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java.lang.Object O2Plib.db.DbBaseSpot O2Plib.db.DbPspot
public class DbPspot
Class DbPspot contains the Composite Sample Database (CSD) spot. This extends DbBaseSpot with fields to encode a single spot pair - i.e., data from both spots in the pair between an Rsample an a Sample. It is used in building the CSD and in data mining.
This includes some fields from the GELLAB-II cgelp2/glbcgl.h gSpot_t typedef.
This file is derived from Open2Dprot, MAExplorer and GELLAB-II code with structures generated by CmpSpots present in the XML SPF data file.
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 |
ccOfGroup
cc of group Rsample spot belongs to if any |
boolean |
lmFlag
set true if spot is a landmark spot |
int |
rArea
spot Rsample area in pixels |
float |
rDensity
Rsample spot density not corrected for background |
float |
rDprime
Rsample Spot density in D' (density corrected for background by subtracting mnBackground*area . |
int |
rDxLM
X distance Rsample spot (x,y) relative to Rsample LM(x,y) |
int |
rDyLM
Y distance Rsample spot (x,y) relative to Rsample LM(x,y) |
float |
rMaxDens
max Rsample pixel density seen in spot |
int |
rMerx1
Rsample Spot minimum enclosing rectangle Left in pixel coords |
int |
rMerx2
Rsample Spot minimum enclosing rectangle Right in pixel coords |
int |
rMery1
Rsample Spot minimum enclosing rectangle Top in pixel coords |
int |
rMery2
Rsample Spot minimum enclosing rectangle Bottom in pixel coords |
float |
rMinDens
min Rsample pixel density seen in spot |
float |
rMnBkgdDens
Mean Background pixel density for the G1 spot. |
int |
rNbrCsamples
# of samples in Rsample Cspot Csample' estimate if not 0. |
int |
rPerimeter
Rsample spot perimeter (pixels) for spot |
float |
rSDarea
Rsample Csample' S.D. |
float |
rSDdPrime
Rsample Csample' S.D. |
float |
rSDxCentroid
Rsample Csample' S.D. |
float |
rSDyCentroid
Rsample Csample' S.D. |
int |
rSpotNbr
spot Rsample spot number |
int |
rSpotOfGroup
NOTE: not used - Rspot group to which this spot belongs. |
float |
rSx
Std Dev of Rsample density weighted X centroid |
float |
rSy
Std Dev of Rsample density weighted Y centroid |
float |
rVolume
Rsample Spot volume (density corrected for background by subtracting mnBackground*area . |
int |
sArea
spot Sample area in pixels |
float |
sDensity
Sample spot density not corrected for background |
float |
sDprime
Sample Spot density in D' (density corrected for background by subtracting mnBackground*area . |
int |
sDxLM
X distance Sample spot (x,y) relative to Sample LM(x,y) |
int |
sDyLM
Y distance Sample spot (x,y) relative to Sample LM(x,y) |
float |
sMaxDens
max Sample pixel density seen in spot |
int |
sMerx1
Sample Spot minimum enclosing rectangle Left in pixel coords |
int |
sMerx2
Sample Spot minimum enclosing rectangle Right in pixel coords |
int |
sMery1
Sample Spot minimum enclosing rectangle Top in pixel coords |
int |
sMery2
Sample Spot minimum enclosing rectangle Bottom in pixel coords |
float |
sMinDens
min Sample pixel density seen in spot |
float |
sMnBkgdDens
Mean Background pixel density for the G2 spot. |
int |
sNbrCsamples
# of samples in Sample Cspot Csample' estimate if not 0. |
int |
sPerimeter
Sample spot perimeter (pixels) for spot |
float |
sSDarea
Sample Csample' S.D. |
float |
sSDdPrime
Sample Csample' S.D. |
float |
sSDxCentroid
Sample Csample' S.D. |
float |
sSDyCentroid
Sample Csample' S.D. |
int |
sSpotNbr
spot Sample spot number |
float |
sSx
Std Dev of Sample density weighted X centroid |
float |
sSy
Std Dev of Sample density weighted Y centroid |
float |
sVolume
Sample Spot volume (density corrected for background by subtracting mnBackground*area . |
static java.lang.String |
VERSION
Version for this module |
float |
xRmom
X Abs Rsample(x,y) spot centroid |
float |
xSmom
X Abs Sample(x,y) spot centroid |
float |
yRmom
Y Abs Rsample(x,y) spot centroid |
float |
ySmom
Y Abs Sample(x,y) spot centroid |
Constructor Summary | |
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DbPspot()
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DbPspot(DbSample dbSample)
DbPspot() - Constructor for new DbPspot. |
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DbPspot(DbSample dbRsample,
DbSample dbSample)
DbPspot() - Constructor for new DbPspot. |
Method Summary | |
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void |
clearRsampleValues()
clearRsampleValues() - clear Rsample values in this spot. |
DbPspot |
clonePspot()
clonePspot() - clone spot sp into this spot. |
DbPspot |
clonePspotRsample()
clonePspotRsample() - clone spot sp into this spot. |
void |
copyRsampleToSampleSpotValues()
copyRsampleToSampleSpotValues() - copy Rsample field values in this Pspot to the Sample field values. |
boolean |
copySpotValues(DbPspot sp,
boolean copyPointersFlag)
copySpotValues() - copy values in spot sp into this spot. |
static java.lang.String |
getSampleOnlyHeaderNames()
getSampleOnlyHeaderNames() - get row of space-separated names of fields used in either toStringSampleOnly() or toStringRsampleOnly() calls. |
static java.lang.String |
getTabDelimitedFields()
getTabDelimitedFields() - get a string representation of the tab-delimited data fields |
boolean |
isLandmarkSpot()
isLandmarkSpot() - test if sample's ccNbr spot is a landmark spot. |
void |
swapSampleValues()
swapSampleValues() - swap the Rsample and Sample field values |
java.lang.String |
toBriefString()
toBriefString() - get brief DbPspot features string of the spot. |
java.lang.String |
toBriefXML()
toBriefXML() - get a brief string representation of this instance as XML. |
java.lang.String |
toDxyBriefString()
toDxyBriefString() - get brief DbPspot features string of the spot. |
java.lang.String |
toDxyDpDlBriefString()
toDxyDpDlBriefString() - get brief DbPspot features string of the spot. |
java.lang.String |
toFullXML()
toFullXML() - get a full string representation of this instance as XML. |
java.lang.String |
toString()
toString() - get DbPspot features string of the spot. |
java.lang.String |
toStringRsampleOnly()
toStringRsampleOnly() - get only Rsample DbPspot features of the spot. |
java.lang.String |
toStringSampleOnly()
toStringSampleOnly() - get only Sample DbPspot features of the spot. |
java.lang.String |
toTabDelimitedData()
toTabDelimitedData() - get a string representation of this instance as tab-delimited data values |
java.lang.String |
toXML()
toXML() - get a full string representation of this instance as XML. |
java.lang.String |
toXML(boolean useFullFlag)
toXML() - get a string representation of this instance as XML. |
Methods inherited from class O2Plib.db.DbBaseSpot |
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copyBaseValues, copyRsampleToSampleBaseValues, setDbSamples, swapBaseValues, verifyNotCircularSSFlist |
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 rSpotNbr
public int sSpotNbr
public int rArea
public int sArea
public int ccOfGroup
public boolean lmFlag
public int rDxLM
public int rDyLM
public int sDxLM
public int sDyLM
public int rPerimeter
public int sPerimeter
public int rSpotOfGroup
public float xRmom
public float yRmom
public float xSmom
public float ySmom
public float rDensity
public float sDensity
public float rDprime
public float sDprime
public float rVolume
public float sVolume
public float rMaxDens
public float sMaxDens
public float rMinDens
public float sMinDens
public int rMerx1
public int rMerx2
public int rMery1
public int rMery2
public int sMerx1
public int sMerx2
public int sMery1
public int sMery2
public float rMnBkgdDens
public float sMnBkgdDens
public float rSx
public float rSy
public float sSx
public float sSy
public int rNbrCsamples
public float rSDxCentroid
public float rSDyCentroid
public float rSDdPrime
public float rSDarea
public int sNbrCsamples
public float sSDxCentroid
public float sSDyCentroid
public float sSDdPrime
public float sSDarea
Constructor Detail |
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public DbPspot()
public DbPspot(DbSample dbSample)
dbSample
- for this spotpublic DbPspot(DbSample dbRsample, DbSample dbSample)
dbRsample
- is sample for pairing with this spotdbSample
- for this spotMethod Detail |
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public boolean isLandmarkSpot()
ps
- is DbPspot to test
public DbPspot clonePspot()
public DbPspot clonePspotRsample()
public boolean copySpotValues(DbPspot sp, boolean copyPointersFlag)
sp
- is spotcopyPointersFlag
- to copy spot pointers as well
public void copyRsampleToSampleSpotValues()
public void swapSampleValues()
public void clearRsampleValues()
public java.lang.String toDxyDpDlBriefString()
public java.lang.String toDxyBriefString()
public java.lang.String toBriefString()
public java.lang.String toString()
toString
in class java.lang.Object
public static java.lang.String getSampleOnlyHeaderNames()
toStringSampleOnly
public java.lang.String toStringSampleOnly()
public java.lang.String toStringRsampleOnly()
public static java.lang.String getTabDelimitedFields()
public java.lang.String toTabDelimitedData()
public java.lang.String toBriefXML()
public java.lang.String toFullXML()
public java.lang.String toXML()
public java.lang.String toXML(boolean useFullFlag)
useFullFlag
- add full details else just brief summary
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