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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDnorm
public class CSDnorm
Class CSDnorm contains a normalization for a sample for the Composite Samples Database (CSD). This is on a per-sample basis.
[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 normalization. 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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float |
bLsqTerm
Least Square normalization intercept: bj to estimate djR'=mj*d'j+bj. |
float |
corCoefLsqTerm
Correlation coefficient when computing Least Square normalization terms: |
int |
curNormMethod
Current normalization method set by NORM_xxx |
DbSample |
dbSample
|
boolean |
didLeastSqCalibFlag
true if EVER did a SET LEAST SQUARES calibration |
boolean |
didRatioListCalibFlag
true if EVER did a SET RATIO LIST calibration |
float |
lsqMcoef
Least Square normalization slope: mj to estimate djR'=mj*d'j+bj |
float[] |
meanDprimeRatioMeanSpots
Median of the D' of the Rspots in the [0:nRatioMeanSpots-1] list of spots used in ratio mean normalization |
float[] |
medianDprimeRatioMeanSpots
Median of the D' of the Rspots in the [0:nRatioMeanSpots-1] list of spots used in ratio mean normalization |
int |
modeDensity
[TODO-REFACTOR] Density mode String 'A P R L C' |
java.lang.String |
name
Name of the normalization |
static int |
NORM_LOESS
Normalization by LOESS |
static int |
NORM_LSQ
Normalization by linear least square fit |
static int |
NORM_NONE
Normalization - none. |
static int |
NORM_OTHER
Normalization by an other (possible plugin) method |
static int |
NORM_PCT_TOT_DENS
Normalization by percent of total density' |
static int |
NORM_RATO_MEANS
Normalization by ratio means |
static int |
NORM_RATO_MEDIANS
Normalization by ratio means |
static java.util.Hashtable |
normHash
hashTable for normalization lookup |
int[] |
normLSQspotNbrs
[0:nSpotsLsq-1] Ratio-mean spot #'s of spots in ratioMeans for normalization. |
DbSpot[] |
normLSQspots
[0:nSpotsLsq-1] list of spots used in least-square fit norm. |
int |
nRatioMeanSpots
#'s of spots in ratioMean normalization. |
int |
nSpotsLsq
Number of spots used in computing Least Square normalization terms |
java.lang.String |
otherNormMethod
|
float |
ratioMean
Slope mj OR Tot D'/sample's ratio list. |
int[] |
ratioMeanSpotNbrs
[0:nRatioMeanSpots-1] Ratio-mean spot #'s of spots in ratioMeans for normalization. |
CSDRspot[] |
ratioMeanSpots
[0:nRatioMeanSpots-1] list of spots used in ratio mean normalization |
int |
reorderModeDens
[TODO-REFACTOR]value of modeDensity at time of REORDER |
float[] |
sumDprimeRatioMeanSpots
Sum of the D' of the Rspots in the [0:nRatioMeanSpots-1] list of spots used in ratio mean normalization |
float |
totDensPrime
Total D' (density corrected for background) for a sample for the percent total density normalization. |
float |
totNbrSpots
# of spots in this sample used in Percent total density normalization. |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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CSDnorm()
CSDnorm() - Constructor for new CSDnorm. |
|
CSDnorm(java.lang.String name)
CSDnorm() - Constructor for new CSDnorm. |
Method Summary | |
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static java.lang.String |
getTabDelimitedFields()
getTabDelimitedFields() - get a string representation of the tab-delimited data fields |
float |
normalizeData(CSDRspot rspot,
float data,
int idxSample)
normalizeData() - normalize data by this normalization. |
float |
normalizeData(float data,
int idxSample)
normalizeData() - normalize data by this normalization. |
void |
set_lsq_norm_calib()
set_lsq_norm_calib() - If least squares mode 'L' is used where we compute D''j=mj*D'i+bi, then store the slopes 'mj' in lsqMcoef[j]. |
boolean |
set_ratio_list(CSDRspot[] rSpotList)
set_ratio_list() - Get a list of Rspots which will serve as a basis to normalize spots in calculations and reporting for ratio-list normalization mode. |
java.lang.String |
toString()
toString() - get a pretty-print string representation of this instance [TODO] add additional state... |
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 [TODO] |
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 static final int NORM_NONE
public static final int NORM_PCT_TOT_DENS
public static final int NORM_RATO_MEANS
public static final int NORM_RATO_MEDIANS
public static final int NORM_LSQ
public static final int NORM_LOESS
public static final int NORM_OTHER
public java.lang.String otherNormMethod
public static java.util.Hashtable normHash
public int reorderModeDens
public int modeDensity
public boolean didRatioListCalibFlag
public boolean didLeastSqCalibFlag
public DbSample dbSample
public java.lang.String name
public int curNormMethod
public float totNbrSpots
public float totDensPrime
public int nRatioMeanSpots
public int[] ratioMeanSpotNbrs
public CSDRspot[] ratioMeanSpots
public float[] sumDprimeRatioMeanSpots
public float[] meanDprimeRatioMeanSpots
public float[] medianDprimeRatioMeanSpots
public float ratioMean
public int nSpotsLsq
public int[] normLSQspotNbrs
public DbSpot[] normLSQspots
public float lsqMcoef
public float bLsqTerm
public float corCoefLsqTerm
Constructor Detail |
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public CSDnorm()
public CSDnorm(java.lang.String name)
name
- of the normalization instanceMethod Detail |
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public float normalizeData(CSDRspot rspot, float data, int idxSample)
rspot
- is Rspot set if needed.data
- to normalizeidxSample
- is the index of the sample for this spot
public float normalizeData(float data, int idxSample)
data
- to normalizeidxSample
- is the index of the sample for this spot
public boolean set_ratio_list(CSDRspot[] rSpotList)
NOTE: if samples are missing from the WORKING SET, then their SUM D' value defaults to 1.0. If the set of spots is specified explicitly then it is also put into the RSL.
[TODO - REFACTOR]
public void set_lsq_norm_calib()
[TODO - REFACTOR]
public java.lang.String toString()
toString
in class java.lang.Object
public static java.lang.String getTabDelimitedFields()
public java.lang.String toTabDelimitedData()
public java.lang.String toXML()
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