O2Plib.db.CSD
Class CSDtotals

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

public class CSDtotals
extends CSDglb

Class CSDtotals contains the state totals information on the Composite Samples Database (CSD).

Note that individual Rsample and Sample pairing statistics are found in the DbPairSamples instances. Individual sample statistics are found in the DbSample instances. We then assemble the groupd statistics here.


 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
 int areaMax
           
 int areaMin
          Minimum area of any spot in DB
 int ctrArea1Failed
          # spots failed area1 sizing, i.e., below lower threshold
 int ctrArea2Failed
          # spots failed area2 sizing, i.e., above lower threshold
 int ctrDensity1Failed
          # spots failed density1 sizing, i.e., below lower threshold
 int ctrDensity2Failed
          # spots failed density2 sizing, i.e., above lower threshold
 int ctrDR1Failed
          # spots failed DR1 sizing, i.e., below lower threshold
 int ctrDR2Failed
          # spots failed DR2 sizing, i.e., above lower threshold
 float dLmax
          Maximum dL of any spot in DB
 float dPmax
          Maximum dP of any spot in DB
 float dPrimeMax
          Maximum dPrime (density) of any spot in DB
 float dPrimeMin
          Minimum dPrime (density) of any spot in DB
 int invalidCentroidsTot
          # of invalid spot centroids found during spot quantification
 int maxAreaFound
          Max area found in accepted spot
 float maxBkgrdDensity
          max background seen in any spot
 int maxBkgrdTot
          Max sample background grayscale (computed elsewhere)
 float maxCalibGrayFound
          Max calibrated grayvalue found in accepted spot
 float maxDensityFound
          Max density found in accepted spot
 float maxDensityPrimeFound
          Max densityPrime found in accepted spot
 float maxDmax
          Maximum maxD of any spot in DB
 float minBkgrdDensity
          min background seen in any spot
 int minBkgrdTot
          Min sample background grayscale (computed elsewhere)
 float minDmax
          Minimum maxD of any spot in DB
 int nbrLblAP
          # AP labeled spots in DB (from all samples)
 int nbrLblCP
          # CP labeled spots in DB (from All samples)
 int nbrLblEP
          # EP labeled spots in DB (from All samples)
 int nbrLblGP
          # GS labeled spots in DB (from All samples)
 int nbrLblPP
          # PP labeled spots in DB (from all samples)
 int nbrLblSP
          # SP labeled spots in DB (from all samples)
 int nbrLblUS
          # US labeled spots in DB (from all samples)
 int nSpotsAborted
          # of spots aborted during assembly.
 int omittedArea
           
 float omittedDensity
          Data statistics read from the SSF files.
 int omittedNumberSpots
           
 float ratioOmittedToAccepted
          "Omitted(D')/Accepted(D')"
 int totSampleArea
           
 int totSampleAreaPrime
           
 float totSampleDensity
          Data statistics read from the SSF files.
 float totSampleDensityPrime
          Data statistics read from the SSF files.
 int totSampleNbrSpots
           
 int totSampleNbrSpotsPrime
           
static java.lang.String VERSION
          Version for this module
 float volumeMax
          Maximum volume (density) of any spot in DB
 float volumeMin
          Minimum volume (density) of any spot in DB
 
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
CSDtotals()
          CSDtotals() - Constructor for new CSDtotals.
 
Method Summary
 boolean allocSpotTotals()
          allocSpotTotals() - allocate spot total arrays for nSamples
 boolean getSpotTotalsFromSamples()
          getSpotTotalsFromSamples() - compile totals from individual sample instances
static java.lang.String getTabDelimFields()
          getTabDelimFields() - get a string representation of this instance as tab delimited fields.
 java.lang.String getTabDelimitedFieldsAndData()
          getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values.
 java.lang.String toString()
          toString() - return the totals as a printable string
 java.lang.String toStringSample(DbPairSamples ps)
          toStringSample() - return the totals as a printable string
 java.lang.String toTabDelimData()
          toTabDelimData() - get a string representation of this instance as tab delimited data.
 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

areaMax

public int areaMax

areaMin

public int areaMin
Minimum area of any spot in DB


dLmax

public float dLmax
Maximum dL of any spot in DB


dPmax

public float dPmax
Maximum dP of any spot in DB


dPrimeMax

public float dPrimeMax
Maximum dPrime (density) of any spot in DB


dPrimeMin

public float dPrimeMin
Minimum dPrime (density) of any spot in DB


volumeMax

public float volumeMax
Maximum volume (density) of any spot in DB


volumeMin

public float volumeMin
Minimum volume (density) of any spot in DB


maxDmax

public float maxDmax
Maximum maxD of any spot in DB


minDmax

public float minDmax
Minimum maxD of any spot in DB


nbrLblSP

public int nbrLblSP
# SP labeled spots in DB (from all samples)


nbrLblPP

public int nbrLblPP
# PP labeled spots in DB (from all samples)


nbrLblAP

public int nbrLblAP
# AP labeled spots in DB (from all samples)


nbrLblUS

public int nbrLblUS
# US labeled spots in DB (from all samples)


nbrLblEP

public int nbrLblEP
# EP labeled spots in DB (from All samples)


nbrLblCP

public int nbrLblCP
# CP labeled spots in DB (from All samples)


nbrLblGP

public int nbrLblGP
# GS labeled spots in DB (from All samples)


totSampleDensity

public float totSampleDensity
Data statistics read from the SSF files. These are spots accepted by spot program before correcting density by background subtraction and that still passed the sizing criteria.


totSampleArea

public int totSampleArea

totSampleNbrSpots

public int totSampleNbrSpots

totSampleDensityPrime

public float totSampleDensityPrime
Data statistics read from the SSF files. These are spots accepted by spot program after correcting density by background subtraction and that still passed the sizing criteria.


totSampleAreaPrime

public int totSampleAreaPrime

totSampleNbrSpotsPrime

public int totSampleNbrSpotsPrime

omittedDensity

public float omittedDensity
Data statistics read from the SSF files. Spots omitted from SSF because they failed the sizing criteria of the spot program.


omittedArea

public int omittedArea

omittedNumberSpots

public int omittedNumberSpots

maxCalibGrayFound

public float maxCalibGrayFound
Max calibrated grayvalue found in accepted spot


maxAreaFound

public int maxAreaFound
Max area found in accepted spot


maxDensityFound

public float maxDensityFound
Max density found in accepted spot


maxDensityPrimeFound

public float maxDensityPrimeFound
Max densityPrime found in accepted spot


invalidCentroidsTot

public int invalidCentroidsTot
# of invalid spot centroids found during spot quantification


nSpotsAborted

public int nSpotsAborted
# of spots aborted during assembly.


ratioOmittedToAccepted

public float ratioOmittedToAccepted
"Omitted(D')/Accepted(D')"


ctrArea1Failed

public int ctrArea1Failed
# spots failed area1 sizing, i.e., below lower threshold


ctrArea2Failed

public int ctrArea2Failed
# spots failed area2 sizing, i.e., above lower threshold


ctrDensity1Failed

public int ctrDensity1Failed
# spots failed density1 sizing, i.e., below lower threshold


ctrDensity2Failed

public int ctrDensity2Failed
# spots failed density2 sizing, i.e., above lower threshold


ctrDR1Failed

public int ctrDR1Failed
# spots failed DR1 sizing, i.e., below lower threshold


ctrDR2Failed

public int ctrDR2Failed
# spots failed DR2 sizing, i.e., above lower threshold


minBkgrdDensity

public float minBkgrdDensity
min background seen in any spot


maxBkgrdDensity

public float maxBkgrdDensity
max background seen in any spot


minBkgrdTot

public int minBkgrdTot
Min sample background grayscale (computed elsewhere)


maxBkgrdTot

public int maxBkgrdTot
Max sample background grayscale (computed elsewhere)

Constructor Detail

CSDtotals

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

Method Detail

allocSpotTotals

public boolean allocSpotTotals()
allocSpotTotals() - allocate spot total arrays for nSamples


getSpotTotalsFromSamples

public boolean getSpotTotalsFromSamples()
getSpotTotalsFromSamples() - compile totals from individual sample instances

Returns:
true if succeed.

toString

public java.lang.String toString()
toString() - return the totals as a printable string

Overrides:
toString in class java.lang.Object
Returns:
true if succeed.

toStringSample

public java.lang.String toStringSample(DbPairSamples ps)
toStringSample() - return the totals as a printable string

Parameters:
s - is DbPairSamples paired sample instance
Returns:
true if succeed.

getTabDelimitedFieldsAndData

public java.lang.String getTabDelimitedFieldsAndData()
getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values. Data is repeated on each line as horizontally stacked data - suitable for reading into R.

Returns:
string representation of this full instance

getTabDelimFields

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

Returns:
string representation of this instance

toTabDelimData

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

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