Class MaHPquantTable

java.lang.Object
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  +--SimpleTable
        |
        +--Table
              |
              +--MaHPquantTable

class MaHPquantTable

extends Table

The class is only used to read a .quant file (File or URL) into an mae.ms instance. The temporary data structures are then garbage collected. It parses data from a quantified microarray tab-delimited file. The data might be from the analysis by various microarray image quantification programs including (Axon's GenePix, Scanarray, R.G.'s Pathways 2.01, MolDyn ImageQuant-NT, etc). Since the data is a tab-delimited format, any program which can generate this type of data could be used. Most quantitative data formats use integers for (grid,row,col) values. However, some formats use letters [A:Z] for the first 26 (i.e. [1:26]), and [a:z] for the next 26 (i.e. [27:52]) values. Sometimes only lower case letters are used - in which case we must map [a:z] to [1:26]. When MAExplorer first sees a letter in reading the data, it checks to see if it is an upper or lowercase letter and generates the proper offset needed to generate the mapping.

HISTORICAL NOTES: The fields were initially derived from the Research Genetics microarray quantitation .txt table for the corresponding microarray. This whole file is a tab delimited file consisting of some of the following fields:

ALL R.G. Pathways 2.01 fields: "TableName" "FilterType_Description" "ShortName" "Header_Description" "Date" "Researcher" "SampleGrid" "BGLow" "BGAvg" "BGRms" "X" "Y" "RawIntensity" "field" "grid" "grid col" "grid row" "release" "plate" "release row" "release col" "clone id" "type" "norm"

NOTE: we do not use the following since we get it from the GeneTable. "release" "plate" "release row" "release col" "clone id"

The .quant file subset of fields that we try to parse are: "X" "Y" "RawIntensity" "field" "grid" "grid col" "grid row"

Additional global data is saved in the SamplesDB file (@see #SampleTable) that contains a row for each sample with the remaining data: "TableName" "FilterType_Description" "ShortName" "Header_Description" "Date" "Researcher" "SampleGrid" "BGLow" "BGAvg" "BGRms"

where "BGLow" "BGAvg" "BGRms" are global background values such as that defined by a R.G. Pathways 2.01 analysis.

NOTE: if you are using the symbolic ImageQuant GIPO symbol "NAME_GRC", it has the grid #, row# and column# specified as follows:

 e.g. in following (grid,row,column) = (8,12,11)
       "GRID-   8-R12C11". 

When the field # is not explicitly specified, the data may be vertically stacked. We handle multiple (vertically stacked) occurances by replicating the GIPO entry for each field for intensity data (not cy3/cy5 ratio data) if maxFIELDS > 1. If "field" exists, then use "RawIntensity", else for each field [1:maxFIELDS] look for "RawIntensity1", "RawIntensity2" when we do the field 1 and field passes of the file.

 We use the QualCheck field derived from the Becker/NIA QualCheck codes:
  1 = analyzable gene (clone or oligo) on array, good clone id.
  2 = analyzable gene (clone or oligo) on array, bad clone id, good gene name.
  3 = non-analyzable gene (clone or oligo) on array, e.g. empty spots, or
      filled with internal testing material.
  4 = analyzable gene (clone or oligo), duplicated genes on the microarray,
      only one duplicate is flagged with the "4".
 We define the legal QualCheck codes in Gene.C_XXXXX properties bits.

NOTE: (6/8/00) - use of "Location"

The optional "Location" entry may be the identifier for some databases.] It might also indicate that a gene is 'good' since bad genes on the array may be missing from both the GIPO and the .quant data files. This missing data is used in Cvt2Mae to synthesize missing genes by creating spot entrys with 0 density.

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: 1.10 $

Author:

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

See Also:

MAExplorer Home, MaHybridSample

Field Summary

private int	allocSize number of spots allocated as map.maxSpots+1.
private CompositeDatabase	cdb link to global CompositeDatabase instance
private Config	cfg link to global Config instance
(package private) static int	DELTA_X_SPACING (opt) Horiz.
(package private) static int	DELTA_Y_SPACING Vert.
private boolean	doRatioFlag flag: if maxFIELD==1 && useRatioDataFlag
private FileIO	fio link to global FileIO vinstance
private char	gridCharOffset Grid alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters
private char	gridColCharOffset Grid Column alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters
private char	gridRowCharOffset Grid Row alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters
(package private) static int	GUARD_REGION # pixels in target image on each edge
private int	idxBkgrd background raw intensity spot data
private int	idxBkgrd1 background raw intensity channel 1, if code mult fields in each row
private int	idxBkgrd2 background raw intensity channel 2, if code mult fields in each row
private int	idxDetValue Opt.
private int	idxfield opt.
private int	idxgrid separate GRC spec.
private int	idxgrid_col separate GRC spec.
private int	idxgrid_row separate GRC spec.
private int	idxLocation opt.
private int	idxNameGridIdx MolDyn GRC coding for (grid,grid-row,grid-column) as "NAME_GRC" e.g.
private int	idxQualCheck Opt.
private int	idxRawIntens raw intensity spot data
private int	idxRawIntens1 raw intensity spot data for channel 1, if code mult fields in each row
private int	idxRawIntens2 raw intensity spot data for channel 2, if code mult fields in each row
private int	idxX opt.
private int	idxY opt.
private boolean	isGridColDigitFlag flag: Grid-Col value is coded as digit else alpha
private boolean	isGridDigitFlag flag: Grid value is coded as digit else alpha
private boolean	isGridRowDigitFlag flag: Grid-Row value is coded as digit else alpha
private boolean	learnGRCcodingFlag flag: once only code when analyze for MolDyn "NAME_GRC" coding
private MAExplorer	mae link to global MAExplorer instance
private java.lang.String	maeTbl name of remap Table
private Maps	map link to global Maps instance
private int	maxFIELDS maximum number of fields allowed
private int	maxGCOLS maximum number of grid cols allowed
private int	maxGRIDS maximum number of grids allowed
private int	maxGROWS maximum number of grid rows allowed
static float	maxHsize
static float	maxVsize
private MaHybridSample	ms HP sample that owns this table instance
private int	nGenes # of genes
private int	nSpots number of spots read.
private boolean	screenGoodGenesFlag flag: if calc glob-stats on only GoodGenes
(package private) static int	SPACING_BETWEEN_SPOTS (opt) spacing between spots
private boolean	swapCy5Cy3DataFlag
(package private) static int	X_GRID_OFFSET value to add to orig data coords to draw GRID labels
(package private) static int	X_SPOTQ_OFFSET value to add to orig data coords x_textQ[].
private int	xRmax max X coordinate from orig .quant data
private int	xRmin min X coordinate from orig .quant data
(package private) static int	Y_SPOTQ_OFFSET value to add to orig data coords y_textQ[] AND to grid coords so they match spots
private int	yRmax max Y coordinate from orig .quant data
private int	yRmin min Y coordinate from orig .quant data

Fields inherited from class Table

bufSize, fileOKflag

Fields inherited from class SimpleTable

fileName, msg, tCols, tData, tFields, title, tRows

Constructor Summary

(package private)

MaHPquantTable(MAExplorer mae, MaHybridSample ms, java.lang.String fileName, java.lang.String hpName, boolean swapCy5Cy3DataFlag) MaHPquantTable() - constructor to read the .quant file table and setup MaHybridSample

Method Summary

private float	cvtQualCheckStrToFloat(java.lang.String sQualCheck) cvtQualCheckStrToFloat() - do conversion from QualCheck string to float value.
private GridCoords	cvtTblRowDataToFGRC(int f, java.lang.String[] data) cvtTblRowDataToFGRC() - convert table row data to GridCoord data by setting (f,g,r,c) in the mae.grcd object.
private boolean	initFGRCtoGTidxMap() initFGRCtoGTidxMap() - create FGRC to quant table row index lookup table.
private boolean	parseGidQmapLookupTable() parseGidQmapLookupTable()- parse FGRC tData[][] to ms.gidMapQ[].
private boolean	parseQuantTableToQarrays() parseQuantTableToQarrays() - cvt Table data to quant xxxC[] arrays data.
private void	setupFieldIndexes() setupFieldIndexes() - setup indexes for common Table fields for speedups.
private void	setupQuantImageTextQGridCoords() setupQuantImageTextQGridCoords() - for .quant data to draw in PseudoImage
private boolean	setupXYQandCorrectSkew() setupXYQandCorrectSkew() - set XY coords and correct XY skew if actual xy coords.

Methods inherited from class Table

copyTable, createFileTable, getArrayOfTabDelimitedTokens, getData, getTableRowsSubset, getTableRowsSubset, insertTblInULHCtable, lookupFieldIdxAndRemapFieldName, makeTabDelimReport, readTable, storeDataBufParser

Methods inherited from class SimpleTable

freeTable, getTableRowFieldByRowIdx, getTableRowFieldIdxByRowIdx, lookupFieldIdx, setFieldData, setRowData, trimWhitespace

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

map

private Maps map

link to global Maps instance

cfg

private Config cfg

link to global Config instance

cdb

private CompositeDatabase cdb

link to global CompositeDatabase instance

fio

private FileIO fio

link to global FileIO vinstance

ms

private MaHybridSample ms

HP sample that owns this table instance

SPACING_BETWEEN_SPOTS

static final int SPACING_BETWEEN_SPOTS

(opt) spacing between spots

DELTA_X_SPACING

static final int DELTA_X_SPACING

(opt) Horiz. spacing between spots. old value was 11

DELTA_Y_SPACING

static final int DELTA_Y_SPACING

Vert. spacing between spots. old value was 11

X_GRID_OFFSET

static final int X_GRID_OFFSET

value to add to orig data coords to draw GRID labels

X_SPOTQ_OFFSET

static final int X_SPOTQ_OFFSET

value to add to orig data coords x_textQ[]. OLD values:40,50

Y_SPOTQ_OFFSET

static final int Y_SPOTQ_OFFSET

value to add to orig data coords y_textQ[] AND to grid coords so they match spots

GUARD_REGION

static final int GUARD_REGION

# pixels in target image on each edge

maeTbl

private final java.lang.String maeTbl

name of remap Table

maxVsize

public static float maxVsize

maxHsize

public static float maxHsize

idxLocation

private int idxLocation

opt. array Location index

idxX

private int idxX

opt. array image X coord

idxY

private int idxY

opt. array image Y coord

idxfield

private int idxfield

opt. explicit "field"

idxgrid

private int idxgrid

separate GRC spec. "grid"

idxgrid_col

private int idxgrid_col

separate GRC spec. "grid col"

idxgrid_row

private int idxgrid_row

separate GRC spec. "grid row"

idxNameGridIdx

private int idxNameGridIdx

MolDyn GRC coding for (grid,grid-row,grid-column) as "NAME_GRC" e.g. "GRID- 8-R12C11".

idxRawIntens

private int idxRawIntens

raw intensity spot data

idxRawIntens1

private int idxRawIntens1

raw intensity spot data for channel 1, if code mult fields in each row

idxRawIntens2

private int idxRawIntens2

raw intensity spot data for channel 2, if code mult fields in each row

idxBkgrd

private int idxBkgrd

background raw intensity spot data

idxBkgrd1

private int idxBkgrd1

background raw intensity channel 1, if code mult fields in each row

idxBkgrd2

private int idxBkgrd2

background raw intensity channel 2, if code mult fields in each row

idxDetValue

private int idxDetValue

Opt. Detection value for spot

idxQualCheck

private int idxQualCheck

Opt. quality code for spot validity

learnGRCcodingFlag

private boolean learnGRCcodingFlag

flag: once only code when analyze for MolDyn "NAME_GRC" coding

isGridDigitFlag

private boolean isGridDigitFlag

flag: Grid value is coded as digit else alpha

isGridRowDigitFlag

private boolean isGridRowDigitFlag

flag: Grid-Row value is coded as digit else alpha

isGridColDigitFlag

private boolean isGridColDigitFlag

flag: Grid-Col value is coded as digit else alpha

gridCharOffset

private char gridCharOffset

Grid alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters

gridRowCharOffset

private char gridRowCharOffset

Grid Row alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters

gridColCharOffset

private char gridColCharOffset

Grid Column alphabetic offset for Uppercase ('A') or Lowercase ('a') if using letters

screenGoodGenesFlag

private boolean screenGoodGenesFlag

flag: if calc glob-stats on only GoodGenes

doRatioFlag

private boolean doRatioFlag

flag: if maxFIELD==1 && useRatioDataFlag

swapCy5Cy3DataFlag

private boolean swapCy5Cy3DataFlag

maxFIELDS

private int maxFIELDS

maximum number of fields allowed

maxGRIDS

private int maxGRIDS

maximum number of grids allowed

maxGROWS

private int maxGROWS

maximum number of grid rows allowed

maxGCOLS

private int maxGCOLS

maximum number of grid cols allowed

allocSize

private int allocSize

number of spots allocated as map.maxSpots+1. Handles dangling null problem

nSpots

private int nSpots

number of spots read. Set to tRows, or map.maxSpots if maxFIELDS>1

nGenes

private int nGenes

# of genes

xRmax

private int xRmax

max X coordinate from orig .quant data

yRmax

private int yRmax

max Y coordinate from orig .quant data

xRmin

private int xRmin

min X coordinate from orig .quant data

yRmin

private int yRmin

min Y coordinate from orig .quant data

Constructor Detail

MaHPquantTable

MaHPquantTable(MAExplorer mae,
               MaHybridSample ms,
               java.lang.String fileName,
               java.lang.String hpName,
               boolean swapCy5Cy3DataFlag)

MaHPquantTable() - constructor to read the .quant file table and setup MaHybridSample

Parameters:

mae - is instance of MAExplorer

ms - is the MaHybridSample instance

fileName - is the .quant file full path name

hpName - the sample name

swapCy5Cy3DataFlag - indicates that swap (Cy3,Cy5) data

See Also:

MAExplorer.logDRYROTerr(java.lang.String), MaHybridSample, MaHybridSample.clearHPglobalStats(), MaHybridSample.cvtRawQdataToMAEdata(boolean), Util.popupDryrotMsgsAndQuit(), Util.showMsg2(java.lang.String), initFGRCtoGTidxMap(), parseQuantTableToQarrays(), setupFieldIndexes(), setupQuantImageTextQGridCoords(), setupXYQandCorrectSkew()

Method Detail

setupFieldIndexes

private void setupFieldIndexes()

setupFieldIndexes() - setup indexes for common Table fields for speedups. Any fields not found are set to -1.

See Also:

Table.lookupFieldIdxAndRemapFieldName(java.lang.String, java.lang.String)

initFGRCtoGTidxMap

private boolean initFGRCtoGTidxMap()

initFGRCtoGTidxMap() - create FGRC to quant table row index lookup table.

Returns:

true if succeed

See Also:

Util.checkImagesDirExists(), parseGidQmapLookupTable()

cvtTblRowDataToFGRC

private GridCoords cvtTblRowDataToFGRC(int f,
                                       java.lang.String[] data)

cvtTblRowDataToFGRC() - convert table row data to GridCoord data by setting (f,g,r,c) in the mae.grcd object. Pick out the fields to assemble the GridCoords obj.

Parameters:

f - is the field number

data - is the full row of table data

Returns:

instance of GridCoords with data from this row, else null if there is a problem.

See Also:

GridCoords.cvtNAME_GCR2FGRC(int, java.lang.String), MAExplorer.logDRYROTerr(java.lang.String), Util.popupDryrotMsgsAndQuit()

parseGidQmapLookupTable

private boolean parseGidQmapLookupTable()

parseGidQmapLookupTable()- parse FGRC tData[][] to ms.gidMapQ[]. Find (f,g,r,c) and then set ms.gidMapQ[row] to map.fgrc2gid[f][g][r][c]. Note: if there is no "field", we compute field value f based on maxFIELDS.

Returns:

true if succeed.

See Also:

FileIO.logMsgln(java.lang.String), MAExplorer.logDRYROTerr(java.lang.String), Util.popupDryrotMsgsAndQuit(), cvtTblRowDataToFGRC(int, java.lang.String[])

setupQuantImageTextQGridCoords

private void setupQuantImageTextQGridCoords()

setupQuantImageTextQGridCoords() - for .quant data to draw in PseudoImage

See Also:

Maps

setupXYQandCorrectSkew

private boolean setupXYQandCorrectSkew()

setupXYQandCorrectSkew() - set XY coords and correct XY skew if actual xy coords. The ms.(xC,yC) are actual or pseudo image coordinates. This data has the same ranges as the image data so it can be used interchangeably (more or less) with the analysis fcts..

Returns:

true if successful.

cvtQualCheckStrToFloat

private float cvtQualCheckStrToFloat(java.lang.String sQualCheck)

cvtQualCheckStrToFloat() - do conversion from QualCheck string to float value.

Parameters:

sQualCheck - is table string value for QualCheck

Returns:

QualCheck value. If there is no QualCheck data then return Gene.C_GOOD_MID.

See Also:

Util.cvs2f(java.lang.String), Util.cvs2i(java.lang.String)

parseQuantTableToQarrays

private boolean parseQuantTableToQarrays()

parseQuantTableToQarrays() - cvt Table data to quant xxxC[] arrays data. Compute min and max of data for use when we convert to std xxxC[] data.

Returns:

true if succeed.

See Also:

MaInfoTable.getTableRowByMaInfoId(java.lang.String), Util.cvs2f(java.lang.String), Util.cvs2i(java.lang.String), Util.showMsg(java.lang.String), cvtQualCheckStrToFloat(java.lang.String), cvtTblRowDataToFGRC(int, java.lang.String[])