Class MaeSampleData

java.lang.Object
  |
  +--MaeSampleData

public class MaeSampleData

extends java.lang.Object

This class tracks the SampleDB.txt file data containing the list of samples. It contains methods to read and write the Sample DB file. Note: the data is kept in MaeConfigData mcd.

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: 1.4 $

Author:

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

See Also:

MAExplorer Home

Field Summary

private int	idxDatabase_File idx of "Database_File" field
private int	idxProject idx of "Project" field
private int	idxSample_ID idx of "Sample_ID" field
MaeConfigData	mcd link to global MaeConfigData database
private int	tCols # of columns in the table
private java.lang.String[][]	tData [0:tRows-1][0:tCols-1] table data that is actually a 1D array [0:tRows-1] of rowData[0:tCols-1]
private java.lang.String[]	tFields Field names in the table
private int	tRows # of rows in the table

Constructor Summary

MaeSampleData(MaeConfigData mcd)
MaeSampleData() - constructor

Method Summary

private boolean	findSampleFields() findSampleFields() - find SampleDB fields in the first row.
private int	lookupFieldIndex(java.lang.String field) lookupFieldIndex() - lookup field index in the tFields[0:tCols-1] data.
boolean	readSamplesFile() readSamplesFile() - read Config/SamplesDB-fn.txt file into mcd state.
boolean	writeSamplesFile() writeSamplesFile() - create Config/SamplesDB-fn.txt file As a minimum it writes the following to mcd.samplesFile:

Methods inherited from class java.lang.Object

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

Field Detail

mcd

public MaeConfigData mcd

link to global MaeConfigData database

tFields

private java.lang.String[] tFields

Field names in the table

tData

private java.lang.String[][] tData

[0:tRows-1][0:tCols-1] table data that is actually a 1D array [0:tRows-1] of rowData[0:tCols-1]

tRows

private int tRows

# of rows in the table

tCols

private int tCols

# of columns in the table

idxSample_ID

private int idxSample_ID

idx of "Sample_ID" field

idxProject

private int idxProject

idx of "Project" field

idxDatabase_File

private int idxDatabase_File

idx of "Database_File" field

Constructor Detail

MaeSampleData

public MaeSampleData(MaeConfigData mcd)

MaeSampleData() - constructor

Parameters:

mcd - is instance of MaeConfigData

Method Detail

lookupFieldIndex

private int lookupFieldIndex(java.lang.String field)

lookupFieldIndex() - lookup field index in the tFields[0:tCols-1] data.

Parameters:

field - to lookup

Returns:

index value >=0 if found, else return -1.

findSampleFields

private boolean findSampleFields()

findSampleFields() - find SampleDB fields in the first row.

Returns:

true if all fields are present.

See Also:

lookupFieldIndex(java.lang.String)

readSamplesFile

public boolean readSamplesFile()

readSamplesFile() - read Config/SamplesDB-fn.txt file into mcd state. As a minimum it reads the following from mcd.samplesFile:

  File Field            MaeConfigData (mcd) variable
  ============          ============================
  "Sample_ID"           mcd.quantName[0:mcd.nQuantFiles-1]
  "Project"             mcd.prjName[0:mcd.nQuantFiles-1)
  "Database_File"       mcd.quantName[0:mcd.nQuantFiles-1]

Returns:

true if succeed.

writeSamplesFile

public boolean writeSamplesFile()

writeSamplesFile() - create Config/SamplesDB-fn.txt file As a minimum it writes the following to mcd.samplesFile:

  File Field            MaeConfigData (mcd) variable
  ============          ============================
  "Sample_ID"           mcd.quantName[0:mcd.nQuantFiles-1]
  "Project"             mcd.prjName[0:mcd.nQuantFiles-1]
  "Database_File"       mcd.quantName[0:mcd.nQuantFiles-1]

Returns:

true if succeed.