O2Plib.db.CSD
Class CSDfilterState

java.lang.Object
  extended by O2Plib.db.CSD.CSDglb
      extended by O2Plib.db.CSD.CSDfilterState

public class CSDfilterState
extends CSDglb

Class CSDfilterState contains the state for a named data filter parameter subset. This is a data-mining filter state search of the Composite Samples Database (CSD).

[TODO] make dynamic using hash tables instead of fixed index values. [TODO] add capability for dynamic Java plugins and RLO R-plugins to do the data filtering. Use CSDlimits stats.


 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 java.util.Hashtable filterHash
          hashTable for filter lookup
static int LB
          Lower bound index constant
 CSDlimits limits
           
 boolean mappingModeFlag
          using Rspot name mapping to foreign Fspot mapping
 java.lang.String name
          Name of the data-mining filter state
 CSDnorm norm
          current density normalization mode
static int PAIRBIT_AP
          Pairing-bit Sure-Pair AP
static int PAIRBIT_CP
          Pairing-bit Sure-Pair CP
static int PAIRBIT_EP
          Pairing-bit Sure-Pair EP
static int PAIRBIT_GS
          Pairing-bit Sure-Pair GS
static int PAIRBIT_LM
          Pairing-bit Sure-Pair LM
static int PAIRBIT_PP
          Pairing-bit Sure-Pair PP
static int PAIRBIT_SP
          Pairing-bit Sure-Pair SP
static int PAIRBIT_US
          Pairing-bit Sure-Pair US
 int pairingBits
          spot pair label bits: from DbLM.PAIRBIT_xx where xx is US, SP, PP, AP, EP, CP, GS, LM.
 java.lang.String timeStamp
           
 java.lang.String title
          title information of data-mining filter state.
static int UB
          Upper bound index constant
static java.lang.String VERSION
          Version for this module
 CSDcond wrkSamples
          list of samples in the working set of samples
 
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
CSDfilterState()
          CSDfilterState() - Constructor for new CSDfilterState.
 
Method Summary
 boolean chkPairingBits(CSDRspot r)
          chkPairingBits() - test the pairing bits agains the Rspot.
 boolean chkPairingBits(CSDRspotList rsl)
          chkPairingBits() - test the pairing bits agains the list of Rspots.
 int clearPairingBit(int pairCode)
          clearPairingBit() - clear the search pairing bit
 int cvPairCode2PairingBit(int pairCode)
          cvPairCode2PairingBit() - set the search pairing bit
 int getPairingBit()
          getPairingBit() - get the search pairing bits
static java.lang.String getPairingBitStr(int pairingBits)
          getPairingBitStr() - get the search pairing bits as a string
 int setPairingBit(int pairCode)
          setPairingBit() - set the search pairing bit
 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 toTabDelimitedFields()
          toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields
 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

LB

public static final int LB
Lower bound index constant

See Also:
Constant Field Values

UB

public static final int UB
Upper bound index constant

See Also:
Constant Field Values

PAIRBIT_SP

public static final int PAIRBIT_SP
Pairing-bit Sure-Pair SP

See Also:
Constant Field Values

PAIRBIT_PP

public static final int PAIRBIT_PP
Pairing-bit Sure-Pair PP

See Also:
Constant Field Values

PAIRBIT_AP

public static final int PAIRBIT_AP
Pairing-bit Sure-Pair AP

See Also:
Constant Field Values

PAIRBIT_US

public static final int PAIRBIT_US
Pairing-bit Sure-Pair US

See Also:
Constant Field Values

PAIRBIT_EP

public static final int PAIRBIT_EP
Pairing-bit Sure-Pair EP

See Also:
Constant Field Values

PAIRBIT_CP

public static final int PAIRBIT_CP
Pairing-bit Sure-Pair CP

See Also:
Constant Field Values

PAIRBIT_GS

public static final int PAIRBIT_GS
Pairing-bit Sure-Pair GS

See Also:
Constant Field Values

PAIRBIT_LM

public static final int PAIRBIT_LM
Pairing-bit Sure-Pair LM

See Also:
Constant Field Values

name

public java.lang.String name
Name of the data-mining filter state


timeStamp

public java.lang.String timeStamp

title

public java.lang.String title
title information of data-mining filter state.


filterHash

public static java.util.Hashtable filterHash
hashTable for filter lookup


mappingModeFlag

public boolean mappingModeFlag
using Rspot name mapping to foreign Fspot mapping


pairingBits

public int pairingBits
spot pair label bits: from DbLM.PAIRBIT_xx where xx is US, SP, PP, AP, EP, CP, GS, LM. 0 means none.


limits

public CSDlimits limits

wrkSamples

public CSDcond wrkSamples
list of samples in the working set of samples


norm

public CSDnorm norm
current density normalization mode

Constructor Detail

CSDfilterState

public CSDfilterState()
CSDfilterState() - Constructor for new CSDfilterState.

Method Detail

setPairingBit

public int setPairingBit(int pairCode)
setPairingBit() - set the search pairing bit

Parameters:
pairCode - to use in setting the pairing bit
Returns:
new pairingBits

clearPairingBit

public int clearPairingBit(int pairCode)
clearPairingBit() - clear the search pairing bit

Parameters:
pairCode - to use in clearing the pairing bit
Returns:
new pairingBits

cvPairCode2PairingBit

public int cvPairCode2PairingBit(int pairCode)
cvPairCode2PairingBit() - set the search pairing bit

Parameters:
pairCode - to use in clearing the pairing bit
Returns:
new pairingBits

getPairingBit

public int getPairingBit()
getPairingBit() - get the search pairing bits

Returns:
list if succeed else null

chkPairingBits

public boolean chkPairingBits(CSDRspot r)
chkPairingBits() - test the pairing bits agains the Rspot. [TODO] add variants to require all spots in Rspot set, some of spots in Rspot set, per condition, etc.

Parameters:
r - is CSDRspot to test
Returns:
true if Rspot set contains pairing codes of the current pairing bits

chkPairingBits

public boolean chkPairingBits(CSDRspotList rsl)
chkPairingBits() - test the pairing bits agains the list of Rspots. [TODO] add variants to require all spots in Rspot set, some of spots in Rspot set, per condition, etc.

Parameters:
r - is CSDRspotList to test
Returns:
true if list of Rspots contains pairing codes of the current pairing bits

getPairingBitStr

public static java.lang.String getPairingBitStr(int pairingBits)
getPairingBitStr() - get the search pairing bits as a string

Parameters:
paringBits - to convert
Returns:
list if succeed else null

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

toTabDelimitedFields

public java.lang.String toTabDelimitedFields()
toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields

Returns:
string representation of this instance

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

toXML

public java.lang.String toXML()
toXML() - get a string representation of this instance as XML

Returns:
string representation of this instance