Class SamplesTable

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

class SamplesTable

extends Table

The SamplesTable class is database for the Samples DB Table. It reads the tab-delimited SamplesDB.txt file from the Config/. It also contains methods to help handle queries on samples in the database. The Samples DB contains descriptive data for all samples - whether they are loaded or not. This lets us then lookup file names for samples that were not initially loaded and then load them. This data also includes (Login, Project) security information as well as Sample_ID and Database_File, and other optional fields.

It reads a subset of the actual table data from FILE/URL. This Samples DB file may consist of the following fields:

   Sample_ID Source Strain Stage Probe Login Project Contributor
   Contrib_Institute Submission_Date Exposure Membrane_Nbr 
   Database_File GeneCard_URL Histology_URL Model_URL Comments 
   Menu_Stage_Name Membrane_Layout 
 

 NOTE: substitute - ("Membrane" is depricated for "Sample" -
 for now parse it both ways 4-18-00.)
         Sample_ID for Membrane_ID  
         Sample_Nbr for Membrane_Nbr   
         Sample_Layout for Membrane_Layout 

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: 2003/02/18 18:02:35 $ $Revision: $

Author:

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

See Also:

MAExplorer Home, Table

Field Summary

(package private) boolean	hasValidDataFlag set if data was read ok
(package private) int	idxBGAvg
(package private) int	idxBGLow
(package private) int	idxBGRms
(package private) int	idxComments The following fields were from the original Membranes.txt file.
(package private) int	idxContrib_Institute The following fields were from the original Membranes.txt file.
(package private) int	idxContributor The following fields were from the original Membranes.txt file.
(package private) int	idxDatabase_File The following fields were from the original Membranes.txt file.
(package private) int	idxDatabaseFileID The following fields were from the original Membranes.txt file.
(package private) int	idxExposure The following fields were from the original Membranes.txt file.
(package private) int	idxFilterType
(package private) int	idxFilterType_Descr
(package private) int	idxGeneCard_URL The following fields were from the original Membranes.txt file.
(package private) int	idxHistology_URL The following fields were from the original Membranes.txt file.
(package private) int	idxLogin The following fields were from the original Membranes.txt file.
(package private) int	idxMenu_Stage_Name The following fields were from the original Membranes.txt file.
(package private) int	idxModel_URL The following fields were from the original Membranes.txt file.
(package private) int	idxProbe The following fields were from the original Membranes.txt file.
(package private) int	idxProject The following fields were from the original Membranes.txt file.
(package private) int	idxSample_ID The following fields were from the original Membranes.txt file.
(package private) int	idxSample_Nbr The following fields were from the original Membranes.txt file.
(package private) int	idxSource The following fields were from the original Membranes.txt file.
(package private) int	idxStage The following fields were from the original Membranes.txt file.
(package private) int	idxStrain The following fields were from the original Membranes.txt file.
(package private) int	idxSubmission_Date The following fields were from the original Membranes.txt file.
private MAExplorer	mae link to global instance of MAExplorer
private java.lang.String	maeTbl remap table name

Fields inherited from class Table

bufSize, fileOKflag, fio

Fields inherited from class SimpleTable

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

Constructor Summary

(package private)

SamplesTable(MAExplorer mae, java.lang.String fileName) SamplesTable() - constructor to read Samples DB and set up table.

Method Summary

(package private) boolean	chkIfHPvisible(java.lang.String hpNameToChk) chkIfHPvisible() - check if allowed to view HP sample.
(package private) java.lang.String	getTableFieldDataByHPname(java.lang.String fieldName, java.lang.String hpName) getTableFieldDataByHPname() - get data of fieldName of particular HP sample
(package private) java.lang.String[]	getUniqueTableFieldData(int fieldIdx) getUniqueTableFieldData() - get list from SamplesDB.txt database Sort the array in ASCENDING order.
(package private) boolean	isHPnameIsAccessible(java.lang.String hpName) isHPnameIsAccessible() - test if HP database name is accessible.
(package private) SimpleTable	makeHPrestrictedTable(Table srcTbl) makeHPrestrictedTable() - make a Table of HPs restricted by login required.
(package private) void	readListOfSampleNames() readListOfSampleNames() - get list of Sample (i.e.
(package private) void	setupFieldIndexes() setupFieldIndexes() - set up indexes for common fields for speedups

Methods inherited from class Table

copyTable, createFileTable, getArrayOfTabDelimitedTokens, getData, getTableRowsSubset, getTableRowsSubset, insertTblInULHCtable, lookupFieldIdxAndRemapFieldName, makeTabDelimReport, readTable, storeDataBufParser

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

maeTbl

private final java.lang.String maeTbl

remap table name

mae

private MAExplorer mae

link to global instance of MAExplorer

idxSample_ID

int idxSample_ID

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxStrain

int idxStrain

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxSource

int idxSource

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxProbe

int idxProbe

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxStage

int idxStage

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxLogin

int idxLogin

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxProject

int idxProject

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxContributor

int idxContributor

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxContrib_Institute

int idxContrib_Institute

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxSubmission_Date

int idxSubmission_Date

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxExposure

int idxExposure

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxSample_Nbr

int idxSample_Nbr

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxDatabase_File

int idxDatabase_File

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxDatabaseFileID

int idxDatabaseFileID

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxGeneCard_URL

int idxGeneCard_URL

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxHistology_URL

int idxHistology_URL

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxModel_URL

int idxModel_URL

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxComments

int idxComments

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxMenu_Stage_Name

int idxMenu_Stage_Name

The following fields were from the original Membranes.txt file. These lookup field indices are used to access the Samples DB.

idxFilterType

int idxFilterType

idxFilterType_Descr

int idxFilterType_Descr

idxBGLow

int idxBGLow

idxBGAvg

int idxBGAvg

idxBGRms

int idxBGRms

hasValidDataFlag

boolean hasValidDataFlag

set if data was read ok

Constructor Detail

SamplesTable

SamplesTable(MAExplorer mae,
             java.lang.String fileName)

SamplesTable() - constructor to read Samples DB and set up table.

Parameters:

mae - is instance of MAExplorer

fileName - is file name of the Samples DB

See Also:

MAExplorer.logDRYROTerr(java.lang.String), setupFieldIndexes()

Method Detail

setupFieldIndexes

void setupFieldIndexes()

setupFieldIndexes() - set up indexes for common fields for speedups

See Also:

Table.lookupFieldIdxAndRemapFieldName(java.lang.String, java.lang.String)

getTableFieldDataByHPname

java.lang.String getTableFieldDataByHPname(java.lang.String fieldName,
                                           java.lang.String hpName)

getTableFieldDataByHPname() - get data of fieldName of particular HP sample

Parameters:

fieldName - is the name of the field

hpName - is the name of the sample

Returns:

data, else null if failed.

See Also:

Table.lookupFieldIdxAndRemapFieldName(java.lang.String, java.lang.String)

getUniqueTableFieldData

java.lang.String[] getUniqueTableFieldData(int fieldIdx)

getUniqueTableFieldData() - get list from SamplesDB.txt database Sort the array in ASCENDING order. It is indexed from [0 : rtnStr.length()-1].

Parameters:

fieldIdx - is the index of the field (column) to retrieve

Returns:

data array, else null if a problem or there is no data.

See Also:

SortMAE.sortArray(java.lang.String[], boolean)

readListOfSampleNames

void readListOfSampleNames()

readListOfSampleNames() - get list of Sample (i.e. HP) names from Config database. These names are setup with the .mae startup file for the stand-alone application or PARAMs for an Applet.

 Samples are defined by the keyword "image" following by the relative
 sample number (e.g. "image4").
 1. First, get all images specified in the PARAM and these are
    candidates for loading the samples. They are named
    "image1", "image2", ..., "imageMAX_HYBRID_SAMPLES".
 This pushes names into:
       mae.iSampleName[++mae.iHPnbr]= baseFile;
       mae.iImageFile[mae.iHPnbr].
    Don't add a name if it is already in the list.

 2. Then, add names to the list (primarily for loading later
    from the menus). These names will come from the Image_File field
    in the Samples.txt database.
    These names will be pushed into
        snHPName[++mae.snHPNbr] and snImageFile[].
    Don't add a name if it is already in the list.

See Also:

GetParams.setDefParam(java.lang.String, boolean), MAExplorer.logDRYROTerr(java.lang.String), Util.showMsg(java.lang.String)

makeHPrestrictedTable

SimpleTable makeHPrestrictedTable(Table srcTbl)

makeHPrestrictedTable() - make a Table of HPs restricted by login required. This test is only performed if running as an Applet. Only include HP rows that are visible in the database i.e. loaded. If the table does not contain the keyword "Database_File", Then simply return the entire table. Otherwise, it creates a new subset table and copies rows of valid data (i.e. pointers).

Parameters:

srcTbl - super table to restrict by login access

Returns:

subtable else null if there is a problem.

See Also:

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

chkIfHPvisible

boolean chkIfHPvisible(java.lang.String hpNameToChk)

chkIfHPvisible() - check if allowed to view HP sample. NOTE: called after all logins so can check verified projects.

Parameters:

hpNameToChk - is the sample to check

Returns:

true if ok.

isHPnameIsAccessible

boolean isHPnameIsAccessible(java.lang.String hpName)

isHPnameIsAccessible() - test if HP database name is accessible. If we are not in workingMAE mode, everything is accessible else look for exact match.

Parameters:

hpName - is the sample to check

Returns:

true if sample is accessible.