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java.lang.Object O2Plib.db.DbBaseSpot O2Plib.db.DbSpot
public class DbSpot
Class DbSpot supports a spot data structure for spot features in Open2Dprot programs. It contains data for a single spot. There are a number of optional fields that may be used depending on the application. Note this class extends DbBaseSpot.
1. In applications where paired spots are used (CSD DB programs), the Rsample, landmark and paired spot related features are used. 2. The spot boundary is optional depending on the application. 3. The statistical features to represent a composite sample are optional depending on the application (CSD DB data mining). 4. Composite Cspots are statistical representations of a set of corresponding spots from replicate samples. These fields are optional (CSD DB data mining).This file is derived from GELLAB-II cmpgl2.c as of "Version November 9, 1999" with major refactoring for use in Open2Dprot.
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[] |
altLMset
Sorted list of next nearest LM sets [0:nbrAltLMs-1] to this spot |
float[] |
altLMsetDistSq
corresponding distances of next nearest landmarks [0:nbrAltLMs-1] |
int |
area
spot area in pixels |
DbSpot |
bestPairedSpot
ptr to best paired spot for spot-pairing, if not null |
DbBoundary |
bnd
Spot boundary for the CC if used |
int |
ccNumber
Spot connected component number (CC#) from spot list . |
int |
ccRsampleIdx
[DEPRICATE] Seg2Dgel CC# index for Rsample spot |
int |
ccSampleIdx
[DEPRICATE] Seg2Dgel CC# index for Rsample spot |
float |
density
Note: store the various density modes in the same array! This could be selected from (densityPrime, %density, volume). |
float |
densityPct
percent spot density |
float |
densityPrime
density' is density corrected for background and is computed as (density - mnBackground*area). |
int |
dLx
relative X distance from Rsample spot to LM |
int |
dLy
relative Y distance from Rsample spot to LM |
float |
dMax
spot MAX OD |
float |
dMin
spot MIN OD |
boolean |
extrapolatedFlag
set if spot is an extrapolated EP spot. |
boolean |
lmFlag
set true if spot is a landmark spot |
static int |
maxNbrAltLMs
Maximum # of alternate paired landmarks (N3). |
int |
merx1
Spot minimum enclosing rectangle x1 in pixel coordinates |
int |
merx2
Spot minimum enclosing rectangle x2 in pixel coordinates |
int |
mery1
Spot minimum enclosing rectangle y1 in pixel coordinates |
int |
mery2
Spot minimum enclosing rectangle y2 in pixel coordinates |
float |
mnBackground
spot mean background density in calibrated OD if available. |
int |
mnBkgrdGrayvalue
spot mean background grayvalue |
float |
mnDensity
mean spot density |
int |
nbrAltLMs
The # of alternate paired landmarks for this spot. |
int |
nCsample
# of samples in Cspot Csample' estimate if not 0. |
DbSpot |
nextLMspot
ptr to Next LM-set spot if not null |
DbSpot |
nextSpot
ptr to Next spot instance in spot list if not null |
DbSpot |
prevSpot
ptr to Previous spot instance in spot list if not null |
DbSpot |
rSpotNext
Next instance for CSD database Rspot linked list |
float |
sdArea
Csample' S.D. |
float |
sdDprime
Csample' S.D. |
float |
sdXcentroid
Csample' S.D. |
float |
sdYcentroid
Csample' S.D. |
java.lang.String |
spotBoundaryStr
spot boundary string if using boundaries |
float |
sx
spot size weight mean std dev |
float |
sxy
spot size weight mean std dev |
float |
sy
spot size weight mean std dev |
static java.lang.String |
VERSION
Version for this module |
float |
volume
percent spot volume |
float |
xMom
spot X density weighted centroid |
int[] |
xyList
List of all packed (x<<16 | y) 16-bit pixel coordinates in the spot which is updated by the particular application - optional. |
float |
yMom
spot Y density weighted centroid |
Constructor Summary | |
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DbSpot()
DbSpot() - Constructor for new DbSpot. |
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DbSpot(DbSample dbSample)
DbSpot() - Constructor for new DbSpot. |
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DbSpot(DbSample dbRsample,
DbSample dbSample)
DbSpot() - Constructor for new DbSpot. |
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DbSpot(DbSample dbRsample,
DbSample dbSample,
int maxNbrAltLandmark)
DbSpot() - Constructor for new DbSpot. |
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DbSpot(DbSample dbSample,
int maxNbrAltLandmark)
DbSpot() - Constructor for new DbSpot. |
Method Summary | |
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boolean |
copyValues(DbSpot sp,
boolean copyPointersFlag)
copyValues() - copy values in spot sp into this spot. |
void |
createAltLMset(int maximumAltLMs)
createAltLMset() - create alternate landmark set for this spot. |
java.lang.String |
cvPrettyPrintSpot()
cvPrettyPrintSpot() - pretty print a spot if it exists else return "Null". |
static java.lang.String |
cvSpotToPrettyPrintListStr(DbSpot p1,
boolean addSubPairListFlag)
cvSpotToPrettyPrintListStr() - get the pretty-print features of the specified spot and its pair spot if it is paired. |
static java.lang.String |
cvSpotToPrettyPrintListStr(DbSpot p1,
boolean addSubPairListFlag,
boolean addCCnbrFlag)
cvSpotToPrettyPrintListStr() - get the pretty-print features of the specified spot and its pair spot if it is paired. |
static java.lang.String |
cvSpotToPrintStr(DbSpot p1,
int spotFormatToUse)
cvSpotToPrintStr() - Debugging print the features of the specified spot and print its paired spot features if it is paired. |
static java.lang.String |
cvSpotToPrintStr(DbSpot p1,
int spotFormatToUse,
boolean addCCdataFlag)
cvSpotToPrintStr() - Debugging print the features of the specified spot and print its paired spot features if it is paired. |
static java.lang.String |
getAllSSFspotsStr(java.lang.String title,
DbSample dbS,
int[] filterByLMsets)
getAllSSFspotsStr() - get the printable list of all spots the specified sample.. |
java.lang.String |
getAltLMsetStr()
getAltLMsetStr() - create an alternate landmark set list string for this spot. |
static java.lang.String |
getPrettyPrintSpotStr(DbSpot p1)
getPrettyPrintSpotStr() - get the pretty-print spot features of specified |
static java.lang.String |
getPrettyPrintSpotStr(DbSpot p1,
boolean addCCnbrFlag)
getPrettyPrintSpotStr() - get the pretty-print spot features of specified |
static DbSpot[] |
getSubListSpotsPairedWithThisSpot(DbSpot spot,
int maxSublistSize)
getSubListSpotsPairedWithThisSpot() - get a sublist of spots (in the other sample) that are paired with this spot. |
void |
setDbSamples(DbSample dbRsample,
DbSample dbSample)
setDbSamples() - set the dbRsample and dbSample objects for this spot. |
static void |
setNbrAltLMsize(int maxNbrAltLandmark)
setNbrAltLMsize() - set the default maximum # of alternate paired landmarks all spots in the database could belong to. |
java.lang.String |
toString()
toString() - print SSF features of the spot. |
Methods inherited from class O2Plib.db.DbBaseSpot |
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copyBaseValues, copyRsampleToSampleBaseValues, 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 ccNumber
public int area
public float density
public float densityPrime
public float densityPct
public float volume
public float dMax
public float dMin
public int mnBkgrdGrayvalue
public float mnBackground
public float mnDensity
public float xMom
public float yMom
public float sx
public float sy
public float sxy
public java.lang.String spotBoundaryStr
public int merx1
public int merx2
public int mery1
public int mery2
public int[] xyList
public DbBoundary bnd
public static int maxNbrAltLMs
public int nbrAltLMs
public int[] altLMset
public float[] altLMsetDistSq
public int nCsample
public float sdXcentroid
public float sdYcentroid
public float sdDprime
public float sdArea
public int dLx
public int dLy
public boolean lmFlag
public boolean extrapolatedFlag
public int ccRsampleIdx
public int ccSampleIdx
public DbSpot prevSpot
public DbSpot nextSpot
public DbSpot nextLMspot
public DbSpot bestPairedSpot
public DbSpot rSpotNext
Constructor Detail |
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public DbSpot(DbSample dbSample, int maxNbrAltLandmark)
dbSample
- for this spotmaxNbrAltLandmark
- - max # of alternative landmark sets this spot
could belong to.public DbSpot(DbSample dbRsample, DbSample dbSample, int maxNbrAltLandmark)
dbRsample
- is sample for pairing with this spotdbSample
- for this spotmaxNbrAltLandmark
- - max # of alternative landmark sets this spot
could belong to.public DbSpot(DbSample dbRsample, DbSample dbSample)
dbRsample
- is sample for pairing with this spotdbSample
- for this spotpublic DbSpot(DbSample dbSample)
dbSample
- for this spotpublic DbSpot()
Method Detail |
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public void createAltLMset(int maximumAltLMs)
maximumAltLMs
- - set the size of the alternate landmark listpublic void setDbSamples(DbSample dbRsample, DbSample dbSample)
setDbSamples
in class DbBaseSpot
dbRsample
- is sample for pairing with this spotdbSample
- for this spotpublic static void setNbrAltLMsize(int maxNbrAltLandmark)
maxNbrAltLandmark
- - max # of alternative landmark sets this spot
could belong to.public boolean copyValues(DbSpot sp, boolean copyPointersFlag)
sp
- is spotcopyPointersFlag
- to copy spot pointers as well
public static DbSpot[] getSubListSpotsPairedWithThisSpot(DbSpot spot, int maxSublistSize)
p
- is DbSpot pointer to list of spots
public java.lang.String getAltLMsetStr()
"B(35) E(42) G(62)"
public static java.lang.String getPrettyPrintSpotStr(DbSpot p1)
p1
- is spot to print and includ ccNumber data
public static java.lang.String getPrettyPrintSpotStr(DbSpot p1, boolean addCCnbrFlag)
p1
- is spot to print
public static java.lang.String cvSpotToPrettyPrintListStr(DbSpot p1, boolean addSubPairListFlag)
p1
- is spot print and include ccNumber dataaddSubPairListFlag
- get all AP spots paired to either spots of
main pair.
public static java.lang.String cvSpotToPrettyPrintListStr(DbSpot p1, boolean addSubPairListFlag, boolean addCCnbrFlag)
p1
- is spot printaddSubPairListFlag
- get all AP spots paired to either spots of
main pair.
public static java.lang.String cvSpotToPrintStr(DbSpot p1, int spotFormatToUse)
p1
- is spot print, include CC number dataspotFormatToUse
- (IO_FORMAT_xxxx)
public static java.lang.String cvSpotToPrintStr(DbSpot p1, int spotFormatToUse, boolean addCCdataFlag)
p1
- is spot printspotFormatToUse
- (IO_FORMAT_xxxx)addCCdataFlag
- to add CC number data
public java.lang.String toString()
toString
in class java.lang.Object
r
- is DbSpot to convert to a string
public java.lang.String cvPrettyPrintSpot()
q
- is the spot to use
public static java.lang.String getAllSSFspotsStr(java.lang.String title, DbSample dbS, int[] filterByLMsets)
E.g., . . . Rsample spot list Rsample spot# 1 (xMom,yMom)=(223,321) LM[A] ltLMs={B(6) C(12) P(37} \ bpSpt#=354 nxtLMspt#=36 nxtSpt#=2 Rsample spot# 2 (xMom,yMom)=(243,361) LM[A] ltLMs={B(8) C(11) P(35} \ bpSpt#=642 nxtLMspt#=38 nxtSpt#=3 . . .
title
- if not nulldbS
- is the sample to list all spotsfilterByLMsets
- of landmark sets to filter spots (if not null).
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