O2Plib.db.CSD
Class CSDlimits

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

public class CSDlimits
extends CSDglb

Class CSDlimits contains the sizing spot/Rspot set feature limits for the Composite Samples Database (CSD).

 [TODO] refactor.
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
 float[] covAreaLimits
          [LB:UB] COV area limits
 float[] covDensLimits
          [LB:UB] COV density limits
 float[] densRangeDiffLimits
          [LB:UB] (maxDensity-mnBkground) diff calibrated density limits/pixel
 float[] dLlimits
          [LB:UB] dL limits
 float dLthr
          Maximum threshold distance from spot-pair center to their corresponding landmark.
 float[] dPlimits
          [LB:UB] dP limits
 float dPthr
          Maximum threshold distance between spots in a spot-pair
static int LB
          Lower bound index constant
static int LIMITS_COV_AREA
          Sizing limits: coefficient of variation of area
static int LIMITS_COV_DENSITY
          Sizing limits: coefficient of variation of density
static int LIMITS_DL
          Sizing limits: dL
static int LIMITS_DP
          Sizing limits: dP
static int LIMITS_MN_AREA
          Sizing limits: mean area
static int LIMITS_MN_DENS_RANGE
          Sizing limits: mean density range (maxdensity-bkgrd density)/pixel
static int LIMITS_MN_DENSITY
          Sizing limits: mean density
static int LIMITS_MW
          Sizing limits: MW
static int LIMITS_MZ
          Sizing limits: MZ (2D-LC-MS)
static int LIMITS_N_SAMPLES_PER_COND
          Sizing limits: # of samples/condition (minimum)
static int LIMITS_P_VALUE
          Sizing limits: pValue
static int LIMITS_PIE
           
static int LIMITS_REL_DIST
          Sizing limits: relative distance from the landmark indicating that the pairing has more certainty if closer.
static int LIMITS_RT
          Sizing limits: RT (retention time 2D LC-MS)
 float[] mnAreaLimits
          [LB:UB] mean area limits
 float[] mnDensLimits
          [LB:UB] mean density limits
 float[] mwLimits
          [LB:UB] mw (y) region limits
 float[] mzLimits
          [LB:UB] mz (2D LC-MS) (y) region limits
 float[] nSampleLimits
          [LB:UB] # samples/class
 float[] pieLimits
          [LB:UB] pIe (x) region limits
 float[] pValueLimit
          PREFILTER: continus p-value limits
 float[] relDistLimits
          [LB:UB] relative distance limits
 float[] rtLimits
          [LB:UB] retention time (2D LC-MS) (x) region limits
 int sizingBits
           
static int UB
          Upper bound index constant
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
CSDlimits()
          CSDlimits() - Constructor for new CSDlimits.
 
Method Summary
 boolean chkPspotLimits(DbPspot pSpot)
          chkPspotLimits() - check a DbPspot's Sample values for MW, pIe, (or RT, MZ) area, density (D'), density range, dP and dL limits.
 boolean chkRspotLimits(CSDRspot rSpot)
          chkRspotLimits() - check if all DbPspots in the Rspot set meet the Sample values for MW, pIe, area, density (D'), density range, dP and dL limits.
 int clearSizingBit(int sizingCode)
          clearSizingBit() - clear the search sizing limits bit
static java.lang.String getSizingBitStr(int sb)
          getSizingBitStr() - get the search sizing limits bits as a string
 int setSizingBit(int sizingCode)
          setSizingBit() - set the search sizing limits 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

LIMITS_PIE

public static final int LIMITS_PIE
See Also:
Constant Field Values

LIMITS_MW

public static final int LIMITS_MW
Sizing limits: MW

See Also:
Constant Field Values

LIMITS_RT

public static final int LIMITS_RT
Sizing limits: RT (retention time 2D LC-MS)

See Also:
Constant Field Values

LIMITS_MZ

public static final int LIMITS_MZ
Sizing limits: MZ (2D-LC-MS)

See Also:
Constant Field Values

LIMITS_DL

public static final int LIMITS_DL
Sizing limits: dL

See Also:
Constant Field Values

LIMITS_DP

public static final int LIMITS_DP
Sizing limits: dP

See Also:
Constant Field Values

LIMITS_REL_DIST

public static final int LIMITS_REL_DIST
Sizing limits: relative distance from the landmark indicating that the pairing has more certainty if closer.

See Also:
Constant Field Values

LIMITS_MN_AREA

public static final int LIMITS_MN_AREA
Sizing limits: mean area

See Also:
Constant Field Values

LIMITS_MN_DENSITY

public static final int LIMITS_MN_DENSITY
Sizing limits: mean density

See Also:
Constant Field Values

LIMITS_MN_DENS_RANGE

public static final int LIMITS_MN_DENS_RANGE
Sizing limits: mean density range (maxdensity-bkgrd density)/pixel

See Also:
Constant Field Values

LIMITS_COV_AREA

public static final int LIMITS_COV_AREA
Sizing limits: coefficient of variation of area

See Also:
Constant Field Values

LIMITS_COV_DENSITY

public static final int LIMITS_COV_DENSITY
Sizing limits: coefficient of variation of density

See Also:
Constant Field Values

LIMITS_N_SAMPLES_PER_COND

public static final int LIMITS_N_SAMPLES_PER_COND
Sizing limits: # of samples/condition (minimum)

See Also:
Constant Field Values

LIMITS_P_VALUE

public static final int LIMITS_P_VALUE
Sizing limits: pValue

See Also:
Constant Field Values

sizingBits

public int sizingBits

pieLimits

public float[] pieLimits
[LB:UB] pIe (x) region limits


mwLimits

public float[] mwLimits
[LB:UB] mw (y) region limits


rtLimits

public float[] rtLimits
[LB:UB] retention time (2D LC-MS) (x) region limits


mzLimits

public float[] mzLimits
[LB:UB] mz (2D LC-MS) (y) region limits


dLlimits

public float[] dLlimits
[LB:UB] dL limits


dPlimits

public float[] dPlimits
[LB:UB] dP limits


relDistLimits

public float[] relDistLimits
[LB:UB] relative distance limits


mnAreaLimits

public float[] mnAreaLimits
[LB:UB] mean area limits


mnDensLimits

public float[] mnDensLimits
[LB:UB] mean density limits


densRangeDiffLimits

public float[] densRangeDiffLimits
[LB:UB] (maxDensity-mnBkground) diff calibrated density limits/pixel


covAreaLimits

public float[] covAreaLimits
[LB:UB] COV area limits


covDensLimits

public float[] covDensLimits
[LB:UB] COV density limits


nSampleLimits

public float[] nSampleLimits
[LB:UB] # samples/class


pValueLimit

public float[] pValueLimit
PREFILTER: continus p-value limits


dPthr

public float dPthr
Maximum threshold distance between spots in a spot-pair


dLthr

public float dLthr
Maximum threshold distance from spot-pair center to their corresponding landmark.

Constructor Detail

CSDlimits

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

Method Detail

chkPspotLimits

public boolean chkPspotLimits(DbPspot pSpot)
chkPspotLimits() - check a DbPspot's Sample values for MW, pIe, (or RT, MZ) area, density (D'), density range, dP and dL limits. NOTE: it does not check additional limits.

Parameters:
pSpot - to check
Returns:
true if meets all of the limits.

chkRspotLimits

public boolean chkRspotLimits(CSDRspot rSpot)
chkRspotLimits() - check if all DbPspots in the Rspot set meet the Sample values for MW, pIe, area, density (D'), density range, dP and dL limits.

Parameters:
rSpot - to check
Returns:
true if meets all of the limits.

setSizingBit

public int setSizingBit(int sizingCode)
setSizingBit() - set the search sizing limits bit

Parameters:
sizingCode - to use in setting the sizing limits bit
Returns:
new sizingBits

clearSizingBit

public int clearSizingBit(int sizingCode)
clearSizingBit() - clear the search sizing limits bit

Parameters:
sizingCode - to use in clearing the sizing limits bit
Returns:
new sizingBits

getSizingBitStr

public static java.lang.String getSizingBitStr(int sb)
getSizingBitStr() - get the search sizing limits bits as a string

Parameters:
sb - is sizing bits 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