Class ArrayLayout

java.lang.Object
  |
  +--ArrayLayout

public class ArrayLayout

extends java.lang.Object

This class specifies vendor and user defined Array Layouts. Cvt2Mae stores array layouts in a subdirectory called "/ArrayLayouts" as *.alo files.

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.

Version:

$Date: 2002/10/14 19:22:28 $ $Revision: 1.5 $

Author:

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

See Also:

MAExplorer Home

Field Summary

boolean	allowNegQuantDataFlag flag: Set if .quant data has negative intensity values otherwise it clips the negative values to 0.0 (eg.
int	alNbr unique ArrayLayout instance number
java.lang.String	aloFileName .alo file name
long	bitProps bit subsets of properties from mcd.PROP_xxxx
boolean	chkAndEditFieldNamesFlag flag: check and edit Samples and Field names data before use.
int	colsPerGrid number of columns of spots per grid
java.lang.String	commentToken if not null, skip lines with this as 1st token
java.lang.String[]	desiredFields A list of desired fields we extract from table header.
int	expectedNbrTokens expected number of tokens for this layout
FieldMap	fieldMap field map of internal (MAE) to external (User) Table Fields
java.lang.String	geoPlatformID Optional GEO Platform ID
boolean	hasBkgrdDataFlag flag: has background intensity data
boolean	hasMultDatasetsFlag flag: true if file contains multiple data sets
boolean	hasQuantXYcoordsFlag flag: has actual quant XY coordinates data
java.lang.String	initialKeyword initial keyword if any for chip
java.lang.String	layoutName unique vendor's name or part number for chip
FileTable	mapTbl Table equivalent of desiredFields[]
(package private) static int	masterNbr used in generating alNbrs'
int	maxFields maximum complete duplicate Fields of grids on chip
int	maxRowsExpected max number of data rows - i.e.
int	nDesiredFields # of desired fields in field mapping
(package private) java.lang.String	newline for newline, Mac= "\r" Sun ="\n" PC= "\r\n"
int	nGridsPerField number of grids in one field
boolean	pseudoArrayFlag flag: pseudo array layout else exact (F,G,R,C)
java.lang.String	quantTool quantification tool used to segment spots
int	rowsPerGrid number of rows of spots per grid
int	rowWithData row in user FieldQ file where expect Data
int	rowWithFields row in user FieldQ file where expect Fields list
int	rowWithSamples optional row in user FieldQ file where expect samples list
int	rowWithSepGIPOData optional row in user FieldG separate GIPO file where expect Data
int	rowWithSepGIPOFields optional row in user FieldG separate GIPO file where expect Fields list
boolean	saveArrayFlag flag: If changes made with arrays thru editing, array must be saved if true
java.lang.String	species species where genes came from on chip
boolean	specifyGeometryByNbrSpotsFlag flag: true if specify pseudo array geometry from number of spots in maxRowsExpected
java.lang.String	strain [TODO] add to constuctors and data?
java.lang.String	tissue [TODO] add to constuctors and data?
java.lang.String	UniGeneSpeciesPrefix Used with UniGene
boolean	useRatioDataFlag flag: data is Cy3/Cy5 type fluorescent ratio data
java.lang.String	vendor chip vendor or manufacture making the chip

Constructor Summary

(package private)

ArrayLayout(java.lang.String aloFileName, java.lang.String vendor, java.lang.String layoutName, java.lang.String species, java.lang.String quantTool, java.lang.String UniGeneSpeciesPrefix, java.lang.String commentToken, java.lang.String initialKeyword, boolean hasMultDatasetsFlag, boolean specifyGeometryByNbrSpotsFlag, int maxFields, int nGridsPerField, int rowsPerGrid, int colsPerGrid, int maxRowsExpected, int expectedNbrTokens, int rowWithSamples, int rowWithFields, int rowWithData, int rowWithSepGIPOFields, int rowWithSepGIPOData, boolean pseudoArrayFlag, boolean useRatioDataFlag, boolean allowNegQuantDataFlag, boolean chkAndEditFieldNamesFlag, boolean hasBkgrdDataFlag, boolean hasQuantXYcoordsFlag, long bitProps, java.lang.String[] desiredFields, java.lang.String geoPlatformID) ArrayLayout() - constructor for Array Layouts.

Method Summary

boolean	buildMapTFentries() buildMapTFentries() - build mapTF DB if mapTbl and fieldMap exists
java.lang.String	toString() toString() - make prettyprint string for Array Layout.

Methods inherited from class java.lang.Object

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

Field Detail

masterNbr

static int masterNbr

used in generating alNbrs'

aloFileName

public java.lang.String aloFileName

.alo file name

vendor

public java.lang.String vendor

chip vendor or manufacture making the chip

layoutName

public java.lang.String layoutName

unique vendor's name or part number for chip

species

public java.lang.String species

species where genes came from on chip

tissue

public java.lang.String tissue

[TODO] add to constuctors and data?

strain

public java.lang.String strain

[TODO] add to constuctors and data?

quantTool

public java.lang.String quantTool

quantification tool used to segment spots

UniGeneSpeciesPrefix

public java.lang.String UniGeneSpeciesPrefix

Used with UniGene

commentToken

public java.lang.String commentToken

if not null, skip lines with this as 1st token

initialKeyword

public java.lang.String initialKeyword

initial keyword if any for chip

alNbr

public int alNbr

unique ArrayLayout instance number

maxFields

public int maxFields

maximum complete duplicate Fields of grids on chip

nGridsPerField

public int nGridsPerField

number of grids in one field

rowsPerGrid

public int rowsPerGrid

number of rows of spots per grid

colsPerGrid

public int colsPerGrid

number of columns of spots per grid

maxRowsExpected

public int maxRowsExpected

max number of data rows - i.e. clones in array

expectedNbrTokens

public int expectedNbrTokens

expected number of tokens for this layout

rowWithSamples

public int rowWithSamples

optional row in user FieldQ file where expect samples list

rowWithFields

public int rowWithFields

row in user FieldQ file where expect Fields list

rowWithData

public int rowWithData

row in user FieldQ file where expect Data

rowWithSepGIPOFields

public int rowWithSepGIPOFields

optional row in user FieldG separate GIPO file where expect Fields list

rowWithSepGIPOData

public int rowWithSepGIPOData

optional row in user FieldG separate GIPO file where expect Data

saveArrayFlag

public boolean saveArrayFlag

flag: If changes made with arrays thru editing, array must be saved if true

hasMultDatasetsFlag

public boolean hasMultDatasetsFlag

flag: true if file contains multiple data sets

specifyGeometryByNbrSpotsFlag

public boolean specifyGeometryByNbrSpotsFlag

flag: true if specify pseudo array geometry from number of spots in maxRowsExpected

pseudoArrayFlag

public boolean pseudoArrayFlag

flag: pseudo array layout else exact (F,G,R,C)

useRatioDataFlag

public boolean useRatioDataFlag

flag: data is Cy3/Cy5 type fluorescent ratio data

allowNegQuantDataFlag

public boolean allowNegQuantDataFlag

flag: Set if .quant data has negative intensity values otherwise it clips the negative values to 0.0 (eg. AFFY)

chkAndEditFieldNamesFlag

public boolean chkAndEditFieldNamesFlag

flag: check and edit Samples and Field names data before use. This is for handling the bad Affy fields data generated by the old Affy software.

hasBkgrdDataFlag

public boolean hasBkgrdDataFlag

flag: has background intensity data

hasQuantXYcoordsFlag

public boolean hasQuantXYcoordsFlag

flag: has actual quant XY coordinates data

bitProps

public long bitProps

bit subsets of properties from mcd.PROP_xxxx

nDesiredFields

public int nDesiredFields

# of desired fields in field mapping

desiredFields

public java.lang.String[] desiredFields

A list of desired fields we extract from table header. The rest are ignored. This list of mapped fields will be analyzed during processing. An entry is

  "< MAE field name >:< user field name >" 

Note: If there is a leading '*', then the field is an instance of a sample field and may be repeated multiple times and is used for extracting data into separate .quant files.

geoPlatformID

public java.lang.String geoPlatformID

Optional GEO Platform ID

fieldMap

public FieldMap fieldMap

field map of internal (MAE) to external (User) Table Fields

mapTbl

public FileTable mapTbl

Table equivalent of desiredFields[]

newline

java.lang.String newline

for newline, Mac= "\r" Sun ="\n" PC= "\r\n"

Constructor Detail

ArrayLayout

ArrayLayout(java.lang.String aloFileName,
            java.lang.String vendor,
            java.lang.String layoutName,
            java.lang.String species,
            java.lang.String quantTool,
            java.lang.String UniGeneSpeciesPrefix,
            java.lang.String commentToken,
            java.lang.String initialKeyword,
            boolean hasMultDatasetsFlag,
            boolean specifyGeometryByNbrSpotsFlag,
            int maxFields,
            int nGridsPerField,
            int rowsPerGrid,
            int colsPerGrid,
            int maxRowsExpected,
            int expectedNbrTokens,
            int rowWithSamples,
            int rowWithFields,
            int rowWithData,
            int rowWithSepGIPOFields,
            int rowWithSepGIPOData,
            boolean pseudoArrayFlag,
            boolean useRatioDataFlag,
            boolean allowNegQuantDataFlag,
            boolean chkAndEditFieldNamesFlag,
            boolean hasBkgrdDataFlag,
            boolean hasQuantXYcoordsFlag,
            long bitProps,
            java.lang.String[] desiredFields,
            java.lang.String geoPlatformID)

ArrayLayout() - constructor for Array Layouts.

Parameters:

aloFileName - is the Array Layout file name

vendor - is the Array Layout vendor name

layoutName - is the Array Layout name

species - is the species name

quantTool - is the quantification tool used to segment spots

UniGeneSpeciesPrefix - is used with UniGene

commentToken - for comments

initialKeyword - initial keyword if any for chip

hasMultDatasetsFlag - flag: true if file contains multiple data sets

specifyGeometryByNbrSpotsFlag - flag: true if specify pseudo array geometry from number of spots in maxRowsExpected

maxFields - maximum number of fields

nGridsPerField - number of grids in one field

rowsPerGrid - number of rows of spots per grid

colsPerGrid - number of columns of spots per grid

maxRowsExpected - max number of data rows - i.e. clones in array

expectedNbrTokens - expected number of tokens for this layout

rowWithSamples - optional row in user FieldQ file where expect samples list

rowWithFields - row in user FieldQ file where expect Fields list

rowWithData - row in user FieldQ file where expect Data to start

rowWithSepGIPOFields - optional row in user FieldG separate GIPO file where expect Fields list

rowWithSepGIPOData - optional row in user FieldG separate GIPO file where expect Data

pseudoArrayFlag - flag: pseudo array layout else exact (F,G,R,C)

useRatioDataFlag - flag: data is Cy3/Cy5 type fluorescent ratio data

allowNegQuantDataFlag - it clips the negative values to 0.0 (eg. AFFY)

chkAndEditFieldNamesFlag - flag: check and edit Samples and Field names data before use.

hasBkgrdDataFlag - flag: has background intensity data

hasQuantXYcoordsFlag - flag: has actual quant XY coordinates data

bitProps - bit subsets of properties from mcd.PROP_xxxx

desiredFields[] - This list of mapped fields will be analyzed during processing

geoPlatformID - optional GEO Platform ID

See Also:

FileTable.cvtStrToTable(java.lang.String), buildMapTFentries()

Method Detail

buildMapTFentries

public boolean buildMapTFentries()

buildMapTFentries() - build mapTF DB if mapTbl and fieldMap exists

Returns:

true if mapTbl and fieldMap exists

See Also:

FieldMap.addEntry(java.lang.String, java.lang.String, java.lang.String, java.lang.String), FieldMap.clearMap(), FileTable.lookupFieldIdx(java.lang.String)

toString

public java.lang.String toString()

toString() - make prettyprint string for Array Layout.

Overrides:

toString in class java.lang.Object

Returns:

prettyprint string for Array Layout