Class MJAhistogram

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

public class MJAhistogram

extends MJAbase

MAExplorer Open Java API class to access MJAhistogram methods and data structures. Access histograms and methods

List of methods available to Plugin-writers

 calcHistOfHP_XYRatios() - calc of ratio hist of HP-X/-Y spot data.
 calcHistOfF1F2Ratios() - calc ratio hist of current HP F1/F2 spot data.
 calcSampleIntensityHistogram() - compute intensity histogram for sample
 calcAndcalcAndGetSampleStats() - get list of sample's global array stats
 getSampleHistStats() - compute Filtered sample intensity histogram & stats
 calcIntensityHistogram() - compute intensity histogram for Sample

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: 2003/04/03 21:03:28 $ $Revision: 1.6 $

Author:

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

See Also:

MAExplorer Home, for additional histogram methods and data

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.util.Hashtable	calcAndGetSampleStats(int sampleNbr, boolean recalcHistFlag) calcAndGetSampleStats() - get list of sample's global array statistics You map recompute the histogram.
java.util.Hashtable	calcHistOfF1F2Ratios(int sampleNbr) calcHistOfF1F2Ratios() - get Hashtable list of features for ratio histogram of the current HP sample F1/F2 spot data.
java.util.Hashtable	calcHistOfHP_XYRatios() calcHistOfHP_XYRatios() - get Hashtable list of features of ratio histogram of HP-X/-Y spot data for the current HP-X and HP-Y samples.
boolean	calcIntensityHistogram(int sampleNbr) calcIntensityHistogram() - compute intensity histogram for Sample for the current normalization.
boolean	calcSampleIntensityHistogram(int sampleNbr) calcSampleIntensityHistogram() - compute intensity histogram for current normalization method.
java.util.Hashtable	getSampleHistStats(int sampleNbr, boolean doRecalcHistFlag) getSampleHistStats() - compute Filtered sample intensity histogram and get list of statistics and return list of statistics

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

calcHistOfHP_XYRatios

public final java.util.Hashtable calcHistOfHP_XYRatios()

calcHistOfHP_XYRatios() - get Hashtable list of features of ratio histogram of HP-X/-Y spot data for the current HP-X and HP-Y samples. The histogram is recomputed on the current data filter. If the Use Multiple X and Y sample 'sets' is on, then the ratios are for the mean HP-X 'set' and the mean HP-Y 'set'. Only genes passing the data Filter are used in computing the data. Note this methods assumes that HP-X and HP-Y have been set.

 The Hashtable list returned is defined as:
 Name           - Value
 "nList"              - int size of gene list
 "ListOfMIDs"         - int[] of gene MIDs indices
 "ListOfRatios"       - float[] of gene ratios
 "maxRatioHistIdx"    - int index of maximum histogram value
 "minRatioHistIdx"    - int index of minimum histogram value
 "NbrBinsInHistogram" - int # of bins in histogram
 "RatioHistFreqList"  - long[] frequency histograms
 "RatioValuesList"    - float[] values corresponding to histogram bins
 

Returns:

a hashtable if ok, else null if error.

calcHistOfF1F2Ratios

public final java.util.Hashtable calcHistOfF1F2Ratios(int sampleNbr)

calcHistOfF1F2Ratios() - get Hashtable list of features for ratio histogram of the current HP sample F1/F2 spot data. If Cy3/Cy5 ratio data is being used, then (F1=Cy3, F2=Cy5) and the histogram is of the (Cy3/Cy5) ratio (modulo that Cy3 and Cy5 are swapped for this particular sample. Only genes passing the data Filter are used in computing data. Note this methods assumes that the current sample has been set.

 The Hashtable list returned is defined as:
 Name           - Value
 "nList"               - int size of gene list
 "ListOfMIDs"          - int[] of gene MIDs indices
 "ListOfRatios"        - float[] of gene ratios
 "maxRatioHistIdx"     - int index of maximum histogram value
 "minRatioHistIdx"     - int index of minimum histogram value
 "NbrBinsInHistogram"  - int # of bins in histogram
 "RatioHistFreqList"   - long[] frequency histograms
 "RatioValuesList"     - float[] values corresponding to histogram bins
 

Parameters:

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

Returns:

a hashtable if ok, else null if error.

calcSampleIntensityHistogram

public final boolean calcSampleIntensityHistogram(int sampleNbr)

calcSampleIntensityHistogram() - compute intensity histogram for current normalization method.

Parameters:

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

Returns:

ok, if were successful, else false if method failed.

calcAndGetSampleStats

public final java.util.Hashtable calcAndGetSampleStats(int sampleNbr,
                                                       boolean recalcHistFlag)

calcAndGetSampleStats() - get list of sample's global array statistics You map recompute the histogram. If not, then you just get the previous values.

 The Hashtable list returned is defined as:
 Name            - Value
 "SampleName"        - String name of sample file (without .quant file
                       extension) in the database
 "SampleNumber"      - int sample number in the database
 "HistMeanIdx"       - int index in histogram of mean raw intensity
 "HistModeIdx"       - int index in histogram of mode raw intensity
 "HistMedianIdx"     - int index in histogram of median raw intensity
 "HistMaxFV"         - float maximum and fractions of dynamic range
 "Mean"              - float histogram mean raw intensity
 "Mode"              - float histogram mode raw intensity
 "Median"            - float histogram median raw intensity
 "MeanAbsDev"        - float hist mean absolute deviation raw intensity
 "logMean"           - float log of histogram mean raw intensity
 "logStdDev"         - float log of histogram StdDev raw intensity
 "logmeanAbsDev"     - float log of histogram mean absolute deviation
                       raw intensity
 "maxDataS"          - float scaled maximum data value for the current
                       normalization
 "minDataS"          - float scaled minimum data value for the current
                       normalization
 "maxRawS"           - float raw maximum data value for cur. normalization
 "minRawS"           - float raw maximum data value for cur. normalization
 "Histogram"         - int[0:nbrBins-1] hist of data Filtered raw intensity
 "nbrBins"           - int number of bins in the histogram
 "WidthOfBin"        - float width of bin in histogram in intensity space
 "HistMedianIntens"  - float histogram value at median intensity
 "HistMeanIntensity" - float histogram value at mean intensity
 "HistModeIntensity" - float histogram value at mode intensity
 "HistMaxIntensity   - float histogram value at max intensity
 "HistMinIntensity"  - float histogram value at min intensity
 "HistNormFactor"    - float normalization factor for all intensity data
                       so we can compare intensity between HP samples.
 

Parameters:

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

Returns:

hashtable list else null if not found or error

getSampleHistStats

public final java.util.Hashtable getSampleHistStats(int sampleNbr,
                                                    boolean doRecalcHistFlag)

getSampleHistStats() - compute Filtered sample intensity histogram and get list of statistics and return list of statistics

 The Hashtable list returned is defined as:
 Name           - Value
 "histogram"        - int[] intensity histogram frequency counts
 "nbrBins"          - int number of bins in intensity histogram
 "minRawIntensity"  - float minimum raw intensity seen in sample
 "maxRawIntensity"  - float maximum raw intensity seen in sample
 "meanIntensity"    - float mean of intensity histogram
 "modeIntensity"    - float mode of intensity histogram
 "minIntensity"     - float minimum scaled intensity seen in sample
 "maxIntensity"     - float maximum scaled intensity seen in sample
 "stdDev"           - float Std Deviation of histogram
 "meanAbsDev"       - float Mean Absolute Deviation of histogram
 "meanIdx"          - int index of mean in intensity histogram
 "modeIdx"          - int index of mode in intensity histogram
 "medianIdx"        - int index of median in intensity histogram
 "deltaBin"         - float width of bin in intensity histogram
 

Parameters:

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

doRecalcHistFlag - recompute histogram before get data

Returns:

hash table else null if not found or error.

calcIntensityHistogram

public final boolean calcIntensityHistogram(int sampleNbr)

calcIntensityHistogram() - compute intensity histogram for Sample for the current normalization.

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.