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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDcal
public class CSDcal
Class CSDcal contains sample calibration data for the Composite Samplex Database (CSD). Note: individual DbSample objects have dbSample.calib sub-objects that can hold a grayscale to calibration-units calibration. This class has other types (spatial) calibrations as well. Be aware of the differences. This class is used in CSD data-mining.
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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boolean |
areaCalibFlag
use Area calibration in OD/mm**2 if set |
CalibrateOD |
calib
(Optional) list of sample's grayscale to calibrated units calibrations. |
static int |
CALIB_MHZ_RT
(MHZ,RT) calibration type |
static int |
CALIB_MW_PIE
(MW,pIE) calibration type |
static int |
CALIB_PIECEWISE_LINEAR
Piecewise-linear curve fitting type |
static int |
CALIB_SMOOTH
Smooth curve fitting type |
java.lang.String |
calibName
name of calibration |
int |
calibType
domain type of calibration: CALIB_MW_PIE or CALIB_MHZ_RT |
int |
curveFittingType
smoothing type of calibration: CALIB_PIECEWISE_LINEAR or CALIB_SMOOTH |
float |
exposureCorrectionFactor
(Optional) exposure correction or decay factor such as might be used to correct for delays in scanning after a pulse label. |
int |
maxCalibrations
Number of calibrations |
int |
nXRspots
# of pIe or RT X calib spots |
int |
nYRspots
# of MW or mhz Y calib spots |
float |
pixelResolutionMicrons
Resolution of scan data. |
int |
pixXsize
max # columns in CSD virtual database |
int |
pixYsize
max # rows in CSD virtual database |
int[] |
rspot_Xcalib
[0:maxCalibrations-1] for [0:nXRspots-1] Rspot# for xCoord[] point |
int[] |
rspot_Ycalib
[0:maxCalibrations-1] for [0:nYRspots-1] Rspot# for yCoord[] point |
boolean |
useCalibFlag
if calibration was performed for rSampleName. |
static java.lang.String |
VERSION
Version for this module |
float[] |
xCalib
[0:maxCalibrations-1] corresponding calibration value |
float[] |
xCoord
[0:maxCalibrations-1] X coordinate for pIe |
java.lang.String |
xName
name of X-axis isoelectric point : "pIe" or Retention time "RT" |
java.lang.String |
xUnits
Scale UNITS of X-axis : "pH" or "seconds" |
float[] |
yCalib
[0:maxCalibrations-1] corresponding calibration value |
float[] |
yCoord
[0:maxCalibrations-1] Y coordinate for MW |
java.lang.String |
yName
name of Y-axis Molecular Mass: "mw" or Mass size "mhz" |
java.lang.String |
yUnits
Scale UNITS of Y-axis : "Dalton" |
Constructor Summary | |
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CSDcal()
CSDcal() - Constructor for new CSDcal. |
Method Summary | |
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boolean |
createCalibrationMaps(int curveFittingType)
createCalibrationMaps() - calibrate X and Y calibration sets using either piecewise-linear or smooth curve fitting [TODO] |
float |
getCalibratedXvalue(float x)
getCalibratedXvalue() - map X coordinate to calibrated value [TODO] |
float |
getCalibratedYvalue(float y)
getCalibratedYvalue() - map X coordinate to calibrated value [TODO] |
static java.lang.String |
getTabDelimitedFields()
getTabDelimitedFields() - get a string representation of the tab-delimited data fields |
boolean |
initCal(java.lang.String calibName,
int calibType)
initCal() - initialize calibration [TODO] add data... |
void |
set_exposure_correction(float eFactor)
set_exposure_correction() - set the exposure correction factors (eFactor) for all samples in the database. |
boolean |
setCalData(float[] xCalib,
float[] xCoord,
float[] yCalib,
float[] yCoord)
setCalData() - set the calibration data lists |
boolean |
setCalDataNames(java.lang.String xName,
java.lang.String xUnits,
java.lang.String yName,
java.lang.String yUnits)
setCalDataNames() - set the calibration data names |
java.lang.String |
toString()
toString() - get a pretty-print string representation of this instance |
java.lang.String |
toStringFull()
toStringFull() - get a pretty-print string representation of this instance including the expanded calibration data |
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 |
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 CALIB_MW_PIE
public static final int CALIB_MHZ_RT
public static final int CALIB_PIECEWISE_LINEAR
public static final int CALIB_SMOOTH
public java.lang.String calibName
public int calibType
public int curveFittingType
public boolean areaCalibFlag
public boolean useCalibFlag
public float pixelResolutionMicrons
public int pixXsize
public int pixYsize
public java.lang.String yName
public java.lang.String yUnits
public java.lang.String xName
public java.lang.String xUnits
public int nXRspots
public int nYRspots
public int maxCalibrations
public float[] xCalib
public float[] yCalib
public float[] xCoord
public float[] yCoord
public int[] rspot_Xcalib
public int[] rspot_Ycalib
public CalibrateOD calib
public float exposureCorrectionFactor
Constructor Detail |
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public CSDcal()
Method Detail |
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public boolean initCal(java.lang.String calibName, int calibType)
calibName
- is name of this calibrationcalibType
- is type of this calibration
CALIB_MW_PIE or CALIB_MHZ_RT
public boolean setCalDataNames(java.lang.String xName, java.lang.String xUnits, java.lang.String yName, java.lang.String yUnits)
xName
- is name of this X axisxUnits
- is units of this X axisyName
- is name of this Y axisyUnits
- is units of this Y axis
public boolean setCalData(float[] xCalib, float[] xCoord, float[] yCalib, float[] yCoord)
xCalib
- is calibration data of this X axisxCoord
- is coordinates of the X axisyCalib
- is calibration data of this Y axisyCoord
- is coordinates of the Y axis
public boolean createCalibrationMaps(int curveFittingType)
curveFittingType
- is CALIB_PIECEWISE_LINEAR or CALIB_SMOOTH
public float getCalibratedXvalue(float x)
x
-
public float getCalibratedYvalue(float y)
y
-
public void set_exposure_correction(float eFactor)
eFactor
- exposure correction or decay factor such as might
be used to correct for delays in scanning after a pulse label.public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String toStringFull()
public static java.lang.String getTabDelimitedFields()
public java.lang.String toTabDelimitedData()
public java.lang.String toXML()
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