawF1F2DataAndBkgdForSample() - get filtered spot list raw intensity and background data for genes and return it in the arrays pre-specified by the user.
int	getRawHP_XandYsamplesData(float[] xData, float[] yData, float[] xBkgd, float[] yBkgd, int[] propList, int sampleNbrX, int sampleNbrY, java.lang.String geneListName) getAllRawHPdataForSample() - get all raw (data,prop) list single sample's intensity data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data by the specified gene list.
java.util.Hashtable	getSampleStatisticsTable() getSampleStatisticsTable() - get list of all Sample statistics table.
java.util.Hashtable	getSampleVsSampleCorrelationsTable() getSampleVsSampleCorrelationsTable() - get list of Sample Vs Sample correlations table.
int	getSizeOf_HP_E_set() getSizeOf_HP_E_set() - get # of HP-E 'set' samples.
int	getSizeOf_HP_X_set() getSizeOf_HP_X_set() - get # of HP-X 'set' samples
int	getSizeOf_HP_Y_set() getSizeOf_HP_Y_set() - get # of HP-Y 'set' samples
boolean	setListOfEsamples(int[] sampleIdxList) setListOfEsamples() - set int[] list of samples in HP-E 'list' list.
boolean	setListOfXsamples(int[] sampleIdxList) setListOfXsamples() - set int[] list of samples in HP-X 'set' list.
boolean	setListOfYsamples(int[] sampleIdxList) setListOfYsamples() - set int[] list of samples in HP-Y 'set' list.

Methods inherited from class MJAbase

cvtHashtable2SimpleTable, cvtTable2Hashtable

Methods inherited from class java.lang.Object

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

Method Detail

getNbrHPsamples

public final int getNbrHPsamples()

getNbrHPsamples() - get # of ALL HP samples currently loaded in DB

Returns:

value else null if not found.

getSizeOf_HP_X_set

public final int getSizeOf_HP_X_set()

getSizeOf_HP_X_set() - get # of HP-X 'set' samples

Returns:

value else null if not found.

getSizeOf_HP_Y_set

public final int getSizeOf_HP_Y_set()

getSizeOf_HP_Y_set() - get # of HP-Y 'set' samples

Returns:

value else null if not found.

getSizeOf_HP_E_set

public final int getSizeOf_HP_E_set()

getSizeOf_HP_E_set() - get # of HP-E 'set' samples.

Returns:

value else null if not found.

getCurrent_HP_index

public final int getCurrent_HP_index()

getCurrent_HP_index() - get Current HP sample index. Sample index numbers are in the range of [1:maxSamples].

Returns:

value else null if not found.

getCurrent_HP_X_index

public final int getCurrent_HP_X_index()

getCurrent_HP_X_index() - get Current HP-X sample index. Sample index numbers are in the range of [1:maxSamples].

Returns:

value else -1 if not found.

getCurrent_HP_Y_index

public final int getCurrent_HP_Y_index()

getCurrent_HP_Y_index() - get Current HP-Y sample index. Sample index numbers are in the range of [1:maxSamples].

Returns:

value else -1 if not found.

getCurrent_HP_name

public final java.lang.String getCurrent_HP_name(boolean getFullNameFlag)

getCurrent_HP_name() - get Current HP sample name

Parameters:

getFullNameFlag - to get fullStageText sample name else sample name

Returns:

name else null if not found.

getCurrent_HP_X_name

public final java.lang.String getCurrent_HP_X_name(boolean getFullNameFlag)

getCurrent_HP_X_name() - get Current HP-X sample name

Parameters:

getFullNameFlag - to get fullStageText sample name else sample name

Returns:

name else null if not found.

getCurrent_HP_Y_name

public final java.lang.String getCurrent_HP_Y_name(boolean getFullNameFlag)

getCurrent_HP_Y_name() - get Current HP-Y sample name

Parameters:

getFullNameFlag - to get fullStageText sample name else sample name

Returns:

name else null if not found.

get_HP_SampleName

public final java.lang.String get_HP_SampleName(int sampleNbr,
                                                boolean getFullNameFlag)

get_HP_SampleName() - get HP sample name for sample number

Parameters:

sampleNbr - is the number of the sample to look up

getFullNameFlag - to get fullStageText sample name else sample name

Returns:

name else null if not found.

getClassXname

public final java.lang.String getClassXname()

getClassXname() - get the current Class X name.

Returns:

class X name

getClassYname

public final java.lang.String getClassYname()

getClassYname() - get the current Class Y name.

Returns:

class Y name

getAllSampleNames

public final java.lang.String[] getAllSampleNames()

getAllSampleNames()- get list of all active sample names used in DB

Returns:

values else null if error

getHP_Xset_SampleNames

public java.lang.String[] getHP_Xset_SampleNames()

getHP_Xset_SampleNames()- get list of HP-X 'set' sample names used in DB

Returns:

values else null if error

getHP_Yset_SampleNames

public final java.lang.String[] getHP_Yset_SampleNames()

getHP_Yset_SampleNames()- get list of HP-Y 'set' sample names used in DB

Returns:

values else null if error

getHP_Elist_SampleNames

public final java.lang.String[] getHP_Elist_SampleNames()

getHP_Elist_SampleNames()- get list of HP-E 'list' sample IDs used in DB

Returns:

values else null if error

getHP_Xset_SampleIDs

public final java.lang.String[] getHP_Xset_SampleIDs()

getHP_Xset_SampleIDs()- get list of HP-X 'set' sample IDs used in DB

Returns:

values else null if error

getHP_Yset_SampleIDs

public final java.lang.String[] getHP_Yset_SampleIDs()

getHP_Yset_SampleIDs()- get list of HP-Y 'set' sample IDs used in DB

Returns:

values else null if error

getHP_Elist_SampleIDs

public final java.lang.String[] getHP_Elist_SampleIDs()

getHP_Elist_SampleIDs()- get list of HP-E 'list' sample IDs used in DB

Returns:

values else null if error

getHP_Xset_SampleNbrs

public final int[] getHP_Xset_SampleNbrs()

getHP_Xset_SampleNbrs()- get list of HP-X 'set' sample numbers used in DB

Returns:

values else null if error

getHP_Yset_SampleNbrs

public final int[] getHP_Yset_SampleNbrs()

getHP_Yset_SampleNbrs()- get list of HP-Y 'set' sample numbers used in DB

Returns:

values else null if error

getHP_Elist_SampleNbrs

public final int[] getHP_Elist_SampleNbrs()

getHP_Elist_SampleNbrs()- get list of HP-E 'list' sample numbers used in DB

Returns:

values else null if error

getListOfAllActiveHPsampleIndices

public final int[] getListOfAllActiveHPsampleIndices()

getListOfAllActiveHPsampleIndices() - get list of all active sample HP indices. Sample index numbers are in the range of [1:maxSamples].

Returns:

list of indices else null if the list is empty.

getListOfHPXsampleIndices

public final int[] getListOfHPXsampleIndices()

getListOfHPXsampleIndices() - get list of sample indices in HP-X set. Sample index numbers are in the range of [1:maxSamples].

Returns:

list of indices else null if the list is empty.

getListOfHPYsampleIndices

public final int[] getListOfHPYsampleIndices()

getListOfHPYsampleIndices() - get list of sample indices in HP-Y set. Sample index numbers are in the range of [1:maxSamples].

Returns:

list of indices else null if the list is empty.

getListOfHPEsampleIndices

public final int[] getListOfHPEsampleIndices()

getListOfHPEsampleIndices() - get list of sample indices in HP-E list. Sample index numbers are in the range of [1:maxSamples].

Returns:

list of indices else null if the list is empty.

getHP_XYsetsStatistics

public final java.util.Hashtable getHP_XYsetsStatistics(int mid)

getHP_XYsetsStatistics() - get HP-X and HP-Y 'set statistics for gene.

 The Hashtable list returned is defined as:
 Property name           - Value
 "HPXsetData"           - float[0:sizeofHPXset-1] array of normalized HP-X
                          set data
 "HPYsetData"           - float[0:sizeofHPYset-1] array of normalized HP-Y
                          set data
 "CVF1F2eachHPX"        - float[0:sizeofHPXset-1] array of (F1,F2) CV for
                          each HP sample in HP-X set
 "CVF1F2eachHPY"        - float[0:sizeofHPYset-1] array of (F1,F2) CV for
                          each HP sample in HP-Y set
 "sizeofHPXset"         - int number of samples in HP-X set
 "sizeofHPYset"         - int number of samples in HP-Y set
 "MeanHPXset"           - float mean of HP-X set
 "MeanHPYset"           - float mean of HP-Y set
 "StdDevHPXset"         - float StdDev of HP-X set
 "StdDevHPYset"         - float StdDev of HP-Y set
 "CoeffVariationHPXset" - float CoeffVariation of HP-X set
 "CoeffVariationHPYset" - float CoeffVariation of HP-Y set
 "LabelForHPXset"       - String Plot label for HP-X set
 "LabelForHPYset"       - String Plot label for HP-Y set
 "ClassNameHPXset"      - String ClassName for HP-X set
 "ClassNameHPYset"      - String ClassName for HP-Y set
 

Parameters:

mid - MID gene data to access

Returns:

value null if mid was not found, otherwise the current values are returned in a Hashtable.

getListOfSampleMenuEntries

public final java.lang.String[] getListOfSampleMenuEntries()

getListOfSampleMenuEntries() - get list of sample menu names as appears in the MAExplorer Samples menu.

Returns:

list[0:nHP-1] if found, else null null if getName was not found.

getListOfSampleProjectEntries

public final java.lang.String[] getListOfSampleProjectEntries()

getListOfSampleProjectEntries() - get list of sample project names.

Returns:

list[0:nHP-1] if found, else null null if getName was not found.

getListOfSampleStageNames

public final java.lang.String[] getListOfSampleStageNames()

getListOfSampleStageNames() - get list of sample full stage text names.

Returns:

list[0:nHP-1] if found, else null null if getName was not found.

getListOfSampleNames

public final java.lang.String[] getListOfSampleNames()

getListOfSampleNames() - get list sample database file name (no .quant).

Returns:

list[0:nHP-1] if found, else null null if getName was not found.

getGrandMeanCalDNA

public final float getGrandMeanCalDNA(boolean doRecalcCalibFlag)

getGrandMeanCalDNA() - get compute grand mean of calibration DNA

Parameters:

doRecalcCalibFlag - recompute calibration before get data

Returns:

value

getGrandMeanUseGeneSet

public final float getGrandMeanUseGeneSet(boolean doRecalcCalibFlag)

getGrandMeanUseGeneSet() - get compute grand mean of 'Use Gene Set'

Parameters:

doRecalcCalibFlag - recompute calibration before get data

Returns:

value

getSampleVsSampleCorrelationsTable

public final java.util.Hashtable getSampleVsSampleCorrelationsTable()

getSampleVsSampleCorrelationsTable() - get list of Sample Vs Sample correlations table. This is computed for the current data Filter data.

 The Hashtable returned is defined as:
 Name          - Value
 "TitleOfTable"     - String title of sample vs sample correlation table
 "NbrCols"          - int number of columns in the table
 "NbrRows"          - int number of rows in the table
 "FieldNames"       - String[0:NbrCols-1] list of field names
 "TableRowsData"    - String[0:NbrRows-1][0:NbrCols-1] rows of data
                      in the table
 

Returns:

null if not found or error, else return list.

getSampleStatisticsTable

public final java.util.Hashtable getSampleStatisticsTable()

getSampleStatisticsTable() - get list of all Sample statistics table. This is computed for the current data Filter data.

 The Hashtable list returned is defined as:
 Name          - Value
 "TitleOfTable"     - String title of the sample statistics table
 "NbrCols"          - int number of columns in the table
 "NbrRows"          - int number of rows in the table
 "FieldNames"       - String[0:NbrCols-1] list of field names
 "TableRowsData"    - String[0:NbrRows-1][0:NbrCols-1] rows of data in tbl
 

Returns:

null if not found or error, else return list.

setListOfXsamples

public final boolean setListOfXsamples(int[] sampleIdxList)

setListOfXsamples() - set int[] list of samples in HP-X 'set' list. The number of samples is the size of the list. Sample index numbers are in the range of [1:maxSamples].

Parameters:

sampleIdxList - list of sample number indices to save in the list.

Returns:

value true if succeed.

setListOfYsamples

public final boolean setListOfYsamples(int[] sampleIdxList)

setListOfYsamples() - set int[] list of samples in HP-Y 'set' list. The number of samples is the size of the list. Sample index numbers are in the range of [1:maxSamples].

Parameters:

sampleIdxList - list of sample number indices to save in the list.

Returns:

value true if succeed.

setListOfEsamples

public final boolean setListOfEsamples(int[] sampleIdxList)

setListOfEsamples() - set int[] list of samples in HP-E 'list' list. The number of samples is the size of the list. Sample index numbers are in the range of [1:maxSamples].

Parameters:

sampleIdxList - list of sample HP number indices to save in the list.

Returns:

value true if succeed.

getRawF1F2DataAndBkgdForSample

public final int getRawF1F2DataAndBkgdForSample(float[] rawF1data,
                                                float[] rawF2data,
                                                float[] rawF1bkgd,
                                                float[] rawF2bkgd,
                                                int[] properties,
                                                int[] midList,
                                                int sampleNbr,
                                                java.lang.String geneListName)

getRawF1F2DataAndBkgdForSample() - get filtered spot list raw intensity and background data for genes and return it in the arrays pre-specified by the user. The preallocated array size should be the maximum # of genes for filtered data by the specified gene list. If you are using ratio data, then F1 is Cy3 and F2 is Cy5 - unless you have swapped channels (see Swap (Cy3,Cy5) in Samples menu). The will get the current intensity data filtered list of nGene genes into (rawF1data, rawF2data, rawF1bkgd, rawF2bkgd, propList) lists. Sample index numbers are in the range of [1:maxSamples].

Parameters:

rawF1data[] - return raw F1 intensity values

rawF2data[] - return raw F2 intensity values

rawF1bkgd[] - return raw F1 background values

rawF2bkgd[] - return raw F2 background values

properties[] - return property bits for each gene if array not null. See mjaBase.GENE_IS_xxxxx properties for the definitions.

midList[] - return MIDs for corresponding data if not null

sampleNbr - specifies the HP sample number data to retrieve

geneListName - name of gene list to copy data filter genes into if it is not null

Returns:

the number of genes pushed. If the list length is shorter than the number of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (nList[] size.

getAllRawF1F2DataAndBkgdForSample

public final int getAllRawF1F2DataAndBkgdForSample(float[] rawF1data,
                                                   float[] rawF2data,
                                                   float[] rawF1bkgd,
                                                   float[] rawF2bkgd,
                                                   int[] properties,
                                                   int[] midList,
                                                   int sampleNbr)

getAllawF1F2DataAndBkgdForSample() - get all spot list raw intensity and background data for genes and return it in the arrays pre-specified by the user. The preallocated array size should be the maximum # of genes in the database. If you are using ratio data, then F1 is Cy3 and F2 is Cy5 - unless you have swapped channels (see Swap (Cy3,Cy5) in Samples menu). The will get the current intensity data filtered list of nGene genes into (rawF1data, rawF2data, rawF1bkgd, rawF2bkgd, properties) lists. Sample index numbers are in the range of [1:maxSamples].

Parameters:

rawF1data[] - return raw F1 intensity values

rawF2data[] - return raw F2 intensity values

rawF1bkgd[] - return raw F1 background values

rawF2bkgd[] - return raw F2 background values

properties[] - return property bits for each gene if array not null. See mjaBase.GENE_IS_xxxxx properties for the definitions.

midList[] - return MIDs for corresponding data if not null

sampleNbr - specifies the HP sample number data to retrieve

Returns:

the number of genes pushed. If the list length is shorter than the number of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (nList[] size.

getF1F2dataForSample

public final int getF1F2dataForSample(float[] f1List,
                                      float[] f2List,
                                      int[] propList,
                                      int sampleNbr,
                                      java.lang.String geneListName)

getF1F2dataForSample() - get filtered (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[], propList[]) for FILTERED data by the specified gene list. The f1List[] and f2List[] are intensity data. If you are using ratio data, then F1 is Cy3 and F2 is Cy5 - unless you have swapped channels (see Swap (Cy3,Cy5) in Samples menu). The will get the current intensity data filtered list of nGene genes into (f1List,f2Llist,PropList,GeneList) lists. Note: preallocate maximum size arrays before call. Sample index numbers are in the range of [1:maxSamples].

Parameters:

f1List - RTN: intensity data[0:nGene-1] for F1 sample

f2List - RTN: intensity data[0:nGene-1] for F2 sample

propList - RTN: gene property list[0:nGene-1], see GENE_xxxx properties. If using propList[], then will set bits to MJAbase.GENE_IS_FILTERED or MJAbase.GENE_IS_NOT_FILTERED.

sampleNbr - specifies the HP sample number data to retrieve

geneListName - name of gene list to copy data filter genes into if it is not null

Returns:

nGenes # of genes in f1List[], f2List[], propList[], else 0 if error or there is no dual channel data available!

getAllF1F2dataForSample

public final int getAllF1F2dataForSample(float[] f1List,
                                         float[] f2List,
                                         int sampleNbr)

getAllF1F2dataForSample() - get all (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[]) for ALL gene data. The f1List[] and f2List[] are intensity data. If you are using ratio data, then F1 is Cy3 and F2 is Cy5 - unless you have swapped channels (see Swap (Cy3,Cy5) in Samples menu). The will get the current intensity data filtered list of nGene genes into (f1List,f2Llist) lists. Sample index numbers are in the range of [1:maxSamples].

Note: preallocate maximum size arrays before call.

Parameters:

f1List - RTN: intensity data[0:nGene-1] for F1 sample

f2List - RTN: intensity data[0:nGene-1] for F2 sample

sampleNbr - specifies the HP sample number data to retrieve

Returns:

nGenes # of genes in f1List[], f2List[], else 0 if error or there is no dual channel data available!

getHPdataForSample

public final int getHPdataForSample(float[] dataList,
                                    int[] propList,
                                    int sampleNbr,
                                    java.lang.String geneListName)

getHPdataForSample() - get normalized filtered (data,prop) list single sample's data for sample in (dataList[], propList[]) for FILTERED data by the specified gene list. The dataList[] is intensity data. If you are using ratio data, this is the ratio data for each sample i.e. (F1/F2) or (Cy3/Cy5) for the sample. Otherwise is the F1 data. Data is corrected for background, and median Ratio correction if applicable and the mode is set in the MAExplorer menus. The will get the current intensity data filtered list of nGene genes into (datalist,PropList,GeneList) lists. Note: preallocate maximum size arrays before call. Sample index numbers are in the range of [1:maxSamples].

Parameters:

dataList - RTN: intensity data[0:nGene-1] for sample if succeed

propList - RTN: gene property list[0:nGene-1] if succeed. See GENE_xxxx properties. If using propList[], then will set bits to MJAbase.GENE_IS_FILTERED or MJAbase.GENE_IS_NOT_FILTERED.

sampleNbr - specifies the HP sample number data to retrieve

geneListName - name of gene list to copy data filter genes into. If the name is null, use the the set of ALL GENES gene list.

Returns:

nGenes # of genes in dataList[] and propList[], if the geneListName is not found, use the data filter, else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the dataList[]) size.

getAllHPdataForSample

public final int getAllHPdataForSample(float[] dataList,
                                       int sampleNbr)

getAllHPdataForSample() - get all normalized (data,prop) list single sample's data for sample in (dataList[]) for ALL genes. The dataList[] is intensity data. If you are using ratio data, this is the ratio data for each sample i.e. (F1/F2) or (Cy3/Cy5) for the sample. Otherwise is the F1 data. Data is corrected for background, and median Ratio correction if applicable and the mode is set in the MAExplorer menus. The will get the current intensity data filtered list of nGene genes into (datalist) lists. Sample index numbers are in the range of [1:maxSamples].

Note: preallocate maximum size arrays before call.

Parameters:

dataList - RTN: intensity data[0:nGene-1] for sample if succeed

sampleNbr - specifies the HP sample number data to retrieve

Returns:

nGenes # of genes in dataList[]. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the dataList[]) size.

getHP_XandYsamplesData

public final int getHP_XandYsamplesData(float[] xList,
                                        float[] yList,
                                        int[] propList,
                                        int sampleNbrX,
                                        int sampleNbrY,
                                        java.lang.String geneListName)

getHP_XandYsamplesData() - get filtered (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data by the specified gene list. The Xdata[] and Ydata[] are normalized intensity data. If you are using ratio data, then sample intensity is the ratio data for each sample i.e. (Cy3X/Cy5X) for HP-X and (Cy3Y/Cy5Y) for HP-Y. The will get the current data filtered list of nGene genes into (Xlist,Ylist,PropList).

If your are using (F1,F2) or (Cy3,Cy5) data and sampleNbrX==sampleNbrY, then it will get the F1 (Cy3) channel in xData[] and the F2 (Cy5) data in the yData[] arrays.

Note: preallocate maximum size arrays before call. Sample index numbers are in the range of [1:maxSamples].

Parameters:

xList - RTN: data[0:nGene-1] for X sample if succeed

yList - RTN: data[0:nGene-1] for Y sample if succeed

propList - RTN: gene property list[0:nGene-1] if succeed. See GENE_xxxx properties. If using propList[], then will set bits to MJAbase.GENE_IS_FILTERED or MJAbase.GENE_IS_NOT_FILTERED.

sampleNbrX - specifies the HP-X sample number data to retrieve

sampleNbrY - specifies the HP-Y sample number data to retrieve

geneListName - name of gene list to copy data filter genes into.

Returns:

nGenes # of genes in xList[], yList[], and propList[], else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xList[], yList[]) sizes.

getRawHP_XandYsamplesData

public final int getRawHP_XandYsamplesData(float[] xData,
                                           float[] yData,
                                           float[] xBkgd,
                                           float[] yBkgd,
                                           int[] propList,
                                           int sampleNbrX,
                                           int sampleNbrY,
                                           java.lang.String geneListName)

getAllRawHPdataForSample() - get all raw (data,prop) list single sample's intensity data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data by the specified gene list. The Xdata[] and Ydata[] are raw intensity data. If you are using ratio data, then sample intensity is the raw ratio data for each sample i.e. (Cy3X/Cy5X) for HP-X and (Cy3Y/Cy5Y) for HP-Y. The will get the current data filtered list of nGene genes into (xData, yData, xBkgr, yBkgd,PropList).

If sampleNbrY==-1, then get (Cy3 into xData, Cy5 into yData).

If your are using (F1,F2) or (Cy3,Cy5) data and sampleNbrX==sampleNbrY, then it will get the F1 (Cy3) channel in xData[] and the F2 (Cy5) data in the yData[] arrays.

Note: preallocate maximum size arrays before call. Sample index numbers are in the range of [1:maxSamples].

Parameters:

xData - RTN: X data[0:nGene-1] for X sample if succeed

yData - RTN: opt. Y data[0:nGene-1] for Y sample if succeed

xBkgd - RTN: opt. X bkgrd data[0:nGene-1] for X sample if succeed

yBkgd - RTN: opt. Y bkgrd data[0:nGene-1] for Y sample if succeed

propList - RTN: gene property list[0:nGene-1] if succeed. See GENE_xxxx properties. If using propList[], then will set bits to MJAbase.GENE_IS_FILTERED or MJAbase.GENE_IS_NOT_FILTERED.

sampleNbrX - specifies the HP-X sample number data to retrieve

sampleNbrY - specifies the HP-Y sample number data to retrieve

geneListName - name of gene list to copy data filter genes into.

Returns:

nGenes # of genes in xData[], yData[], xBkgd[], yBkgd[], and propList[], else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xList[], yList[]) sizes.

getAllHP_XandYsamplesData

public final int getAllHP_XandYsamplesData(float[] xList,
                                           float[] yList,
                                           int sampleNbrX,
                                           int sampleNbrY)

getAllHP_XandYsamplesData() - get all (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[]) for ALL genes. The Xdata[] and Ydata[] are intensity data. If you are using ratio data, then sample intensity is the ratio data for each sample i.e. (Cy3X/Cy5X) for HP-X and (Cy3Y/Cy5Y) for HP-Y. The will get the current data filtered list of nGene genes into the (Xlist,Ylist) arrays. Sample index numbers are in the range of [1:maxSamples].

Note: preallocate maximum size arrays before call.

Parameters:

xList - RTN: data[0:nGene-1] for X sample if succeed

yList - RTN: data[0:nGene-1] for Y sample if succeed

sampleNbrX - specifies the HP-X sample number data to retrieve

sampleNbrY - specifies the HP-Y sample number data to retrieve

Returns:

nGenes # of genes in xList[], yList[], else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xList[], yList[]) sizes.

getHP_XandYsetDataForSample

public final int getHP_XandYsetDataForSample(float[] xList,
                                             float[] yList,
                                             int[] propList,
                                             java.lang.String geneListName)

getHP_XandYsetDataForSample() - get normalized HP-X, -Y 'sets' (X,Y,prop) data lists for sample in (Xdata[],Ydata[], propList[] for FILTERED data by the specified gene list. The will get the current data filtered list of nGene genes mean 'set' intensity data into (Xlist,Ylist,PropList). Note: preallocate maximum size arrays before call.

Parameters:

xList - RTN: mean intensity data[0:nGene-1] for X sample

yList - RTN: mean intensity data[0:nGene-1] for Y sample

propList - RTN: gene property list[0:nGene-1]

geneListName - name of gene list specifying genes to filter by. If you specify null, it will use the set of ALL GENES gene list.

Returns:

nGenes # of genes in xList[], yList[], propList, else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xList[], yList[]) sizes.

getAllHP_XandYsetDataForSample

public final int getAllHP_XandYsetDataForSample(float[] xList,
                                                float[] yList)

getAllHP_XandYsetDataForSample() - get all HP-X, -Y 'sets' (X,Y) normalized data lists for sample in (Xdata[],Ydata[] for ALL genes. The will get the current data list ofall nGene genes mean 'set' intensity data into (Xlist,Ylist). Note: preallocate maximum size arrays before call.

Parameters:

xList - RTN: mean intensity data[0:nGene-1] for X sample

yList - RTN: mean intensity data[0:nGene-1] for Y sample

Returns:

nGenes # of genes in xList[], yList[] else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the (xList[], yList[]) sizes.

getMeanDataForCondition

public final int getMeanDataForCondition(float[] meanData,
                                         float[] stdDevData,
                                         int[] propList,
                                         java.lang.String condListName,
                                         java.lang.String geneListName)

getMeanDataGeneListDataForCondition() - get filtered (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in (meanData[], stdDevData[], propList[]) for data filtered by the specified gene list. The dataList[] is intensity data. If you are using ratio data, this is the ratio data for each sample i.e. (F1/F2) or (Cy3/Cy5) for the sample. Otherwise is the F1 data. Data is corrected for background, and median Ratio correction if applicable and the mode is set in the MAExplorer menus. The will get the current intensity data filtered list of nGene genes into (datalist,PropList,GeneList) lists. Note: preallocate maximum size arrays before call.

Parameters:

meanData - RTN: mean intensity data[0:nGene-1] for samples if succeed

stdDevData - RTN: StdDev intensity data[0:nGene-1] for samples if succeed. If this is null, don't return the StdDev data.

propList - RTN: gene property list[0:nGene-1] if succeed see GENE_xxxx properties. If this is null, don't return the properties data.

condListName - specifies the condition list of samples data to retrieve

geneListName - name of gene list to copy data filter genes into. If the name is null, use the set of ALL GENES gene list.

Returns:

nGenes # of genes in dataList[] and propList[], if the geneListName is not found, use the data filter, else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the dataList[]) size.

getAllMeanDataForCondition

public final int getAllMeanDataForCondition(float[] meanData,
                                            float[] stdDevData,
                                            java.lang.String condListName)

getAllMeanDataGeneListDataForCondition() - get all (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in in (meanData[], stdDevData[]) for data filtered by the specified gene list. The dataList[] is intensity data. If you are using ratio data, this is the ratio data for each sample i.e. (F1/F2) or (Cy3/Cy5) for the sample. Otherwise is the F1 data. Data is corrected for background, and median Ratio correction if applicable and the mode is set in the MAExplorer menus. The will get the current intensity data filtered list of nGene genes into (datalist) lists. Note: preallocate maximum size arrays before call.

Parameters:

meanData - RTN: mean intensity data[0:nGene-1] for samples if succeed

stdDevData - RTN: StdDev intensity data[0:nGene-1] for samples if succeed

condListName - specifies the condition list of samples data to retrieve

Returns:

nGenes # of genes in dataList[] else 0 if error. If the list length is shorter than the # of genes to be copied, then do not save the remaining genes, but return the total count so the caller can test if they got them all if the return size equals the dataList[]) size.