Class MJAsample

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

public class MJAsample

extends MJAbase

MAExplorer Open Java API class to access MJAsample methods and data structures. Access get and put single sample top-level data.

List of methods available to Plugin-writers

 setSampleNameMethod() - sets sample name method to  name domain to be used.
 lookupSampleName() - Return sample number by SampleID (free-text) name
 lookupSampleNameByDBfileName() - Return sample number by sample DB file name
 lookupSampleNameByDBfileID() - lookup sample number by sample databaseFileID
 lookupSampleByFreeTextName() - lookup sample number by SampleID (free-text) name.

 getSampleIDbySampleNbr() - lookup the sample ID name by sample number
 getProjectNameBySampleNbr() - lookup the sample project name by sample number
 getFullSampleTextBySampleNbr() - lookup full sample text description by sample number
 
 getRawIntensityQuantDataList() - get raw spot intensity quant data list 
 getRawBkgrdQuantDataList() - get raw spot background quant data 
 getQualCheckQuantDataList() - get spot QualCheck good spot data list 
 getCorrCoefQuantDataList() - get spot intensity correlation coeff. data
 getXYdataList() - get list of XY coordinates data for sample
 getQualCheckList() - get list of QualCheck data for sample
 getSampleScaleFactors() - get list of a sample's scale factors
 getSampleF1F2Extrema() - get list of sample's F1F2 intensity extrema
 setSampleF1F2Extrema() - set normalized list of sample's F1F2 intensity extrema
 setSampleCurScaledExtrema() - set sample's current normalized scaled intensity extrema. 
 getSampleTypeFlags() - get list of a sample's property flags
 getSampleTotHistStats() - get list of a sample's total histogram statistics
 getSampleCalibDNAdata() - get list of a Sample calibration DNA data
 calcIntensityScaleExtrema() - compute intensity scale extrema for Sample.
 calcMeanCalibrationDNA() - compute (mean,StdDev) gene for Sample
 calcMeanUseNormGeneSet() - compute (mean,StdDev) normalization gene set
 swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics 
 getSamplesDataVector() - get sample data for sample indexes for gene mid.

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: 2003/03/03 16:15:16 $ $Revision: 1.12 $

Author:

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

See Also:

MAExplorer Home, for other Sample Histogram methods

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

boolean	calcIntensityScaleExtrema(int sampleNbr) calcIntensityScaleExtrema() - compute intensity scale extrema for Sample.
boolean	calcMeanCalibrationDNA(int sampleNbr) calcMeanCalibrationDNA() - compute (mean,StdDev) gene for Sample for calibration cDNA for the current normalization.
boolean	calcMeanUseNormGeneSet(int sampleNbr) calcMeanUseNormGeneSet() - compute (mean,StdDev) normalization gene set for Sample.
float[]	getCorrCoefQuantDataList(int sampleNbr) getCorrCoefQuantDataList() - get spot intensity correlation coefficient data for the given sample.
java.lang.String	getFullSampleTextBySampleNbr(int sampleNbr) getFullSampleTextBySampleNbr() - lookup the full sample text description by sample number.
java.lang.String	getProjectNameBySampleNbr(int sampleNbr) getProjectNameBySampleNbr() - lookup the sample project name by sample number.
float[]	getQualCheckList(int sampleNbr) getQualCheckList() - get list of QualCheck data for sample number.
float[]	getQualCheckQuantDataList(int sampleNbr) getQualCheckQuantDataList() - get spot QualCheck good spot data list for the given sample.
float[]	getRawBkgrdQuantDataList(int sampleNbr) getRawBkgrdQuantDataList() - get raw spot background quant data for the given sample.
float[]	getRawIntensityQuantDataList(int sampleNbr) getRawIntensityQuantDataList() - get raw spot intensity quant data list for the given sample.
java.util.Hashtable	getRawSampleData(int sampleNbr) getRawSampleData() - get list of a sample's total histogram statistics.
java.util.Hashtable	getSampleCalibDNAdata(int sampleNbr, boolean recalcCalDNAcalibFlag) getSampleCalibDNAdata() - get list of a Sample calibration DNA data this sample.
java.util.Hashtable	getSampleF1F2Extrema(int sampleNbr) getSampleF1F2Extrema() - get list of sample's normalized F1F2 intensity extrema and 1st order histogram statistics.
java.lang.String	getSampleIDbySampleNbr(int sampleNbr) getSampleIDbySampleNbr() - lookup the sample ID name by sample number.
boolean	getSamplesDataVector(float[] sampleData, int[] samplesIndex, int mid) getSamplesDataVector() - get sample data for sample indexes for gene mid.
java.util.Hashtable	getSampleTotHistStats(int sampleNbr) getSampleTotHistStats() - get list of a sample's total histogram statistics.
java.util.Hashtable	getSampleTypeFlags(int sampleNbr)
java.util.Hashtable	getScaleFactors(int sampleNbr) getSampleScaleFactors() - get list of a sample's scale factors.
java.awt.Point[]	getXYdataList(int sampleNbr) getXYdataList() - get list of XY coordinates data for sample.
int	lookupSampleByFreeTextName(java.lang.String sampleFreeTextName, java.lang.String condName) lookupSampleByFreeTextName() - lookup sample number by SampleID (free-text) name.
int	lookupSampleName(java.lang.String databaseFileID, java.lang.String condName) lookupSampleName() - lookup sample number by sample databaseFileID.
int	lookupSampleNameByDBfileID(java.lang.String databaseFileID, java.lang.String condName) lookupSampleNameByDBfileID() - lookup sample number by sample databaseFileID.
int	lookupSampleNameByDBfileName(java.lang.String sampleDBfileName, java.lang.String condName) lookupSampleNameByDBfileName() - lookup sample number by sample DB file name.
void	setSampleCurScaledExtrema(int sampleNbr, float maxDataS, float minDataS, float maxRawS, float minRawS) setSampleCurScaledExtrema() - set sample's current normalized scaled intensity extrema.
void	setSampleF1F2Extrema(int sampleNbr, float minDataF1, float minDataF2, float maxDataF1, float maxDataF2) setSampleF1F2Extrema() - set list of sample's normalized F1F2 intensity extrema.
static boolean	setSampleNameMethod(int nameMethodToUse) setSampleNameMethod() - sets the sample name method to the name domain to be used.
boolean	swapCy5Cy3AndReCalcStats(int sampleNbr) swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics for sample.

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

setSampleNameMethod

public static final boolean setSampleNameMethod(int nameMethodToUse)

setSampleNameMethod() - sets the sample name method to the name domain to be used.

Parameters:

nameMethodToUse - may be NAME_METHOD_DB_FILE_NAME, NAME_METHOD_DB_FILE_ID, or NAME_METHOD_DB_SAMPLE_ID

Returns:

true if the nameMethod is legal.

lookupSampleName

public final int lookupSampleName(java.lang.String databaseFileID,
                                  java.lang.String condName)

lookupSampleName() - lookup sample number by sample databaseFileID. Sample numbers are in the range of [1:maxSamples].

Parameters:

databaseFileID - sample file name to search for. Note: don't include the file extension in the name.

condName - name of condition

Returns:

sample number or -1 if failed

lookupSampleNameByDBfileName

public final int lookupSampleNameByDBfileName(java.lang.String sampleDBfileName,
                                              java.lang.String condName)

lookupSampleNameByDBfileName() - lookup sample number by sample DB file name.

Parameters:

sampleDBfileName - sample file name to search for. Note: don't include the file extension in the name.

condName - name of condition

Returns:

sample number or -1 if failed

lookupSampleNameByDBfileID

public final int lookupSampleNameByDBfileID(java.lang.String databaseFileID,
                                            java.lang.String condName)

lookupSampleNameByDBfileID() - lookup sample number by sample databaseFileID. Sample numbers are in the range of [1:maxSamples].

Parameters:

databaseFileID - sample file name to search for. Note: don't include the file extension in the name.

condName - name of condition

Returns:

sample number or -1 if failed

lookupSampleByFreeTextName

public final int lookupSampleByFreeTextName(java.lang.String sampleFreeTextName,
                                            java.lang.String condName)

lookupSampleByFreeTextName() - lookup sample number by SampleID (free-text) name. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleFreeTextName - sample free-text name to search for sample

condName - name of condition

Returns:

sample number or -1 if failed

getSampleIDbySampleNbr

public final java.lang.String getSampleIDbySampleNbr(int sampleNbr)

getSampleIDbySampleNbr() - lookup the sample ID name by sample number. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - is the number of the sample to lookup

Returns:

the result if found, else null

getProjectNameBySampleNbr

public final java.lang.String getProjectNameBySampleNbr(int sampleNbr)

getProjectNameBySampleNbr() - lookup the sample project name by sample number. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - is the number of the sample to lookup

Returns:

the result if found, else null

getFullSampleTextBySampleNbr

public final java.lang.String getFullSampleTextBySampleNbr(int sampleNbr)

getFullSampleTextBySampleNbr() - lookup the full sample text description by sample number. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - is the number of the sample to lookup

Returns:

the result if found, else null

getRawIntensityQuantDataList

public final float[] getRawIntensityQuantDataList(int sampleNbr)

getRawIntensityQuantDataList() - get raw spot intensity quant data list for the given sample. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

data array if sampleNbr is found, otherwise the data array for the current sample is returned.

getRawBkgrdQuantDataList

public final float[] getRawBkgrdQuantDataList(int sampleNbr)

getRawBkgrdQuantDataList() - get raw spot background quant data for the given sample. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

data array if sampleNbr is found, otherwise the data array for the current sample is returned.

getQualCheckQuantDataList

public final float[] getQualCheckQuantDataList(int sampleNbr)

getQualCheckQuantDataList() - get spot QualCheck good spot data list for the given sample. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

data array if sampleNbr is found, otherwise the data array for the current sample is returned.

getCorrCoefQuantDataList

public final float[] getCorrCoefQuantDataList(int sampleNbr)

getCorrCoefQuantDataList() - get spot intensity correlation coefficient data for the given sample. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

data array if sampleNbr is found, otherwise the data array for the current sample is returned.

getXYdataList

public final java.awt.Point[] getXYdataList(int sampleNbr)

getXYdataList() - get list of XY coordinates data for sample. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

data array if sampleNbr is found, otherwise the data array for the current sample is returned.

getQualCheckList

public final float[] getQualCheckList(int sampleNbr)

getQualCheckList() - get list of QualCheck data for sample number. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

data array if sampleNbr is found, otherwise the data array for the current sample is returned.

getScaleFactors

public final java.util.Hashtable getScaleFactors(int sampleNbr)

getSampleScaleFactors() - get list of a sample's scale factors. Sample numbers are in the range of [1:maxSamples]. These are used in various built-in normalization modes. Call calcIntensityScaleExtrema()to refresh the data.

 The Hashtable list returned is defined as:
 Name                - Value
 "ratioMedianScale"     - float may be set if Cy3/Cy5 median scale
                          correction
 "ratioMedianBkgdScale" - float may be set if Cy3/Cy5 median background
                          scale correction
 "stdDevUseGeneSet"     - float StdDev 'User Filter Gene Set' intensity
 "meanUseGeneSet"       - float mean 'User Filter Gene Set' intensity
 "scaleUseGeneSet"      - float scale factor for 'User Filter Gene set'
 "scaleUseGeneSetTo65K" - float scale factor for 'User Filter Gene Set'
                          but max for all HPs is 65K
 "stdDevCalDNA"         - float StdDev 'calibration DNA' intensity
 "meanCalDNA"           - float mean 'calibration DNA' intensity
 "scaleCalDNA"          - float scale factor for scaling by 'calibration
                          DNA' intensity
 "scaleCalDNAto65K"     - float scale factor for scaling by 'calibration
                          DNA' intensity, but max for all HPs is 65K
 "normFactor"           - float normalization factor for all intensity
                          data so can compare intensity between HPs

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

hashtable list else null if not found or error.

See Also:

calcIntensityScaleExtrema(int)

getSampleF1F2Extrema

public final java.util.Hashtable getSampleF1F2Extrema(int sampleNbr)

getSampleF1F2Extrema() - get list of sample's normalized F1F2 intensity extrema and 1st order histogram statistics. Also get the raw intensity extrema. Sample numbers are in the range of [1:maxSamples].

 The Hashtable list returned is defined as:
 Name        - Value
     --- normalized intensity data -----
 "minDataF1"     - float minimum intensity data for F1 channel
 "minDataF2"     - float minimum intensity data for F2 channel
 "maxDataF1"     - float maximum intensity data for F1 channel
 "maxDataF2"     - float maximum intensity data for F2 channel
 "medianF1"      - float median intensity of F1 channel data
 "medianF2"      - float median intensity of F2 channel data
 "medianF1Bkgd"  - float median background intensity of F1 channel data
 "medianF2Bkgd"  - float median background intensity of F2 channel data
     --- Raw intensity data -----
 "minRI"         - float min raw intensity
 "maxRI"         - float max raw intensity
 "minRI1"        - float min raw intensity F1 (Cy3)
 "maxRI1"        - float max raw intensity F1 (Cy3)
 "minRI2"        - float min raw intensity F2 (Cy5)
 "maxRI2"        - float max raw intensity F2 (Cy5)
 "minRatioRI"    - float min raw intensity ratio F1/F2
 "maxRatioRI"    - float max raw intensity ratio F1/F2
 

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

hash table else null if not found or error.

setSampleF1F2Extrema

public final void setSampleF1F2Extrema(int sampleNbr,
                                       float minDataF1,
                                       float minDataF2,
                                       float maxDataF1,
                                       float maxDataF2)

setSampleF1F2Extrema() - set list of sample's normalized F1F2 intensity extrema. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

minDataF1 - is minimum normalized data for F1 channel

minDataF2 - is minimum normalized data for F1 channel

maxDataF1 - is maximum normalized data for F1 channel

maxDataF2 - is maximum normalized data for F2 channel

setSampleCurScaledExtrema

public final void setSampleCurScaledExtrema(int sampleNbr,
                                            float maxDataS,
                                            float minDataS,
                                            float maxRawS,
                                            float minRawS)

setSampleCurScaledExtrema() - set sample's current normalized scaled intensity extrema. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

maxDataS - is current norm: scaled max data

minDataS - is current norm: scaled min data

maxRawS - is current norm: scaled maxRaw data

minRawS - is current norm: scaled minRaw data

getSampleTypeFlags

public final java.util.Hashtable getSampleTypeFlags(int sampleNbr)

getRawSampleData

public final java.util.Hashtable getRawSampleData(int sampleNbr)

getRawSampleData() - get list of a sample's total histogram statistics. Sample numbers are in the range of [1:maxSamples]. This data is currently computed on non-data Filtered (i.e. all genes) list of data.

 The Hashtable list returned is defined as:
 Name          - Value
 "scaleToMaxIV"    - float total array: maxFV/maxRI scale factor to
                     compute the maximum range
 "maxFV"           - float maximum and fraction
 "minRI"           - float min raw intensity
 "maxRI"           - float max raw intensity
 "minRI1"          - float min raw intensity F1 (Cy3)
 "maxRI1"          - float max raw intensity F1 (Cy3)
 "minRI2"          - float min raw intensity F2 (Cy5)
 "maxRI2"          - float max raw intensity F2 (Cy5)
 "minRaw"          - float min raw intensity (@)
 "maxRaw"          - float max raw intensity (@)
 "minRatioRI"      - float min Ratio of raw intensity
 "maxRatioRI"      - float max Ratio of raw intensity
 "xCmin"           - int min X coord mapped to MAE coord
 "yCmin"           - int min Y coord mapped to MAE coord
 "xCmax"           - int max X coord mapped to MAE coord
 "yCmax"           - int max Y coord mapped to MAE coord
 

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

null if not found or error, else return list.

getSampleTotHistStats

public final java.util.Hashtable getSampleTotHistStats(int sampleNbr)

getSampleTotHistStats() - get list of a sample's total histogram statistics. Sample numbers are in the range of [1:maxSamples]. This data is currently computed on non-data Filtered (i.e. all genes) list of data.

 The Hashtable list returned is defined as:
 Name          - Value
 "minHistData"     - float total array: min hist data value
 "maxHistData"     - float total array: max hist data value
 "mnHPri"          - float total array: rawIntens mean, all genes in HP
                     sample without background
 "sdHPri"          - float total array: rawIntens StdDev, all genes in
                     HP sample without background
 "madHPri"         - float total array: rawIntens meanAbsDev,
                     all genes in HP sample without background
 "mnHPri1"         - float total array: rawIntens f1 mean, all
                     genes in HP sample without background
 "sdHPri1"         - float total array: rawIntens f1 StdDev, all
                     genes in HP sample without background
 "mnHPri2"         - float total array: rawIntens f2 mean, all
                     genes in HP sample without background
 "sdHPri2"         - float total array: rawIntens f2 StdDev, all
                     genes in HP sample without background
 "scaleToMaxIV"    - float total array: maxFV/maxRI scale factor to
                     compute the maximum range
 "maxFV"           - float maximum and fractions of dynamic range
 "logMeanRI"       - float total array: std dev of log of means
 "logStdDevRI"     - float total array: std dev of log of means
 "logMeanAbsDevRI" - float total array: Filter hist: log of mean
                     absolute deviation raw intensity
 "logMaxRI"        - float total array: log of maxRI
 "logMinRI"        - float total array: log of minRI
 "medianRI"        - float median raw intensity
 "modeRI"          - float mode raw intensity
 "minRI"           - float min raw intensity
 "maxRI"           - float max raw intensity
 "minRI1"          - float min raw intensity F1 (Cy3)
 "maxRI1"          - float max raw intensity F1 (Cy3)
 "minRI2"          - float min raw intensity F2 (Cy5)
 "maxRI2"          - float max raw intensity F2 (Cy5)
 "minRaw"          - float min raw intensity (@)
 "maxRaw"          - float max raw intensity (@)
 "deltaHistBin"    - float delta Hist Bin (bin width)
 "minRatioRI"      - float min Ratio of raw intensity
 "maxRatioRI"      - float max Ratio of raw intensity
 "logMinRatioRI"   - float log minRatioRI
 "logMaxRatioRI"   - float log maxRatioRI
 "logRange"        - float log ratio range [Rmin:Rmax]
 "logDeltaBin"     - float (MAX_INTENSITY/logRange)
 "logMiddle"       - float -logMinRatioRI for finding RI==1.0
 "xCmin"           - int min X coord mapped to MAE coord
 "yCmin"           - int min Y coord mapped to MAE coord
 "xCmax"           - int max X coord mapped to MAE coord
 "yCmax"           - int max Y coord mapped to MAE coord
 

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

null if not found or error, else return list.

getSampleCalibDNAdata

public final java.util.Hashtable getSampleCalibDNAdata(int sampleNbr,
                                                       boolean recalcCalDNAcalibFlag)

getSampleCalibDNAdata() - get list of a Sample calibration DNA data this sample. If recalcCalDNAcalibFlag is set, then recompute it. Sample numbers are in the range of [1:maxSamples].

 The Hashtable list returned is defined as:
 Name           - Value
 "sampleNbr"        - int sample number
 "meanCalDNA"       - float mean of calibration DNA
 "stdDevCalDNA"     - float Std-Dev of calibration DNA
 "scaleCalDNA"      - float scale factor for calibration DNA
 "scaleUseGeneSet"  - float scale factor for 'Use Gene Set'
 "scaleCalDNAto65K" - float scale factor for calibration DNA to 65K
 

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

recalcCalDNAcalibFlag - recompute calibration before get data

Returns:

null if not found or error, else return list.

calcIntensityScaleExtrema

public final boolean calcIntensityScaleExtrema(int sampleNbr)

calcIntensityScaleExtrema() - compute intensity scale extrema for Sample. Find intensity scale extrema for current normalization. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

true if succeed, else false if problems.

calcMeanCalibrationDNA

public final boolean calcMeanCalibrationDNA(int sampleNbr)

calcMeanCalibrationDNA() - compute (mean,StdDev) gene for Sample for calibration cDNA for the current normalization. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

true if succeed else false if problems.

calcMeanUseNormGeneSet

public final boolean calcMeanUseNormGeneSet(int sampleNbr)

calcMeanUseNormGeneSet() - compute (mean,StdDev) normalization gene set for Sample. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

false if method was not found or method failed, otherwise the flag returned by the method.

swapCy5Cy3AndReCalcStats

public final boolean swapCy5Cy3AndReCalcStats(int sampleNbr)

swapCy5Cy3AndReCalcStats() - swap Cy3 and Cy5, recalculate statistics for sample. Toggle swapCy5Cy3DataFlag for this sample. Sample numbers are in the range of [1:maxSamples].

Parameters:

sampleNbr - sample number to use, else current HP sample if 0

Returns:

true if succeed else false if problems.

getSamplesDataVector

public final boolean getSamplesDataVector(float[] sampleData,
                                          int[] samplesIndex,
                                          int mid)

getSamplesDataVector() - get sample data for sample indexes for gene mid. Save the data in precomputed sampleData[] array of 1D vectors.

Parameters:

sampleData - - array to return samples data

samplesIndex - - list of sample indices [1:N] (not [0:N-1] to lookup data

mid - gene to lookup

Returns:

true if succeed