Class Cvt2Mae

java.lang.Object
  |
  +--Cvt2Mae

public class Cvt2Mae

extends java.lang.Object

MicroArray Cvt2Mae main class. This application converts microarray data files to MAExplorer files format. Data types includes: user-defined, Incyte GEM, Affymetrix, and others. The data is stored in MaeConfigData and may be edited prior to saving in the MAExplorer tree maePrj/(Config/ MAE/ Quant/ State/ Report/). Cvt2Mae stores array layouts in /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: 1.24 $

Author:

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

See Also:

MAExplorer Home

Field Summary

static java.lang.String	AFFY_TMP_FILE Affy MAS-5 temp file name
static java.lang.String	ALO_VERSION Current Version number for Array layout.
static boolean	CONSOLE_FLAG flag: for debugging - always TRUE
java.lang.String	date date captured when this program is run
static boolean	DBUG_FLAG flag: primary debug flag - only while debugging
static java.lang.String	DBUG_IN_DIR if USE_DBUG_DIR, then can save time when debugging by going directly to debugging input source and output directories.
static java.lang.String	DBUG_OUT_DIR if USE_DBUG_DIR, then can save time when debugging by going directly to debugging input source and output directories.
static boolean	DBUG_READ_WRITE flag: extra debugging for I/O in readData()
DataIO	dio Global data DataIO instance
boolean	enableMapQueryFlag flag: enabled when may edit MapUserToMae
java.lang.Exception	exceptErr Possible global exception error for error reporting
java.lang.String	fileSep JVM ("file.separator")
FieldMapGUI	fmg single MODAL instance of popup FieldMapGUI if not null
boolean	fmgFirstTimeFlagGipo for fieldMapGUI, setting first time defaults
boolean	fmgFirstTimeFlagQuant for fieldMapGUI, setting first time defaults
boolean	fmgFirstTimeFlagSample for fieldMapGUI, setting first time defaults
static CvtGUI	gui Global GUI popup frame
boolean	isMacFlag flag: use Max list of required fields
boolean	isSunFlag flag: true if SUNOS
boolean	isWinPCflag flag: true if Windows PC
static int	MAX_ARRAY_LAYOUTS max # of Array Layouts
static int	MAX_IMG_ANALY_METHODS max # of image analysis methods that were used to quantify data - possibly in separate data files.
static int	MAX_IN_TOKENS_PER_ROW max # of tokens/row of an input file
static int	MAX_SRC_FILES max # of source files that can convert
MaeConfigData	mcd Mae Config Data
static boolean	NEVER flag: for debugging - always FALSE
java.lang.String	newline for newline, Mac= "\r" Sun ="\n" PC= "\r\n"
java.lang.String	osName JVM ("os.name") that we are running in
static java.lang.String	RCS RCS Version number and dat1
boolean	rmvTrailingWhiteSpaceFlag flag: if clean up user data whitespace
boolean	selectedChipLayoutFlag flag: user has selected chip layout
boolean	selectedImageAnalysisFlag flag: user has selected quantification method
boolean	selectedInputFileFlag flag: user has selected input file
boolean	selectedOutputPathFlag flag: user has selected output path
java.lang.String	sExceptErr Possible global exception error string for error reporting
SetupLayouts	sul Global SetupLayouts layouts instance
java.lang.String	title top level GUI title
static boolean	USE_DBUG_DIR flag: Force source and output files directories to use hardwired definitions while debugging
static boolean	USE_IAM_FLAG Add Image Analysis Method GUI
static boolean	USE_LOG_WINDOW flag: set if want log windows
boolean	useMaxFieldsRequiredFlag
java.lang.String	userDir user directory - JVM ("user.dir")+fileSep
UtilCM	util Global utilities UtilCM instance
static java.lang.String	VERSION Title line version numbers

Constructor Summary

Cvt2Mae()
Cvt2Mae() - Constructor

Method Summary

void	init() init() - initialize data structures and create and start the GUI.
static void	main(java.lang.String[] args) main() - for Cvt2Mae started by stand-alone application

Methods inherited from class java.lang.Object

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

Field Detail

VERSION

public static final java.lang.String VERSION

Title line version numbers

RCS

public static final java.lang.String RCS

RCS Version number and dat1

ALO_VERSION

public static final java.lang.String ALO_VERSION

Current Version number for Array layout. Don't read older versions!

AFFY_TMP_FILE

public static final java.lang.String AFFY_TMP_FILE

Affy MAS-5 temp file name

mcd

public MaeConfigData mcd

Mae Config Data

dio

public DataIO dio

Global data DataIO instance

util

public UtilCM util

Global utilities UtilCM instance

sul

public SetupLayouts sul

Global SetupLayouts layouts instance

gui

public static CvtGUI gui

Global GUI popup frame

fmg

public FieldMapGUI fmg

single MODAL instance of popup FieldMapGUI if not null

CONSOLE_FLAG

public static boolean CONSOLE_FLAG

flag: for debugging - always TRUE

NEVER

public static boolean NEVER

flag: for debugging - always FALSE

USE_LOG_WINDOW

public static boolean USE_LOG_WINDOW

flag: set if want log windows

DBUG_FLAG

public static boolean DBUG_FLAG

flag: primary debug flag - only while debugging

USE_DBUG_DIR

public static boolean USE_DBUG_DIR

flag: Force source and output files directories to use hardwired definitions while debugging

DBUG_READ_WRITE

public static boolean DBUG_READ_WRITE

flag: extra debugging for I/O in readData()

USE_IAM_FLAG

public static boolean USE_IAM_FLAG

Add Image Analysis Method GUI

DBUG_IN_DIR

public static final java.lang.String DBUG_IN_DIR

if USE_DBUG_DIR, then can save time when debugging by going directly to debugging input source and output directories.

DBUG_OUT_DIR

public static final java.lang.String DBUG_OUT_DIR

if USE_DBUG_DIR, then can save time when debugging by going directly to debugging input source and output directories.

MAX_IN_TOKENS_PER_ROW

public static final int MAX_IN_TOKENS_PER_ROW

max # of tokens/row of an input file

MAX_SRC_FILES

public static final int MAX_SRC_FILES

max # of source files that can convert

MAX_ARRAY_LAYOUTS

public static final int MAX_ARRAY_LAYOUTS

max # of Array Layouts

MAX_IMG_ANALY_METHODS

public static final int MAX_IMG_ANALY_METHODS

max # of image analysis methods that were used to quantify data - possibly in separate data files.

title

public java.lang.String title

top level GUI title

osName

public java.lang.String osName

JVM ("os.name") that we are running in

fileSep

public java.lang.String fileSep

JVM ("file.separator")

userDir

public java.lang.String userDir

user directory - JVM ("user.dir")+fileSep

date

public java.lang.String date

date captured when this program is run

isWinPCflag

public boolean isWinPCflag

flag: true if Windows PC

isSunFlag

public boolean isSunFlag

flag: true if SUNOS

isMacFlag

public boolean isMacFlag

flag: use Max list of required fields

useMaxFieldsRequiredFlag

public boolean useMaxFieldsRequiredFlag

rmvTrailingWhiteSpaceFlag

public boolean rmvTrailingWhiteSpaceFlag

flag: if clean up user data whitespace

enableMapQueryFlag

public boolean enableMapQueryFlag

flag: enabled when may edit MapUserToMae

selectedInputFileFlag

public boolean selectedInputFileFlag

flag: user has selected input file

selectedChipLayoutFlag

public boolean selectedChipLayoutFlag

flag: user has selected chip layout

selectedOutputPathFlag

public boolean selectedOutputPathFlag

flag: user has selected output path

selectedImageAnalysisFlag

public boolean selectedImageAnalysisFlag

flag: user has selected quantification method

sExceptErr

public java.lang.String sExceptErr

Possible global exception error string for error reporting

exceptErr

public java.lang.Exception exceptErr

Possible global exception error for error reporting

fmgFirstTimeFlagGipo

public boolean fmgFirstTimeFlagGipo

for fieldMapGUI, setting first time defaults

fmgFirstTimeFlagQuant

public boolean fmgFirstTimeFlagQuant

for fieldMapGUI, setting first time defaults

fmgFirstTimeFlagSample

public boolean fmgFirstTimeFlagSample

for fieldMapGUI, setting first time defaults

newline

public java.lang.String newline

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

Constructor Detail

Cvt2Mae

public Cvt2Mae()

Cvt2Mae() - Constructor

See Also:

init()

Method Detail

main

public static void main(java.lang.String[] args)

main() - for Cvt2Mae started by stand-alone application

Parameters:

args - is the command line arg list

init

public void init()

init() - initialize data structures and create and start the GUI.

See Also:

CvtGUI, DataIO, MaeConfigData, SetupLayouts, SetupLayouts.setupImageAnalysisMethods(), UtilCM, UtilCM.dateStr(), UtilCM.logMsg(java.lang.String, java.awt.Color), UtilCM.timeStr()