Class FileTable

java.lang.Object
  |
  +--FileTable

public class FileTable

extends java.lang.Object

This class reads data from files and writes data to files. It also reads tab-delimited data from a file into a Table (tRows,tCols,tFields,tData). It can be used to create an empty table (not associated with a file).

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 19:22:30 $ $Revision: 1.6 $

Author:

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

See Also:

MAExplorer Home

Field Summary

int	bufSize size of input buffer
private static boolean	DBUG_FILE_TABLE Local debugging switch
java.lang.String	errMsgLog error message log it not null
static int	estFieldsRowNbr estimated row number where Fields are listed
static int	estLinesInFile number of lines found in file
static int	estMaxColsInFile estimated max number Cols in file
static int	estMaxGridsInFile estimated max number Grids found in file
static int	estMaxNbrField estimated number of Fields
static int	estMaxRowsInFile estimated max number Rows in file
static int	estRowWithData estimated row where data starts
static int	estSamplesRowNbr estimated row number where Samples are listed
private java.io.File	file file descriptor for I/O
java.lang.String	fileName file to read or write I/O
int	tCols number of columns/row
java.lang.String[][]	tData row vectors [0:tRows-1][0:tCols-1]
java.lang.String[]	tFields names of table fields
java.lang.String	tName Table name
int	tRows number of rows.

Constructor Summary

FileTable(java.lang.String tableName)
FileTable() - generic Constructor, set some defaults to 0.

FileTable(java.lang.String tableName, int rows, int cols)
FileTable() - Constructor to make empty table of known size

Method Summary

boolean	checkForBadTable() checkForBadTable() - verify that it is a well formed table with all field names present and with no duplicate entries.
private boolean	computeTableSize(java.lang.String rawData) computeTableSize() - setup the (tRows,tCols) of table data.
static int	countLinesAndTabCountsInFile(Cvt2Mae cvt, java.lang.String fileName, boolean lookForSampleTabsFlag, java.lang.String msg, java.awt.Color color) countLinesAndTabCountsInFile() - open file and count number of lines & tabs Set estLinesInFile to # lines found. Set estSamplesRowNbr to estimated row # where Samples are listed. Set estFieldsRowNbr to estimated row # where Fields are listed.
static int	countLinesInFile(java.lang.String fileName) countLinesInFile() - open file and count # of lines in the file.
static int	countNonNullTabData(java.lang.String sLine) countNonNullTabData() - count Non-Null data tabs in line Do not count tabs after reach field with no data.
boolean	cvtStrToTable(java.lang.String sData) cvtStrToTable() - convert tab-delim String data to Table data structure.
static boolean	findMaxGridRowColInFile(Cvt2Mae cvt, java.lang.String fileName, java.lang.String msg, java.awt.Color color, int rowWithFields, int rowNbrDataStarts) findMaxGridRowColInFile() - open file and find Max Grid Row Col in file This assumes that ("grid, grid_row, and grid_col") are in the FieldMap.
static int	findRowWithKeywordsInFile(Cvt2Mae cvt, java.lang.String fileName, java.lang.String[] keyWords, boolean needAllKeywordsFlag, int maxLinesToCheck, java.lang.String msg, java.awt.Color color) findRowWithKeywordsInFile() - open file and look for first line with keywords (case-independent) in it.
void	freeTable() freeTable() - free Table tData[][] and tFields so can garbage collect it Also zero tRows, tCols
int	lookupFieldIdx(java.lang.String fieldName) lookupFieldIdx() - lookup index of field if exists.
static int	lookupSubstringFieldIdx(java.lang.String[] tblFields, java.lang.String fieldName) lookupSubstringFieldIdx() - lookup index of case independent field substring if exists and startsWith tblField[].
java.lang.String	promptFileName(java.lang.String promptDir, java.lang.String msg) promptFileName() - prompt for file name
java.lang.String	readFileAsString(java.io.File f) readFileAsString() - Will read file from disk & returns as String
java.lang.String	readFileAsString(java.lang.String fileName) readFileAsString() - read file from disk and return data as String
boolean	readFileAsTable(java.lang.String fileName) readFileAsTable() - read file and tab-delim data as Table.
java.lang.String[]	readTableFieldsFromFile(java.lang.String fileName, int r) readTableFieldsFromFile() - open file and read row r tab-delim data.
private boolean	storeDataBufParser(java.lang.String rawData) storeDataBufParser() - Put data into Table tData[r][c] and tFields[c], given a raw data String from the whole file.
boolean	writeData(java.lang.String fileName, java.lang.String data) writeData() - write string data to file
boolean	writeStringToFile(java.lang.String fileName, java.lang.String data) writeStringToFile() - write data to disk file

Methods inherited from class java.lang.Object

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

Field Detail

DBUG_FILE_TABLE

private static boolean DBUG_FILE_TABLE

Local debugging switch

estLinesInFile

public static int estLinesInFile

number of lines found in file

estSamplesRowNbr

public static int estSamplesRowNbr

estimated row number where Samples are listed

estFieldsRowNbr

public static int estFieldsRowNbr

estimated row number where Fields are listed

estMaxNbrField

public static int estMaxNbrField

estimated number of Fields

estMaxGridsInFile

public static int estMaxGridsInFile

estimated max number Grids found in file

estMaxRowsInFile

public static int estMaxRowsInFile

estimated max number Rows in file

estMaxColsInFile

public static int estMaxColsInFile

estimated max number Cols in file

estRowWithData

public static int estRowWithData

estimated row where data starts

bufSize

public int bufSize

size of input buffer

tCols

public int tCols

number of columns/row

tRows

public int tRows

number of rows. i.e. number row Clone Id's

errMsgLog

public java.lang.String errMsgLog

error message log it not null

fileName

public java.lang.String fileName

file to read or write I/O

tName

public java.lang.String tName

Table name

tFields

public java.lang.String[] tFields

names of table fields

tData

public java.lang.String[][] tData

row vectors [0:tRows-1][0:tCols-1]

file

private java.io.File file

file descriptor for I/O

Constructor Detail

FileTable

public FileTable(java.lang.String tableName)

FileTable() - generic Constructor, set some defaults to 0.

Parameters:

tableName - String name of table

FileTable

public FileTable(java.lang.String tableName,
                 int rows,
                 int cols)

FileTable() - Constructor to make empty table of known size

Parameters:

tableName - String name of table

rows - max rows in table

cols - max columns in table

Method Detail

promptFileName

public java.lang.String promptFileName(java.lang.String promptDir,
                                       java.lang.String msg)

promptFileName() - prompt for file name

Parameters:

promptDir - default dir

msg - message to display in file dialog

Returns:

full file path if successfull else null

checkForBadTable

public boolean checkForBadTable()

checkForBadTable() - verify that it is a well formed table with all field names present and with no duplicate entries.

Returns:

true if successful, also stuff error mesasge into "errMsgLog" to be displayed later.

readTableFieldsFromFile

public java.lang.String[] readTableFieldsFromFile(java.lang.String fileName,
                                                  int r)

readTableFieldsFromFile() - open file and read row r tab-delim data.

Parameters:

fileName - file name

r - row to read

Returns:

rFields is array of fields to return if successful else null.

countLinesInFile

public static int countLinesInFile(java.lang.String fileName)

countLinesInFile() - open file and count # of lines in the file. Set estLinesInFile to number lines found.

Parameters:

fileName - of file to read

Returns:

number of lines else 0.

countLinesAndTabCountsInFile

public static int countLinesAndTabCountsInFile(Cvt2Mae cvt,
                                               java.lang.String fileName,
                                               boolean lookForSampleTabsFlag,
                                               java.lang.String msg,
                                               java.awt.Color color)

countLinesAndTabCountsInFile() - open file and count number of lines & tabs
Set estLinesInFile to # lines found.
Set estSamplesRowNbr to estimated row # where Samples are listed.
Set estFieldsRowNbr to estimated row # where Fields are listed.

Try to estimate row numbers for Samples row and for Field row If lookForSampleTabsFlag is FALSE, it assumes that the first row with initial max number tabs with non-null data is the Fields row, otherwise] it is the Samples row.

Note that the Samples row may contain fewer tabs than the Fields row - but it is assumed that both contain more tabs than any other row. When we have satisfied the initial counts, just stop analyzing the tab counts to make it run MUCH MUCH faster.

Parameters:

cvt - instance of Cvt2Mae

fileName - file to count

lookForSampleTabsFlag - if true, look for sample tabs

msg - message for logMsg

color - is the logMsg color

Returns:

number of lines in file else 0.

See Also:

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

findMaxGridRowColInFile

public static boolean findMaxGridRowColInFile(Cvt2Mae cvt,
                                              java.lang.String fileName,
                                              java.lang.String msg,
                                              java.awt.Color color,
                                              int rowWithFields,
                                              int rowNbrDataStarts)

findMaxGridRowColInFile() - open file and find Max Grid Row Col in file This assumes that ("grid, grid_row, and grid_col") are in the FieldMap. then set

    estMaxGridsInFile   as estimated max # Grids found in file
    estMaxRowsInFile    as estimated max # Rows in file
    estMaxColsInFile    as estimated max # Cols in file

Parameters:

cvt - instance of Cvt2Mae

fileName - file to count

msg - message for logMsg

color - logMsg color

rowNbrDataStarts - row that data starts

Returns:

true if successful

See Also:

FileTable, readTableFieldsFromFile(java.lang.String, int), ParseTable, ParseTable.getDelimTokens(java.lang.String, boolean[], java.lang.String[], boolean, java.lang.String), UtilCM.cvs2i(java.lang.String, int), UtilCM.logMsg(java.lang.String, java.awt.Color), countNonNullTabData(java.lang.String)

countNonNullTabData

public static int countNonNullTabData(java.lang.String sLine)

countNonNullTabData() - count Non-Null data tabs in line Do not count tabs after reach field with no data.

Parameters:

sLine - line to count lines on

Returns:

number of non-null data tabs

findRowWithKeywordsInFile

public static int findRowWithKeywordsInFile(Cvt2Mae cvt,
                                            java.lang.String fileName,
                                            java.lang.String[] keyWords,
                                            boolean needAllKeywordsFlag,
                                            int maxLinesToCheck,
                                            java.lang.String msg,
                                            java.awt.Color color)

findRowWithKeywordsInFile() - open file and look for first line with keywords (case-independent) in it. If needAllKeywordsFlag is set then all keywords need to be present.

Parameters:

cvt - instance of Cvt2Mae

fileName - file to open and search

keyWords - array of keywords to search

needAllKeywordsFlag - boolean look at all keywords flag

maxLinesToCheck - only look at max number of lines

msg - Not used, Future

color - Not used, Future

Returns:

line number (starting at line 1), else return 0

cvtStrToTable

public boolean cvtStrToTable(java.lang.String sData)

cvtStrToTable() - convert tab-delim String data to Table data structure. Set up the table data structures in this instance of FileTable: (tRows, tCols, tFields[], tData[][]).

Parameters:

sData - data to convert to table

Returns:

true if successful

See Also:

computeTableSize(java.lang.String), storeDataBufParser(java.lang.String)

readFileAsTable

public boolean readFileAsTable(java.lang.String fileName)

readFileAsTable() - read file and tab-delim data as Table. Set up the table data structures in this instance of FileTable: (tRows, tCols, tFields[], tData[][]).

Parameters:

fileName - to open and read to get data to convert

Returns:

true if successful

See Also:

computeTableSize(java.lang.String), readFileAsString(java.lang.String), storeDataBufParser(java.lang.String)

writeData

public boolean writeData(java.lang.String fileName,
                         java.lang.String data)

writeData() - write string data to file

Parameters:

fileName - file to write data to disk

data - write data to disk

Returns:

true if successful

See Also:

writeStringToFile(java.lang.String, java.lang.String)

readFileAsString

public java.lang.String readFileAsString(java.lang.String fileName)

readFileAsString() - read file from disk and return data as String

Parameters:

fileName - file name to read data

Returns:

data as String, null if failed

readFileAsString

public java.lang.String readFileAsString(java.io.File f)

readFileAsString() - Will read file from disk & returns as String

Parameters:

f - File to read

Returns:

data read from the file, else null if failed.

writeStringToFile

public boolean writeStringToFile(java.lang.String fileName,
                                 java.lang.String data)

writeStringToFile() - write data to disk file

Parameters:

fileName - is name of the file to write

data - to write to the file

Returns:

true if successful false if failed

storeDataBufParser

private boolean storeDataBufParser(java.lang.String rawData)

storeDataBufParser() - Put data into Table tData[r][c] and tFields[c], given a raw data String from the whole file. The tData[0:tRow-1][0:tCol-1] and tFields[0:tRow-1]

Parameters:

rawData - is raw data string read from file to convert into Table

Returns:

true if successful false if failed

computeTableSize

private boolean computeTableSize(java.lang.String rawData)

computeTableSize() - setup the (tRows,tCols) of table data. This is a tab-delimited file consisting of the field names in the first row followed by data fields. and set (tRows,tCols, tFields[], tData[][]) to (0,0,null,null).

Parameters:

rawData - raw data representing string table to analyze

Returns:

true if successful false if failed

lookupFieldIdx

public int lookupFieldIdx(java.lang.String fieldName)

lookupFieldIdx() - lookup index of field if exists. if it does not exist, return -1

Parameters:

fieldName -

Returns:

index if successful, -1 if not found

lookupSubstringFieldIdx

public static int lookupSubstringFieldIdx(java.lang.String[] tblFields,
                                          java.lang.String fieldName)

lookupSubstringFieldIdx() - lookup index of case independent field substring if exists and startsWith tblField[]. if it does not exist, return -1

Parameters:

fieldName - field name to look up

tblFields - array of fields

Returns:

index if successful, -1 if not found

freeTable

public void freeTable()

freeTable() - free Table tData[][] and tFields so can garbage collect it Also zero tRows, tCols