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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDtotals
public class CSDtotals
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/.
Field Summary | |
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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 |
Constructor Summary | |
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CSDtotals()
CSDtotals() - Constructor for new CSDtotals. |
Method Summary | |
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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 |
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initGlb |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final java.lang.String VERSION
public int areaMax
public int areaMin
public float dLmax
public float dPmax
public float dPrimeMax
public float dPrimeMin
public float volumeMax
public float volumeMin
public float maxDmax
public float minDmax
public int nbrLblSP
public int nbrLblPP
public int nbrLblAP
public int nbrLblUS
public int nbrLblEP
public int nbrLblCP
public int nbrLblGP
public float totSampleDensity
public int totSampleArea
public int totSampleNbrSpots
public float totSampleDensityPrime
public int totSampleAreaPrime
public int totSampleNbrSpotsPrime
public float omittedDensity
public int omittedArea
public int omittedNumberSpots
public float maxCalibGrayFound
public int maxAreaFound
public float maxDensityFound
public float maxDensityPrimeFound
public int invalidCentroidsTot
public int nSpotsAborted
public float ratioOmittedToAccepted
public int ctrArea1Failed
public int ctrArea2Failed
public int ctrDensity1Failed
public int ctrDensity2Failed
public int ctrDR1Failed
public int ctrDR2Failed
public float minBkgrdDensity
public float maxBkgrdDensity
public int minBkgrdTot
public int maxBkgrdTot
Constructor Detail |
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public CSDtotals()
Method Detail |
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public boolean allocSpotTotals()
public boolean getSpotTotalsFromSamples()
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String toStringSample(DbPairSamples ps)
s
- is DbPairSamples paired sample instance
public java.lang.String getTabDelimitedFieldsAndData()
public static java.lang.String getTabDelimFields()
public java.lang.String toTabDelimData()
public java.lang.String toXML()
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