Class Table

java.lang.Object
  |
  +--SimpleTable
        |
        +--Table

Direct Known Subclasses:

ConfigTable, GipoTable, MaHPquantTable, MaInfoTable, SamplesTable

class Table

extends SimpleTable

This class creates a table object with no data or data read from a tab-delimited file. It extens SimpleTable. In turn, Table is the base class for other Table object extensions. Note: I/O is not done in this class but rather in FileIO.java.

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. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/04/08 13:25:08 $ $Revision: 1.11 $

Author:

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

See Also:

MAExplorer Home, ConfigTable, GipoTable, MaHPquantTable, SamplesTable

Field Summary

(package private) int	bufSize size of input buffer when read file
(package private) boolean	fileOKflag File exists and was able to be read
private FileIO	fio link to global instance of FileIO
(package private) MAExplorer	mae link to global instance of MAExplorer

Fields inherited from class SimpleTable

fileName, msg, tCols, tData, tFields, title, tRows

Constructor Summary

(package private)	Table(MAExplorer mae, int nRows, int nCols, java.lang.String title, java.lang.String msg) Table() - constructor for creating empty table of (nRows,nCols).
(package private)	Table(MAExplorer mae, java.lang.String fileName, java.lang.String msg) Table() - constructor for creating table from file
(package private)	Table(MAExplorer mae, java.lang.String fileName, java.lang.String msg, java.lang.String[] overideFieldNames, boolean dontReadHeaderLineFlag) Table() - constructor for creating table from file
(package private)	Table(SimpleTable st) Table() - constructor for creating table from a SimpleTable

Method Summary

(package private) Table	copyTable(SimpleTable st) copyTable() - copy SimpleTable data to this Table.
private boolean	createFileTable(MAExplorer mae, java.lang.String fileName, java.lang.String msg, java.lang.String[] overideFieldNames, boolean dontReadHeaderLineFlag) createFileTable() - create table from file on this Table.
(package private) java.lang.String[]	getArrayOfTabDelimitedTokens(java.lang.String line, int nCols) getArrayOfTabDelimitedTokens() - get array of tab-delim tokens from table.
private boolean	getData(java.lang.String fileName, java.lang.String msg, java.lang.String[] overideFieldNames, boolean dontReadHeaderLineFlag) getData() - read the data and store it in the table.
(package private) SimpleTable	getTableRowsSubset(SimpleTable t, java.lang.String key, java.lang.String fieldName, java.lang.String newTitle) getTableRowsSubset() - make new table subset of table by (field,key)
(package private) SimpleTable	getTableRowsSubset(Table t, java.lang.String[] fieldList, java.lang.String[] newFieldList, java.lang.String[] urlPrefix, java.lang.String[] urlSuffix, int nFields, java.lang.String newTitle) getTableRowsSubset() - make new table of specified fields by fieldList[] and in the order in which they appear in the fieldList[].
(package private) SimpleTable	insertTblInULHCtable(int nRows, int nCols, java.lang.String nTitle) insertTblInULHCtable() - insert table into U.L.H.C.
(package private) int	lookupFieldIdxAndRemapFieldName(java.lang.String maeTbl, java.lang.String maeField) lookupFieldIdxAndRemapFieldName() - lookup field idx and remap name if need to.
(package private) java.lang.String	makeTabDelimReport(java.lang.String title) makeTabDelimReport() - make tab-delimited string report string from this Table
private java.lang.String	readTable(java.lang.String fileName, java.lang.String msg) readTable() - read a tab-delimited table from FILE/URL.
private boolean	storeDataBufParser(java.lang.String rawData, java.lang.String msg, java.lang.String[] overideFieldNames, boolean dontReadHeaderLineFlag) storeDataBufParser() - Put data into Table tData[r][c] and tFields[c], given a String from the whole file.

Methods inherited from class SimpleTable

freeTable, getTableRowFieldByRowIdx, getTableRowFieldIdxByRowIdx, lookupFieldIdx, setFieldData, setRowData, trimWhitespace

Methods inherited from class java.lang.Object

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

Field Detail

mae

MAExplorer mae

link to global instance of MAExplorer

fio

private FileIO fio

link to global instance of FileIO

fileOKflag

boolean fileOKflag

File exists and was able to be read

bufSize

int bufSize

size of input buffer when read file

Constructor Detail

Table

Table(MAExplorer mae,
      java.lang.String fileName,
      java.lang.String msg)

Table() - constructor for creating table from file

Parameters:

mae - is MAExplorer instance

fileName - is file name to read into Table instance

msg - is the loading message

See Also:

FileIO.logMsgln(java.lang.String), MAExplorer.logDRYROTerr(java.lang.String), MAExplorer.percentDone(), Util.showMsg(java.lang.String), getData(java.lang.String, java.lang.String, java.lang.String[], boolean), storeDataBufParser(java.lang.String, java.lang.String, java.lang.String[], boolean)

Table

Table(MAExplorer mae,
      java.lang.String fileName,
      java.lang.String msg,
      java.lang.String[] overideFieldNames,
      boolean dontReadHeaderLineFlag)

Table() - constructor for creating table from file

Parameters:

mae - is MAExplorer instance

fileName - is file name to read into Table instance

msg - is the loading message

overideFieldNames - is array of names to use for the file names if not null, else use the names from the first line in the file.

dontReadHeaderLineFlag - if using the overideFieldNames[] data, don't read the header line (treat it as data) and use the rest of the fields

See Also:

createFileTable(MAExplorer, java.lang.String, java.lang.String, java.lang.String[], boolean)

Table

Table(MAExplorer mae,
      int nRows,
      int nCols,
      java.lang.String title,
      java.lang.String msg)

Table() - constructor for creating empty table of (nRows,nCols). The fileName is set to "*NONE*".

Parameters:

mae - is MAExplorer instance

nRows - is the size of table to create

nCols - is the size of table to create

fileName - is file name to read into Table instance

msg - is the loading message

Table

Table(SimpleTable st)

Table() - constructor for creating table from a SimpleTable

Parameters:

st - is a Simple table instance.

See Also:

copyTable(SimpleTable)

Method Detail

createFileTable

private boolean createFileTable(MAExplorer mae,
                                java.lang.String fileName,
                                java.lang.String msg,
                                java.lang.String[] overideFieldNames,
                                boolean dontReadHeaderLineFlag)

createFileTable() - create table from file on this Table.

Parameters:

mae - is MAExplorer instance

fileName - is file name to read into Table instance

msg - is the loading message if not null

overideFieldNames - is array of names to use for the file names if not null, else use the names from the first line in the file.

dontReadHeaderLineFlag - if using the overideFieldNames[] data, don't read the header line (treat it as data) and use the rest of the fields

Returns:

true if succeed

See Also:

FileIO.logMsgln(java.lang.String), MAExplorer.logDRYROTerr(java.lang.String), MAExplorer.percentDone(), Util.showMsg(java.lang.String), getData(java.lang.String, java.lang.String, java.lang.String[], boolean), storeDataBufParser(java.lang.String, java.lang.String, java.lang.String[], boolean)

getData

private boolean getData(java.lang.String fileName,
                        java.lang.String msg,
                        java.lang.String[] overideFieldNames,
                        boolean dontReadHeaderLineFlag)

getData() - read the data and store it in the table.

Parameters:

fileName - is file name to read into Table instance

msg - is the loading message

overideFieldNames - is array of names to use for the file names if not null, else use the names from the first line in the file.

dontReadHeaderLineFlag - if using the overideFieldNames[] data, don't read the header line (treat it as data) and use the rest of the fields

Returns:

true if can read the table from the file

See Also:

FileIO.logMsgln(java.lang.String), MAExplorer.percentDone(), Util.showMsg(java.lang.String), readTable(java.lang.String, java.lang.String), storeDataBufParser(java.lang.String, java.lang.String, java.lang.String[], boolean)

lookupFieldIdxAndRemapFieldName

int lookupFieldIdxAndRemapFieldName(java.lang.String maeTbl,
                                    java.lang.String maeField)

lookupFieldIdxAndRemapFieldName() - lookup field idx and remap name if need to.

Parameters:

maeTbl - is table to lookup

maeField - to find

Returns:

index if found, -1 if failed.

See Also:

ConfigTable.mapUsrFieldToMaeField(java.lang.String, java.lang.String), SimpleTable.lookupFieldIdx(java.lang.String)

getArrayOfTabDelimitedTokens

java.lang.String[] getArrayOfTabDelimitedTokens(java.lang.String line,
                                                int nCols)

getArrayOfTabDelimitedTokens() - get array of tab-delim tokens from table. The number of expected columns is specified and if there is no more data, it will leave those cells null.

Parameters:

line - of tokens to parse

nCols - is the # of tokens to parse (may be less than actual #)

Returns:

array of data or null line if is empty

storeDataBufParser

private boolean storeDataBufParser(java.lang.String rawData,
                                   java.lang.String msg,
                                   java.lang.String[] overideFieldNames,
                                   boolean dontReadHeaderLineFlag)

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

Parameters:

rawData - is data to be parsed into a Table

msg - is the converting msg

overideFieldNames - is array of names to use for the file names if not null, else use the names from the first line in the file.

dontReadHeaderLineFlag - if using the overideFieldNames[] data, don't read the header line (treat it as data) and use the rest of the fields

Returns:

true if store data correctly

See Also:

MAExplorer.logDRYROTerr(java.lang.String), Util.showMsg(java.lang.String)

readTable

private java.lang.String readTable(java.lang.String fileName,
                                   java.lang.String msg)

readTable() - read a tab-delimited table from FILE/URL. This file consisting of the field names in the first row followed by data fields.

Parameters:

fileName - is file name to read

msg - is the converting msg

Returns:

raw data string if succeed, else null

See Also:

FileIO.readData(java.lang.String, java.lang.String), Util.showMsg(java.lang.String)

getTableRowsSubset

SimpleTable getTableRowsSubset(SimpleTable t,
                               java.lang.String key,
                               java.lang.String fieldName,
                               java.lang.String newTitle)

getTableRowsSubset() - make new table subset of table by (field,key)

Parameters:

t - is the instance of a SimpleTable to subset

key - is the values to look for

fieldName - is the column field name to check

newTitle - is the new table title

Returns:

new SimpleTable or null if failed.

See Also:

SimpleTable.lookupFieldIdx(java.lang.String), Table

getTableRowsSubset

SimpleTable getTableRowsSubset(Table t,
                               java.lang.String[] fieldList,
                               java.lang.String[] newFieldList,
                               java.lang.String[] urlPrefix,
                               java.lang.String[] urlSuffix,
                               int nFields,
                               java.lang.String newTitle)

getTableRowsSubset() - make new table of specified fields by fieldList[] and in the order in which they appear in the fieldList[]. If an newFieldList[] entry is not null, then use a new field name. If a urlPrefix[] (urlSuffix[]) entry is not null, then prepend (append) it to the data item. This is how we generate clickable URLs by attaching the URL base address and possible suffix. Note: only add the URL links if the data for that cell is not "".

Parameters:

t - is the instance of a SimpleTable to subset

fieldList - is list of fields to use

newFieldList[] - is names of new fields entries are not null

urlPrefix - is URL entry prefixes for URL fields if not null

urlSuffix - is URL entry suffixes if entry not null

nFields - is # of new fields

newTitle - is the new table title

Returns:

new SimpleTable or null if failed.

See Also:

SimpleTable, SimpleTable.lookupFieldIdx(java.lang.String)

makeTabDelimReport

java.lang.String makeTabDelimReport(java.lang.String title)

makeTabDelimReport() - make tab-delimited string report string from this Table

Parameters:

title - to put at top of the string report

Returns:

string report

insertTblInULHCtable

SimpleTable insertTblInULHCtable(int nRows,
                                 int nCols,
                                 java.lang.String nTitle)

insertTblInULHCtable() - insert table into U.L.H.C. of new larger table Where this.tRows<=nRows, this.tCols<=nCols. Fill all null entries with "".

Parameters:

nRows - is the number of rows in the table

nCols - is the number of columns in the table

nTitle - is the new title

Returns:

old table if (this.tRows>=nRows && this.tCols>=nCols else return new table if successful, else null.

See Also:

SimpleTable

copyTable

Table copyTable(SimpleTable st)

copyTable() - copy SimpleTable data to this Table. This handles potential casting problems.

Parameters:

st - is SimpleTable to copy into a Table

Returns:

instance of new Table derived from st