Class SetupLayouts

java.lang.Object
  |
  +--SetupLayouts

public class SetupLayouts

extends java.lang.Object

This class sets upthe array layouts from either preloads or files. Cvt2Mae stores array layouts in /ArrayLayouts as *.alo files. When the user presses "Done" after Editing an array layout (make sure it has a unique name) it should then copy that layout to an .alo file and also move it to the top of the sul.alList[i].layoutName[] list and then update the GUI by redoing the cvt.gui.chipsetChoice Choice widget and refresh the screen.

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 19:22:31 $ $Revision: 1.19 $

Author:

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

See Also:

MAExplorer Home

Field Summary

ArrayLayout[]	alList [0:maxAL-1] array layouts to choose from max of MAX_ARRAY_LAYOUTS
private boolean	alo_allowNegQuantDataFlag ALO variable: allow negative quant dat
private long	alo_bitProps ALO variable: bit mcd.PROP_xxxx properties
private boolean	alo_chkAndEditFieldNamesFlag flag: check and edit Samples and Field names data before use.
private int	alo_colsPerGrid ALO variable: # of columns/grid
private java.lang.String	alo_commentToken ALO variable: optional comment token
private java.lang.String[]	alo_desiredFields ALO variable: list of FieldMaps for the layout
private int	alo_expectedNbrTokens ALO variable: # of expected tokens
private java.lang.String	alo_geoPlatformID Optional GEO Platform ID
boolean	alo_hasBkgrdDataFlag ALO variable: has background intensity data
private boolean	alo_hasMultDatasetsFlag ALO variable: input file has multiple samples
boolean	alo_hasQuantXYcoordsFlag ALO variable: has actual quant XY coordinates data
private java.lang.String	alo_initialKeyword ALO variable: optional initial keyword in leftmost field
private java.lang.String	alo_layoutName ALO variable: name of the layout
private int	alo_maxFields ALO variable: number of duplicate Fields of Grids/array
private int	alo_maxRowsExpected ALO variable: maximum number of spots (elements or rows)/sample
private int	alo_nGridsPerField ALO variable: # of grids/field
private boolean	alo_pseudoArrayFlag ALO variable: use generated PseudoArray image
private java.lang.String	alo_quantTool ALO variable: name of the quantification program
private int	alo_rowsPerGrid ALO variable: # of rows/grid
private int	alo_rowWithData ALO variable: # of row of FieldQ input file that contains data
private int	alo_rowWithFields ALO variable: # of row of FieldQ input file that contains Field names
private int	alo_rowWithSamples ALO variable: # of row of FieldQ input file that contains sample names
private int	alo_rowWithSepGIPOData ALO variable: # of row of FieldG separate GIPO input file that contains data
private int	alo_rowWithSepGIPOFields ALO variable: # of row of FieldG separate GIPO input file that contains Field names
private java.lang.String	alo_species ALO variable: species of sample
private boolean	alo_specifyGeometryByNbrSpotsFlag ALO variable: specify (F,G,R,C) from # of spots in PseudoArray
private java.lang.String	alo_UniGeneSpeciesPrefix ALO variable: UniGene 2 letter prefix (eg.
private boolean	alo_useRatioDataFlag ALO variable: data is ratio data (eg.
private java.lang.String	alo_vendor ALO variable: vendor making the array
java.lang.String[]	aloFile [0:nALOfilesFound-1] *.alo ALO files found the the ArrayLayout/ directory
private java.lang.String	aloFileName ALO variable: variables for parsed .alo file
private java.lang.String	aloFileVersion ALO variable: Version # of .alo file
Cvt2Mae	cvt Global link to Cvt2Mae instance
private Element[]	datum data elements from the input table
private java.lang.String[]	defDesiredFields Default desired fields table with no data.
private int	expectedNbrTokens expected # of tokens for this layout if not 0.
int	firstAL index of first default array layout in the ALO list
int	firstUserALO the index of the first user defined ALO.
private java.lang.String	fullPathAloFile full path of AL file trying to read
ImageAnalysisMethod[]	iam [0:nIAused-1] image analysis methods to choose from max of MAX_IMG_ANALY_METHODS
int	lastAL index of last default array layout in the ALO list
int	maxAL max # of array layouts in the ALO list
int	maxIAM max # of image analysis methods
MaeConfigData	mcd Global link to MaeConfigData instance
int	nALOfilesFound # of all *.alo files found in the ArrayLayout/ directory
boolean	readALOflag set to true if read .alo files
static int	REMAP_GIPO REMAP codes - remapping GIPO.
static int	REMAP_QUANT REMAP codes - remapping QUANT.
static int	REMAP_SAMPLE REMAP codes - remapping SAMPLE.
static FieldMap	specialFM Special Field Map for mapping our symbols see getMinReqFieldList()
int	useAL array layout to use, -1 means failed
int	useIAM method to use, -1 means failed
UtilCM	util Global link to UtilCM instance

Constructor Summary

SetupLayouts(Cvt2Mae cvt)
SetupLayouts() - Constructor

Method Summary

private boolean	checkAndMakeALOdir(java.lang.String aloDir) checkAndMakeALOdir()- check for ArrayLayout/ directory tree.
private boolean	chkUniqueLayoutName(java.lang.String layoutName) chkUniqueLayoutName() - return TRUE if layout name is unique.
void	copyALOtoMCDstate() copyALOtoMCDstate() - Copy al[useAL].XXX state to mcd.XXX state.
void	copyMCDtoALOstate() copyMCDtoALOstate() - Copy mcd.XXX state to al[useAL].XXX state.
private java.lang.String	cvArrayLayoutToTableDataStr(ArrayLayout al) cvArrayLayoutToTableDataStr() - make prettyprint (N,V) string for writing to .alo file.
private void	deleteOldStyleAffyALOnamesatV70() deleteOldStyleAffyALOnamesatV70() - hack to remove bogus .alo names from the ArrayLayout directory so they don't appear in the list with the new names.
boolean	getMaeToUserFields(java.lang.String fileName, FieldMap fm, int row, int remapMode, boolean useMaxFieldsFlag) getMaeToUserFields() - extract desired fields from row of tokens by reading them from the fileName.
private java.lang.String[]	getMinReqFieldList(int remapMode) getMinReqFieldList() - get minimal required list of fields based on current mcd state.
java.lang.String	getPrintStringFieldRow(java.lang.String dirName, java.lang.String srcFileName, int row, java.lang.String msg) getPrintStringFieldRow() - get print string of specified row of file
private java.lang.String	getValueByName(FileTable ft, java.lang.String name) getValueByName() - get Value by Name for Table with Fields[0:1] = {Name","Value"}.
private boolean	getValueByNameBool(FileTable ft, java.lang.String name) getValueByNameBool() - get int Value by Name for Table with Fields[0:1] = {Name","Value"}.
private int	getValueByNameInt(FileTable ft, java.lang.String name) getValueByNameInt() - get int Value by Name for Table with Fields[0:1] = {Name","Value"}.
private long	getValueByNameLong(FileTable ft, java.lang.String name) getValueByNameLong() - get long Value by Name for Table with Fields[0:1] = {Name","Value"}.
private boolean	parseArrayLayoutToTableData(FileTable ft) parseArrayLayoutToTableData() - parse (N,V) table data to alo_XXXX vars.
private boolean	readArrayLayouts() readArrayLayouts() - read list of known array layouts from disk layout database directory.
boolean	removeALOfileFromALOlist(java.lang.String aloFName) removeALOfileFromALOlist() - remove ALO entry if match file name
boolean	setPseudoArrayToCurALO() setPseudoArrayToCurALO() - set PseudoArray values to al[useAL].XXX state.
boolean	setPseudoArrayToCurMCD() setPseudoArrayToCurMCD() - set PseudoArray values to mcd.XXX state.
boolean	setupArrayLayouts() setupArrayLayouts() - setup list of known array layouts.
private void	setupDefaultArrayLayouts() setupDefaultArrayLayouts() - setup list of default array layouts These are hardwired values.
boolean	setupImageAnalysisMethods() setupImageAnalysisMethods() - setup list of image analysis methods [DEPRICATED FOR NOW].
boolean	writeArrayLayout(ArrayLayout a, boolean logMsgFlag) writeArrayLayout() - write edited ArrayLayout 'a' else no-op.

Methods inherited from class java.lang.Object

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

Field Detail

REMAP_GIPO

public static final int REMAP_GIPO

REMAP codes - remapping GIPO. Code of 0 means no remap in progress

REMAP_QUANT

public static final int REMAP_QUANT

REMAP codes - remapping QUANT. Code of 0 means no remap in progress

REMAP_SAMPLE

public static final int REMAP_SAMPLE

REMAP codes - remapping SAMPLE. Code of 0 means no remap in progress

cvt

public Cvt2Mae cvt

Global link to Cvt2Mae instance

mcd

public MaeConfigData mcd

Global link to MaeConfigData instance

util

public UtilCM util

Global link to UtilCM instance

alList

public ArrayLayout[] alList

[0:maxAL-1] array layouts to choose from max of MAX_ARRAY_LAYOUTS

maxAL

public int maxAL

max # of array layouts in the ALO list

firstAL

public int firstAL

index of first default array layout in the ALO list

lastAL

public int lastAL

index of last default array layout in the ALO list

useAL

public int useAL

array layout to use, -1 means failed

readALOflag

public boolean readALOflag

set to true if read .alo files

iam

public ImageAnalysisMethod[] iam

[0:nIAused-1] image analysis methods to choose from max of MAX_IMG_ANALY_METHODS

maxIAM

public int maxIAM

max # of image analysis methods

useIAM

public int useIAM

method to use, -1 means failed

firstUserALO

public int firstUserALO

the index of the first user defined ALO. This is so we dont' delete internally defined ALOs.

nALOfilesFound

public int nALOfilesFound

# of all *.alo files found in the ArrayLayout/ directory

aloFile

public java.lang.String[] aloFile

[0:nALOfilesFound-1] *.alo ALO files found the the ArrayLayout/ directory

fullPathAloFile

private java.lang.String fullPathAloFile

full path of AL file trying to read

datum

private Element[] datum

data elements from the input table

expectedNbrTokens

private int expectedNbrTokens

expected # of tokens for this layout if not 0.

specialFM

public static FieldMap specialFM

Special Field Map for mapping our symbols see getMinReqFieldList()

aloFileVersion

private java.lang.String aloFileVersion

ALO variable: Version # of .alo file

aloFileName

private java.lang.String aloFileName

ALO variable: variables for parsed .alo file

alo_vendor

private java.lang.String alo_vendor

ALO variable: vendor making the array

alo_layoutName

private java.lang.String alo_layoutName

ALO variable: name of the layout

alo_species

private java.lang.String alo_species

ALO variable: species of sample

alo_quantTool

private java.lang.String alo_quantTool

ALO variable: name of the quantification program

alo_UniGeneSpeciesPrefix

private java.lang.String alo_UniGeneSpeciesPrefix

ALO variable: UniGene 2 letter prefix (eg. "Hs" for human)

alo_commentToken

private java.lang.String alo_commentToken

ALO variable: optional comment token

alo_initialKeyword

private java.lang.String alo_initialKeyword

ALO variable: optional initial keyword in leftmost field

alo_hasMultDatasetsFlag

private boolean alo_hasMultDatasetsFlag

ALO variable: input file has multiple samples

alo_specifyGeometryByNbrSpotsFlag

private boolean alo_specifyGeometryByNbrSpotsFlag

ALO variable: specify (F,G,R,C) from # of spots in PseudoArray

alo_allowNegQuantDataFlag

private boolean alo_allowNegQuantDataFlag

ALO variable: allow negative quant dat

alo_hasBkgrdDataFlag

public boolean alo_hasBkgrdDataFlag

ALO variable: has background intensity data

alo_hasQuantXYcoordsFlag

public boolean alo_hasQuantXYcoordsFlag

ALO variable: has actual quant XY coordinates data

alo_maxFields

private int alo_maxFields

ALO variable: number of duplicate Fields of Grids/array

alo_nGridsPerField

private int alo_nGridsPerField

ALO variable: # of grids/field

alo_rowsPerGrid

private int alo_rowsPerGrid

ALO variable: # of rows/grid

alo_colsPerGrid

private int alo_colsPerGrid

ALO variable: # of columns/grid

alo_maxRowsExpected

private int alo_maxRowsExpected

ALO variable: maximum number of spots (elements or rows)/sample

alo_expectedNbrTokens

private int alo_expectedNbrTokens

ALO variable: # of expected tokens

alo_rowWithSamples

private int alo_rowWithSamples

ALO variable: # of row of FieldQ input file that contains sample names

alo_rowWithFields

private int alo_rowWithFields

ALO variable: # of row of FieldQ input file that contains Field names

alo_rowWithData

private int alo_rowWithData

ALO variable: # of row of FieldQ input file that contains data

alo_rowWithSepGIPOFields

private int alo_rowWithSepGIPOFields

ALO variable: # of row of FieldG separate GIPO input file that contains Field names

alo_rowWithSepGIPOData

private int alo_rowWithSepGIPOData

ALO variable: # of row of FieldG separate GIPO input file that contains data

alo_pseudoArrayFlag

private boolean alo_pseudoArrayFlag

ALO variable: use generated PseudoArray image

alo_useRatioDataFlag

private boolean alo_useRatioDataFlag

ALO variable: data is ratio data (eg. Cy3/Cy5) vs. single sample intensity data.

alo_chkAndEditFieldNamesFlag

private boolean alo_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.

alo_desiredFields

private java.lang.String[] alo_desiredFields

ALO variable: list of FieldMaps for the layout

alo_bitProps

private long alo_bitProps

ALO variable: bit mcd.PROP_xxxx properties

alo_geoPlatformID

private java.lang.String alo_geoPlatformID

Optional GEO Platform ID

defDesiredFields

private final java.lang.String[] defDesiredFields

Default desired fields table with no data. This may be added later.

Constructor Detail

SetupLayouts

public SetupLayouts(Cvt2Mae cvt)

SetupLayouts() - Constructor

Parameters:

cvt - is instance of Cvt2Mae

Method Detail

removeALOfileFromALOlist

public boolean removeALOfileFromALOlist(java.lang.String aloFName)

removeALOfileFromALOlist() - remove ALO entry if match file name

Parameters:

aloFName - is name of .alo file

deleteOldStyleAffyALOnamesatV70

private void deleteOldStyleAffyALOnamesatV70()

deleteOldStyleAffyALOnamesatV70() - hack to remove bogus .alo names from the ArrayLayout directory so they don't appear in the list with the new names. If the name is found, it removes it from the list & deletes the file.

readArrayLayouts

private boolean readArrayLayouts()

readArrayLayouts() - read list of known array layouts from disk layout database directory. Note: new types could be added. by just adding them to the directory.

 1. read directory contents
 2. read the layouts into alList[1:maxAL-1]. Note: slot [0] is for
  entry that is pushed before we get here so maxAL
 starts at 1.

Returns:

return true if you can set up at least ONE ALO, else return false if can't find or setup ANY of the layouts.

See Also:

ArrayLayout, FileTable.readFileAsTable(java.lang.String), FileTable, getValueByName(FileTable, java.lang.String), parseArrayLayoutToTableData(FileTable)

parseArrayLayoutToTableData

private boolean parseArrayLayoutToTableData(FileTable ft)

parseArrayLayoutToTableData() - parse (N,V) table data to alo_XXXX vars.

Parameters:

ft - is FileTable of array layouts

Returns:

false if problem...

See Also:

getValueByName(FileTable, java.lang.String), getValueByNameBool(FileTable, java.lang.String), getValueByNameInt(FileTable, java.lang.String)

getValueByName

private java.lang.String getValueByName(FileTable ft,
                                        java.lang.String name)

getValueByName() - get Value by Name for Table with Fields[0:1] = {Name","Value"}.

Parameters:

ft - is FileTable

name - to lookup

Returns:

value if found, else null if failed.

getValueByNameLong

private long getValueByNameLong(FileTable ft,
                                java.lang.String name)

getValueByNameLong() - get long Value by Name for Table with Fields[0:1] = {Name","Value"}.

Parameters:

ft - is FileTable

name - to lookup

Returns:

value if found, else 0 if failed.

See Also:

UtilCM.cvs2l(java.lang.String, long), getValueByName(FileTable, java.lang.String)

getValueByNameInt

private int getValueByNameInt(FileTable ft,
                              java.lang.String name)

getValueByNameInt() - get int Value by Name for Table with Fields[0:1] = {Name","Value"}.

Parameters:

ft - is FileTable

name - to lookup

Returns:

value if found, else 0 if failed.

See Also:

UtilCM.cvs2i(java.lang.String, int), getValueByName(FileTable, java.lang.String)

getValueByNameBool

private boolean getValueByNameBool(FileTable ft,
                                   java.lang.String name)

getValueByNameBool() - get int Value by Name for Table with Fields[0:1] = {Name","Value"}.

Parameters:

ft - is FileTable

name - to lookup

Returns:

value if found, else false if failed.

See Also:

UtilCM.cvs2b(java.lang.String, boolean), getValueByName(FileTable, java.lang.String)

cvArrayLayoutToTableDataStr

private java.lang.String cvArrayLayoutToTableDataStr(ArrayLayout al)

cvArrayLayoutToTableDataStr() - make prettyprint (N,V) string for writing to .alo file. Note: no final CRLF.

Parameters:

al - is array layout to use

Returns:

String table for this array layout else null if not found

See Also:

FieldMap

checkAndMakeALOdir

private boolean checkAndMakeALOdir(java.lang.String aloDir)

checkAndMakeALOdir()- check for ArrayLayout/ directory tree. If not found, make the directory

Parameters:

aloDir - is location of ArrayLayout/ directory

Returns:

true if successful.

writeArrayLayout

public boolean writeArrayLayout(ArrayLayout a,
                                boolean logMsgFlag)

writeArrayLayout() - write edited ArrayLayout 'a' else no-op. Save file in the disk layout database directory. Note: new types could be added. by just adding them to the directory.

Parameters:

a - is array layout to write

logMsgFlag - to log this transaction

Returns:

true if write the array layout.

See Also:

UtilCM.logMsg(java.lang.String, java.awt.Color), UtilCM.logMsg2(java.lang.String, java.awt.Color), UtilCM.logMsg3(java.lang.String, java.awt.Color), cvArrayLayoutToTableDataStr(ArrayLayout)

chkUniqueLayoutName

private boolean chkUniqueLayoutName(java.lang.String layoutName)

chkUniqueLayoutName() - return TRUE if layout name is unique.

Parameters:

layoutName - to check

Returns:

true if name is unique

setupArrayLayouts

public boolean setupArrayLayouts()

setupArrayLayouts() - setup list of known array layouts. Read from configuration file where new types could be added.

Returns:

true if find or setup the layouts.

See Also:

ArrayLayout, UtilCM.logMsg(java.lang.String, java.awt.Color), UtilCM.logMsg2(java.lang.String, java.awt.Color), UtilCM.logMsg3(java.lang.String, java.awt.Color), readArrayLayouts(), setupDefaultArrayLayouts(), writeArrayLayout(ArrayLayout, boolean)

setupDefaultArrayLayouts

private void setupDefaultArrayLayouts()

setupDefaultArrayLayouts() - setup list of default array layouts These are hardwired values. Note: put generic types FIRST - then add special instances that may contain other options such as species specific or in the case of the Affy data, getting the genomic IDs from the Description, etc..

See Also:

ArrayLayout, chkUniqueLayoutName(java.lang.String)

setupImageAnalysisMethods

public boolean setupImageAnalysisMethods()

setupImageAnalysisMethods() - setup list of image analysis methods [DEPRICATED FOR NOW]. [TODO] read from configuration file where new types could be added.

Returns:

false if can't find or setup the image analysis methods.

See Also:

ImageAnalysisMethod

setPseudoArrayToCurMCD

public boolean setPseudoArrayToCurMCD()

setPseudoArrayToCurMCD() - set PseudoArray values to mcd.XXX state. But only if mcd.specifyGeometryByNbrSpotsFlag is true.

Returns:

true if generated pseudo array data in ALO.

See Also:

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

setPseudoArrayToCurALO

public boolean setPseudoArrayToCurALO()

setPseudoArrayToCurALO() - set PseudoArray values to al[useAL].XXX state. But only if al.specifyGeometryByNbrSpotsFlag is true.

Returns:

true if generated pseudo array data in ALO.

See Also:

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

copyMCDtoALOstate

public void copyMCDtoALOstate()

copyMCDtoALOstate() - Copy mcd.XXX state to al[useAL].XXX state.

copyALOtoMCDstate

public void copyALOtoMCDstate()

copyALOtoMCDstate() - Copy al[useAL].XXX state to mcd.XXX state.

See Also:

MaeConfigData.setMCDstateFromBitProp(long), ArrayLayout

getMinReqFieldList

private java.lang.String[] getMinReqFieldList(int remapMode)

getMinReqFieldList() - get minimal required list of fields based on current mcd state. Based on the semantics of the current state that is set by "Edit Layout", we may not want to require particular fields or we may want to rename them (eg. use Cy3, Cy5 instead of RawIntensity1, RawIntensity2 if if mcd.useRatioDataFlag is set, etc.

Parameters:

remapMode - to enable remaping of field names

Returns:

list of minimum required fields else null if error

See Also:

FieldMap.addEntry(java.lang.String, java.lang.String, java.lang.String, java.lang.String), FieldMap

getMaeToUserFields

public boolean getMaeToUserFields(java.lang.String fileName,
                                  FieldMap fm,
                                  int row,
                                  int remapMode,
                                  boolean useMaxFieldsFlag)

getMaeToUserFields() - extract desired fields from row of tokens by reading them from the fileName. This is used in the Assign GIPO/QUANT fields operations.

Parameters:

fileName - to read

fm - is field map to use

row - to use

remapMode -

useMaxFieldsFlag -

Returns:

true if successful.

See Also:

FieldMapGUI, FileTable, FileTable.readTableFieldsFromFile(java.lang.String, int), UtilCM.logMsg(java.lang.String, java.awt.Color), UtilCM.logMsg2(java.lang.String, java.awt.Color), getMinReqFieldList(int)

getPrintStringFieldRow

public java.lang.String getPrintStringFieldRow(java.lang.String dirName,
                                               java.lang.String srcFileName,
                                               int row,
                                               java.lang.String msg)

getPrintStringFieldRow() - get print string of specified row of file

Parameters:

dirName - is directory name of file

srcFileName - file name

row - to read

msg - to display while reading file

Returns:

print string of the row else "" if failed

See Also:

FileTable, FileTable.readTableFieldsFromFile(java.lang.String, int)