Class DataIO

java.lang.Object
  |
  +--DataIO

public class DataIO

extends java.lang.Object

This class contains methods to read and write array data, GIPO, .quant, and MAE 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 19:22:29 $ $Revision: 1.17 $

Author:

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

See Also:

MAExplorer Home

Field Summary

private static int	affyFieldDescriptionCol Special hack for Affy files - see chkAndEditFieldNames().
Cvt2Mae	cvt Global links
Element[]	datum data elements from the input table
int	expectedNbrTokens expected # of tokens for this layout
CvtGUI	gui Global GUI popup frame
int	idxClone_ID GIPO index for clone ID
int	idxDbEst3 GIPO index 'dbEST' identifier data.
int	idxDbEst5 GIPO index 'dbEST' identifier data.
int	idxDetValue GIPO index for Spot Detection value
int	idxDiffCall GIPO index for Affy Diff Call
int	idxField GIPO index
int	idxFoldChange GIPO index for Fole Change
int	idxGenBankAcc GIPO index 'GenBank' identifier data.
int	idxGenBankAcc3 GIPO index 'GenBank' identifier data.
int	idxGenBankAcc5 GIPO index 'GenBank' identifier data.
int	idxGeneName GIPO index for gene name
int	idxGrid GIPO index for Grid
int	idxGridCol GIPO index for grid column
int	idxGridRow GIPO index for grid row
int	idxIdentifier generic Genomic ID - used when no other ids
int	idxLocation GIPO index fields for fieldNames[]
int	idxLocusLinkID GIPO index
int	idxNAME_GRC GIPO index for NAME_GRC; (Molecular Dynamics "NAME_GRC" spec )
int	idxPlate GIPO index for plate
int	idxPlateCol GIPO index for plate column
int	idxPlateRow GIPO index for plate row
int	idxQualCheck GIPO index
int	idxQualCheckGIPO GIPO index for 'GIPO' QualCheck data
int	idxRawBackground GIPO index
int	idxRawBackground1 GIPO index
int	idxRawBackground2 GIPO index
int	idxRawIntensity GIPO index
int	idxRawIntensity1 GIPO index
int	idxRawIntensity2 GIPO index
int	idxSwissProtID GIPO index SwissProtID
int	idxUnigene_cluster_ID GIPO index Unigene cluster ID
int	idxUnigene_cluster_name GIPO index Unigene cluster name
int	idxX Quant index fields are for fieldNames[]
int	idxY GIPO index
int	infillCnt # of infill spots generated
MaeConfigData	mcd Mae Config Data
SetupLayouts	sul Global layouts
java.lang.String	title GUI title
java.lang.String[]	tokArray [MAX_IN_TOKENS_PER_ROW] holds input tokens
boolean[]	useTokFlagGQ [MAX_IN_TOKENS_PER_ROW] tokens to get for FieldGQ data
UtilCM	util Global utilities

Constructor Summary

DataIO(Cvt2Mae cvt)
DataIO() - Constructor

Method Summary

java.lang.String	addGenomicDataFromDescr(java.lang.String sDescr) addGenomicDataFromDescr() - setup Affy genomic ids data from Description "Cluster Incl AW208667:uo62e02.x1 Mus musculus cDNA, 3 end /clone=IMAGE-2647130 /clone_end=3 /gb=AW208667 /gi=6514607 /ug=Mm.4609 /len=474" Add field "Clone_ID" from /clone=IMAGE-2647130 Add field "GenBankAcc" from /gb=AW208667 Add field "UniGeneID from /ug=Mm.4609 Add field "LocusID" from /gb=AW208667
java.lang.String	addGenomicFieldsNamesFromDescr() addGenomicFieldsNamesFromDescr() - setup genomic ids field names from Description "Cluster Incl AW208667:uo62e02.x1 Mus musculus cDNA, 3 end /clone=IMAGE-2647130 /clone_end=3 /gb=AW208667 /gi=6514607 /ug=Mm.4609 /len=474" Add field "Clone_ID" from /clone=IMAGE-2647130 Add field "GenBankAcc" from /gb=AW208667 Add field "UniGeneID from /ug=Mm.4609 Add field "LocusID" from /gb=AW208667
private boolean	checkIfRequiredFieldsAreNull(boolean[] useTokFlagGQ, java.lang.String[] tokArray) checkIfRequiredFieldsAreNull() - test if the Required fields are "" Return true if the required fields are ""
boolean	chkAndEditFieldNames(java.lang.String[] tokArray, java.lang.String lookForOpr) chkAndEditFieldNames() - check and edit Sample or Field names.
java.lang.String	cvtGipoDatumToTabDelimStr(Element d) cvtGipoDatumToTabDelimStr() - convert Element to tab-delimited GIPO string
java.lang.String	cvtQuantDatumToTabDelimStr(Element d) cvtQuantDatumToTabDelimStr() - convert Element to tab-delimited Quant string
private java.lang.String	cvtUserDataToQualCheck(java.lang.String qcData) cvtUserDataToQualCheck() map user data range to valid QualCheck range
private int	extractDatumFromDataRow(java.lang.String[] tokArray, int rowNbr, int spotNbr, java.lang.String line, int grid, int gRow, int gCol) extractDatumFromDataRow() - extract datum[spotID] from row of token data Return spotID # (Location#) if ok else -1
boolean	genMultIdxMapOfFieldNameData(java.lang.String[] fieldNamesGQ, int nDataFields, int n) genMultIdxMapOfFieldNameData() - generate quant idx map of data from field map and sames of input file fields. [1] Generate a map of fields where Samples starts to the indices for each .quant sample to be generated. [2] Generate useTokFlag[] from fieldNames[] and FieldMap data.
java.lang.String	makeGipoFieldsTabDelimStr() makeGipoFieldsTabDelimStr() - make tab-delimited GIPO Fields string
java.lang.String	makeQuantFieldsTabDelimStr() makeQuantFieldsTabDelimStr() - make tab-delimited Quant Fields string
(package private) void	quickSortByIntLoc(Element[] d, int lo0, int hi0) quickSortByIntLoc() - recursive sort the Element list datum[].iLocation.
(package private) void	quickSortByLocStr(Element[] d, int lo0, int hi0) quickSortByLocStr() - sort the Element list datum[].location.
boolean	readData(int n) readData() - read composite vendor or user data from file.
void	setupFieldNameIndices()
void	setupFilenames() setupFilenames() - setup proper file names based on path analysis These are kept in the mcd.XXXX state.
private boolean	updateInfillLocationIDs() updateInfillLocationIDs() - if using Location IDs, then sort datum[1:mcd.maxRowsExpected] by Location add infill spots and renumber grid coordinates.
private boolean	writeConfigFile(MaeConfigData mcd) writeConfigFile() - create Config/MaExplorerConfig-fn.txt file
boolean	writeGipoData() writeGipoData() - write out the MAExplorer GIPO data file xxxx.gipo
private boolean	writeMAEstartupFile() writeMAEstartupFile() - create MAE/Start.mae file
boolean	writeQuantData(int n) writeQuantData() - write out the MAExplorer Quant data files These include the set of xxxxnnn.quant files

Methods inherited from class java.lang.Object

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

Field Detail

cvt

public Cvt2Mae cvt

Global links

mcd

public MaeConfigData mcd

Mae Config Data

util

public UtilCM util

Global utilities

sul

public SetupLayouts sul

Global layouts

gui

public CvtGUI gui

Global GUI popup frame

title

public java.lang.String title

GUI title

tokArray

public java.lang.String[] tokArray

[MAX_IN_TOKENS_PER_ROW] holds input tokens

useTokFlagGQ

public boolean[] useTokFlagGQ

[MAX_IN_TOKENS_PER_ROW] tokens to get for FieldGQ data

datum

public Element[] datum

data elements from the input table

infillCnt

public int infillCnt

# of infill spots generated

expectedNbrTokens

public int expectedNbrTokens

expected # of tokens for this layout

idxLocation

public int idxLocation

GIPO index fields for fieldNames[]

idxField

public int idxField

GIPO index

idxGrid

public int idxGrid

GIPO index for Grid

idxGridRow

public int idxGridRow

GIPO index for grid row

idxGridCol

public int idxGridCol

GIPO index for grid column

idxNAME_GRC

public int idxNAME_GRC

GIPO index for NAME_GRC; (Molecular Dynamics "NAME_GRC" spec )

idxPlate

public int idxPlate

GIPO index for plate

idxPlateRow

public int idxPlateRow

GIPO index for plate row

idxPlateCol

public int idxPlateCol

GIPO index for plate column

idxQualCheckGIPO

public int idxQualCheckGIPO

GIPO index for 'GIPO' QualCheck data

idxIdentifier

public int idxIdentifier

generic Genomic ID - used when no other ids

idxClone_ID

public int idxClone_ID

GIPO index for clone ID

idxGeneName

public int idxGeneName

GIPO index for gene name

idxUnigene_cluster_ID

public int idxUnigene_cluster_ID

GIPO index Unigene cluster ID

idxUnigene_cluster_name

public int idxUnigene_cluster_name

GIPO index Unigene cluster name

idxGenBankAcc

public int idxGenBankAcc

GIPO index 'GenBank' identifier data. See http://ncbi.nlm.nih.gov/

idxGenBankAcc3

public int idxGenBankAcc3

GIPO index 'GenBank' identifier data. See http://ncbi.nlm.nih.gov/

idxGenBankAcc5

public int idxGenBankAcc5

GIPO index 'GenBank' identifier data. See http://ncbi.nlm.nih.gov/

idxDbEst3

public int idxDbEst3

GIPO index 'dbEST' identifier data.

idxDbEst5

public int idxDbEst5

GIPO index 'dbEST' identifier data.

idxSwissProtID

public int idxSwissProtID

GIPO index SwissProtID

idxLocusLinkID

public int idxLocusLinkID

GIPO index

idxX

public int idxX

Quant index fields are for fieldNames[]

idxY

public int idxY

GIPO index

idxRawIntensity

public int idxRawIntensity

GIPO index

idxRawIntensity1

public int idxRawIntensity1

GIPO index

idxRawIntensity2

public int idxRawIntensity2

GIPO index

idxRawBackground

public int idxRawBackground

GIPO index

idxRawBackground1

public int idxRawBackground1

GIPO index

idxRawBackground2

public int idxRawBackground2

GIPO index

idxQualCheck

public int idxQualCheck

GIPO index

idxDetValue

public int idxDetValue

GIPO index for Spot Detection value

idxDiffCall

public int idxDiffCall

GIPO index for Affy Diff Call

idxFoldChange

public int idxFoldChange

GIPO index for Fole Change

affyFieldDescriptionCol

private static int affyFieldDescriptionCol

Special hack for Affy files - see chkAndEditFieldNames(). This will contain the column for the Field "Description" if needed, else -1.

Constructor Detail

DataIO

public DataIO(Cvt2Mae cvt)

DataIO() - Constructor

Parameters:

cvt - Cvt2Mae instance

Method Detail

extractDatumFromDataRow

private int extractDatumFromDataRow(java.lang.String[] tokArray,
                                    int rowNbr,
                                    int spotNbr,
                                    java.lang.String line,
                                    int grid,
                                    int gRow,
                                    int gCol)

extractDatumFromDataRow() - extract datum[spotID] from row of token data Return spotID # (Location#) if ok else -1

Parameters:

tokArray - tokens in row

rowNbr - row number in file

spotNbr - sequential spot number

line - raw line

grid - computed Grid

gRow - computed Row

gCol - computed Column

Returns:

SpotID number location if ok, else -1

See Also:

Element

setupFilenames

public void setupFilenames()

setupFilenames() - setup proper file names based on path analysis These are kept in the mcd.XXXX state.

setupFieldNameIndices

public void setupFieldNameIndices()

readData

public boolean readData(int n)

readData() - read composite vendor or user data from file. This assumes that the current state is setup in the MCD config data structure.

Parameters:

n - is the nth user data file to read

Returns:

true if successful

See Also:

Element, FieldMap.genUseTokFlags(java.lang.String[]), FileTable, FileTable.readTableFieldsFromFile(java.lang.String, int), ParseTable, ParseTable.getAllDelimTokens(java.lang.String, java.lang.String[], boolean), TextFrame.appendLog(java.lang.String), UtilCM.logMsg(java.lang.String, java.awt.Color), checkIfRequiredFieldsAreNull(boolean[], java.lang.String[]), chkAndEditFieldNames(java.lang.String[], java.lang.String), extractDatumFromDataRow(java.lang.String[], int, int, java.lang.String, int, int, int), genMultIdxMapOfFieldNameData(java.lang.String[], int, int), updateInfillLocationIDs()

checkIfRequiredFieldsAreNull

private boolean checkIfRequiredFieldsAreNull(boolean[] useTokFlagGQ,
                                             java.lang.String[] tokArray)

checkIfRequiredFieldsAreNull() - test if the Required fields are "" Return true if the required fields are ""

Parameters:

useTokFlagGQ - boolean array

tokArray - String array

Returns:

true if required fields are null, false if required fields are not null

genMultIdxMapOfFieldNameData

public boolean genMultIdxMapOfFieldNameData(java.lang.String[] fieldNamesGQ,
                                            int nDataFields,
                                            int n)

genMultIdxMapOfFieldNameData() - generate quant idx map of data from field map and sames of input file fields.
[1] Generate a map of fields where Samples starts to the indices for each .quant sample to be generated.
[2] Generate useTokFlag[] from fieldNames[] and FieldMap data. This analyzes the field map and extracts only the data required.
[3] Setup lookup FieldName indices for mapping data. Note: for multiple samples/file this will remap things like rawIntensity by flaging other fields.
Return true if succeed.

Parameters:

fieldNamesGQ - array of field names

nDataFields - max number of data fields

n - nth data file from 0

Returns:

true if successful

See Also:

FieldMap.genUseTokFlags(java.lang.String[]), FieldMap.lookupUserIndex(java.lang.String, java.lang.String), UtilCM.logMsg(java.lang.String, java.awt.Color), setupFieldNameIndices()

chkAndEditFieldNames

public boolean chkAndEditFieldNames(java.lang.String[] tokArray,
                                    java.lang.String lookForOpr)

chkAndEditFieldNames() - check and edit Sample or Field names. This does special handling required for various types of data. Change the names in the tokArray[]. Return true if made a change.

Parameters:

tokArray - array of tokens to search through

lookForOpr - look for this

Returns:

true if a change was made to the field

updateInfillLocationIDs

private boolean updateInfillLocationIDs()

updateInfillLocationIDs() - if using Location IDs, then sort datum[1:mcd.maxRowsExpected] by Location add infill spots and renumber grid coordinates. This may grow it to datum[1:mcd.maxRowsComputed] where mcd.maxRowsComputed= mcd.highestID or spotNbr if no "Location".

Returns:

true if updated

See Also:

Element, PseudoArray, UtilCM.logMsg(java.lang.String, java.awt.Color), UtilCM.logMsg2(java.lang.String, java.awt.Color), UtilCM.logMsg3(java.lang.String, java.awt.Color)

quickSortByIntLoc

void quickSortByIntLoc(Element[] d,
                       int lo0,
                       int hi0)

quickSortByIntLoc() - recursive sort the Element list datum[].iLocation. Based on the QuickSort method by James Gosling from Sun's SortDemo applet

Parameters:

d - array of Elements to sort

lo0 - low index

hi0 - high index

quickSortByLocStr

void quickSortByLocStr(Element[] d,
                       int lo0,
                       int hi0)

quickSortByLocStr() - sort the Element list datum[].location. Note: d.location is a String and may not be a numeric string. Based on the QuickSort method by James Gosling from Sun's SortDemo applet

Parameters:

d - array of Elements to sort

lo0 - low index

hi0 - high index

addGenomicFieldsNamesFromDescr

public java.lang.String addGenomicFieldsNamesFromDescr()

addGenomicFieldsNamesFromDescr() - setup genomic ids field names from Description "Cluster Incl AW208667:uo62e02.x1 Mus musculus cDNA, 3 end /clone=IMAGE-2647130 /clone_end=3 /gb=AW208667 /gi=6514607 /ug=Mm.4609 /len=474" Add field "Clone_ID" from /clone=IMAGE-2647130 Add field "GenBankAcc" from /gb=AW208667 Add field "UniGeneID from /ug=Mm.4609 Add field "LocusID" from /gb=AW208667

Returns:

field names based on Description

addGenomicDataFromDescr

public java.lang.String addGenomicDataFromDescr(java.lang.String sDescr)

addGenomicDataFromDescr() - setup Affy genomic ids data from Description "Cluster Incl AW208667:uo62e02.x1 Mus musculus cDNA, 3 end /clone=IMAGE-2647130 /clone_end=3 /gb=AW208667 /gi=6514607 /ug=Mm.4609 /len=474" Add field "Clone_ID" from /clone=IMAGE-2647130 Add field "GenBankAcc" from /gb=AW208667 Add field "UniGeneID from /ug=Mm.4609 Add field "LocusID" from /gb=AW208667

Parameters:

sDescr - Description

Returns:

field names based on Description

writeGipoData

public boolean writeGipoData()

writeGipoData() - write out the MAExplorer GIPO data file xxxx.gipo

Returns:

true if successful

See Also:

CvtGUI.getChipsetStr(), CvtGUI.getProjectStr(), Element, TextFrame.appendLog(java.lang.String)

writeQuantData

public boolean writeQuantData(int n)

writeQuantData() - write out the MAExplorer Quant data files These include the set of xxxxnnn.quant files

Parameters:

n - is the nth quant file to write

Returns:

true if successful

See Also:

CvtGUI.getChipsetStr(), CvtGUI.getProjectStr(), TextFrame.appendLog(java.lang.String), UtilCM.logMsg(java.lang.String, java.awt.Color), UtilCM.logMsg2(java.lang.String, java.awt.Color), UtilCM.logMsg3(java.lang.String, java.awt.Color), cvtQuantDatumToTabDelimStr(Element), makeQuantFieldsTabDelimStr()

makeGipoFieldsTabDelimStr

public java.lang.String makeGipoFieldsTabDelimStr()

makeGipoFieldsTabDelimStr() - make tab-delimited GIPO Fields string

Returns:

tab-delimited GIPO Fields string

See Also:

addGenomicFieldsNamesFromDescr()

makeQuantFieldsTabDelimStr

public java.lang.String makeQuantFieldsTabDelimStr()

makeQuantFieldsTabDelimStr() - make tab-delimited Quant Fields string

Returns:

tab-delimited Quant Fields string

cvtUserDataToQualCheck

private java.lang.String cvtUserDataToQualCheck(java.lang.String qcData)

cvtUserDataToQualCheck() map user data range to valid QualCheck range

Parameters:

qcData - QualCheck data

Returns:

qcData, else if GenePix data then bad spot data

cvtGipoDatumToTabDelimStr

public java.lang.String cvtGipoDatumToTabDelimStr(Element d)

cvtGipoDatumToTabDelimStr() - convert Element to tab-delimited GIPO string

Parameters:

d - Element to convert

Returns:

tab-delimited GIPO string

See Also:

addGenomicDataFromDescr(java.lang.String), cvtUserDataToQualCheck(java.lang.String)

cvtQuantDatumToTabDelimStr

public java.lang.String cvtQuantDatumToTabDelimStr(Element d)

cvtQuantDatumToTabDelimStr() - convert Element to tab-delimited Quant string

writeMAEstartupFile

private boolean writeMAEstartupFile()

writeMAEstartupFile() - create MAE/Start.mae file

Returns:

true if successful, false if error

See Also:

MaeStartupData.writeMAEstartupFile()

writeConfigFile

private boolean writeConfigFile(MaeConfigData mcd)

writeConfigFile() - create Config/MaExplorerConfig-fn.txt file

Returns:

true if successful, false if error

See Also:

MaeConfigData.writeConfigFile()