O2Plib.db.CSD
Class CSDacc

java.lang.Object
  O2Plib.db.CSD.CSDglb
      O2Plib.db.CSD.CSDacc

public class CSDacc
extends CSDglb

Class CSDacc contains the accession database information for the Composite Samples Database (CSD).

This file is derived from Open2Dprot, MAExplorer and GELLAB-II code.

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 Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.

Version:

$Date: 2005/12/09 15:04:26 $ $Revision: 1.10 $

Author:

P. Lemkin, NCI-Frederick, Frederick, MD, 21702

Field Summary

static DbAccession	acc Accession database if it exists
java.lang.String	accFile Accession database file if it exists
java.lang.String	accFilePath Full Accession database file if it exists
int[]	idxSampleList index values of the samples [0:nSamples-1]
int	maxFields maximum # of MIAPE accession fields used to define the study string, Size of miapeStudyFields[] (optional).
int	maxSamples maximum # of samples in accession database (optional).
java.lang.String[][]	miapeStudyData [0:nSamples-1][0:nMiapeFields-1] A short version of a samples's accession info is assembled from MIAPE/accession fields specified by miapeStudyFields[].
java.lang.String[]	miapeStudyFields [0:nMiapeFields-1] list of names of MIAPE accession fields used to define the study string
int	nMiapeFields # of MIAPE accession fields used to define the study string, Size of miapeStudyFields[].
int	nSamples # samples
java.lang.String[]	sampleNames names of the samples [0:nSamples-1]
static java.lang.String	VERSION Version for this module

Fields inherited from class O2Plib.db.CSD.CSDglb

allSetSamples, AP, batchDir, BF_IS_LMS_SPOT, BF_ISVALIDSPOT, cacheDir, cdbIsOpenFlag, condListDB, CONSOLE_FLAG, CP, CSD_DBTYPE_CACHE, CSD_DBTYPE_RDBMS, CSD_DBTYPE_TAB_DELIM, CSD_DBTYPE_UNKNOWN, CSD_DBTYPE_XML, csdAcc, csdCache, csdCacheFile, csdDatabaseFile, csdFormatMode, csdIO, csdLMS, csdName, csdRdbmsFile, csdSizes, csdTabDelimFile, csdTotals, CSDversion, csdXMLfile, dataFiltersListDB, dateCreation, dateLastSession, dbRsample, dbSample, dbSamplesListDB, dbSPFlistsDB, dBugLMsetNbr, dBugPspotNbr, dBugRspotNbr, dBugSampleNbr, EP, epSetSamples, exprListsDB, GS, LM, MAX_NODE_SAFTY_FACTOR, mrl, nbrTimesInitialized, nCondListDB, nDataFiltersDB, needToSaveCSDdataFlag, NEVER, nExprListsDB, nOclDB, nodeSaftyFactor, normListDB, nRmapsDB, nRspotListsDB, nSamplesDB, nSPFfilesUsedDB, nSPFlistsDB, oclListDB, oclNameDB, PP, ppxDir, projDir, rdbmsDir, rMapsListDB, RSAMPLE, rspotListsDB, SAMPLE, sampleNamesDB, sampleNamesUsedDB, SP, tmpDir, US, useInternalDTDflag, wrkAnotation, wrkCalib, wrkERspot, wrkExpr, wrkSetSamples, xmlDir, xSetSamples, ySetSamples

Constructor Summary

CSDacc()
CSDacc() - Constructor for new CSDacc.

Method Summary

java.lang.String[][]	getStudyDataForAllSamples() getStudyDataForAllSamples() - get the accession database study data for all samples
java.lang.String[]	getStudyDataForSample(int sampleIdx) getStudyDataForSample() - get the accession database study data for a particular sample
java.lang.String[]	getStudyFields() getStudyFields() - get the accession database study fields
static java.lang.String	getTabDelimitedFields() getTabDelimitedFields() - get a string representation of the tab-delimited data fields
void	setAccessionDB(java.lang.String accFile, java.lang.String accFilePath, DbAccession acc) setAccessionDB() - assign the accession DB
boolean	setStudyFields(java.lang.String[] studyFields) setStudyFields() - set the accession database study fields.
java.lang.String	toString() toString() - get a pretty-print string representation of this instance
java.lang.String	toTabDelimitedData() toTabDelimitedData() - get a string representation of this instance as tab-delimited data values
java.lang.String	toXML() toXML() - get a string representation of this instance as XML

Methods inherited from class O2Plib.db.CSD.CSDglb

initGlb

Methods inherited from class java.lang.Object

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

Field Detail

VERSION

public static final java.lang.String VERSION

Version for this module

See Also:

Constant Field Values

acc

public static DbAccession acc

Accession database if it exists

accFile

public java.lang.String accFile

Accession database file if it exists

accFilePath

public java.lang.String accFilePath

Full Accession database file if it exists

nSamples

public int nSamples

# samples

maxSamples

public int maxSamples

maximum # of samples in accession database (optional).

sampleNames

public java.lang.String[] sampleNames

names of the samples [0:nSamples-1]

idxSampleList

public int[] idxSampleList

index values of the samples [0:nSamples-1]

miapeStudyFields

public java.lang.String[] miapeStudyFields

[0:nMiapeFields-1] list of names of MIAPE accession fields used to define the study string

miapeStudyData

public java.lang.String[][] miapeStudyData

[0:nSamples-1][0:nMiapeFields-1] A short version of a samples's accession info is assembled from MIAPE/accession fields specified by miapeStudyFields[].

nMiapeFields

public int nMiapeFields

# of MIAPE accession fields used to define the study string, Size of miapeStudyFields[].

maxFields

public int maxFields

maximum # of MIAPE accession fields used to define the study string, Size of miapeStudyFields[] (optional).

Constructor Detail

CSDacc

public CSDacc()

CSDacc() - Constructor for new CSDacc.

Method Detail

setAccessionDB

public void setAccessionDB(java.lang.String accFile,
                           java.lang.String accFilePath,
                           DbAccession acc)

setAccessionDB() - assign the accession DB

Parameters:

accFile - is accession database file

accFilePath - is full path accession database file

acc - is the accession database instance

getStudyFields

public java.lang.String[] getStudyFields()

getStudyFields() - get the accession database study fields

Returns:

study fields miapeStudyFields[0:nMiapeFields-1], null if none

setStudyFields

public boolean setStudyFields(java.lang.String[] studyFields)

setStudyFields() - set the accession database study fields. If the studyFields.length is different from current miapeStudyFields.length, then fail since the existing data will be the wrong matrix shape. Note: be aware this could put the wrong field names for the corresponding data.

Parameters:

study - fields

Returns:

true if succeed

getStudyDataForAllSamples

public java.lang.String[][] getStudyDataForAllSamples()

getStudyDataForAllSamples() - get the accession database study data for all samples

Returns:

study data miapeStudyData[0:nSamples-1][0:nMiapeFields-1], null if none

getStudyDataForSample

public java.lang.String[] getStudyDataForSample(int sampleIdx)

getStudyDataForSample() - get the accession database study data for a particular sample

Parameters:

sampleIdx - is the sample to use

Returns:

study data miapeStudyData[sampleIdx], null if none

toString

public java.lang.String toString()

toString() - get a pretty-print string representation of this instance

Overrides:

toString in class java.lang.Object

Returns:

string representation of this instance

getTabDelimitedFields

public static java.lang.String getTabDelimitedFields()

getTabDelimitedFields() - get a string representation of the tab-delimited data fields

Returns:

string representation of this instance, no "\n"

toTabDelimitedData

public java.lang.String toTabDelimitedData()

toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

Returns:

string representation of this instance, no "\n"

toXML

public java.lang.String toXML()

toXML() - get a string representation of this instance as XML

Returns:

string representation of this instance