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| Packages that use DbSample | |
|---|---|
| O2Plib.db | |
| O2Plib.db.CSD | |
| O2Plib.image | |
| O2Plib.misc | |
| Uses of DbSample in O2Plib.db |
|---|
| Fields in O2Plib.db declared as DbSample | |
|---|---|
DbSample |
DbBaseSpot.dbRsample
|
DbSample |
DbPairSamples.dbRsample
Rsample object |
DbSample |
DbPairSamples.SpfContentHandler.dbRsample
Rsample instance |
DbSample |
DbBaseSpot.dbSample
|
DbSample |
DbBoundary.dbSample
|
DbSample |
DbPairSamples.dbSample
Sample object |
DbSample |
DbPairSamples.SpfContentHandler.dbSample
Sample instance |
DbSample |
DbSample.SsfContentHandler.dbSample
where most of the data is |
| Methods in O2Plib.db with parameters of type DbSample | |
|---|---|
boolean |
DbSample.assignRsampleToAllSpotsInSpotList(DbSample dbRsample)
assignRsampleToAllSpotsInSpotList() - assign the dbRsample field in all spots in the current spot list |
boolean |
DbLM.deleteLMsetFromLmsTable(DbSample dbRsample,
DbSample dbSample,
boolean clearBothSamplesFlag)
deleteLMsetFromLmsTable() - delete old landmark set from the landmark database table. |
static java.lang.String |
DbSpot.getAllSSFspotsStr(java.lang.String title,
DbSample dbS,
int[] filterByLMsets)
getAllSSFspotsStr() - get the printable list of all spots the specified sample.. |
java.lang.String |
DbLM.getLMSDBstr(DbSample dbRsample,
DbSample dbSample)
getLMSDBstr() - get landmark set summary as a printable string. |
DbSpot[] |
DbLM.getLMsetSpotList(DbSample dbS,
int k)
getLMsetSpotList() - get a list of spots in landmark set k for sample dbS if it exists. |
boolean |
DbSample.SsfContentHandler.goParse(java.lang.String fileName,
DbSample dbSample)
goParse() - parse XML file for prologue, spot, and epilogue data. |
boolean |
DbLM.lookupSamplePairLMS(DbSample dbRsample,
DbSample dbSample,
boolean commutativeLMSflag)
lookupSamplePairLMS() - lookup specific LMset pair (Rsample,Sample) from landmarks data table. |
void |
DbBaseSpot.setDbSamples(DbSample dbRsample,
DbSample dbSample)
setDbSamples() - set the dbRsample and dbSample objects for this DbBaseSpot. |
void |
DbSpot.setDbSamples(DbSample dbRsample,
DbSample dbSample)
setDbSamples() - set the dbRsample and dbSample objects for this spot. |
void |
DbPairSamples.setPairSamples(DbSample dbRsample,
DbSample dbSample,
DbLM dbLM)
setPairSamples() - setup DbSPF instance of the database and reset data |
| Constructors in O2Plib.db with parameters of type DbSample | |
|---|---|
DbBaseSpot(DbSample dbSample)
DbBaseSpot() - Constructor for new DbBaseSpot. |
|
DbBaseSpot(DbSample dbRsample,
DbSample dbSample)
DbBaseSpot() - Constructor for new DbBaseSpot. |
|
DbBoundary(DbSample dbSample)
DbBoundary() - Constructor |
|
DbBoundary(DbSample dbSample,
DbSpot dbSpot)
DbBoundary() - Constructor |
|
DbPairSamples(DbSample dbRsample,
DbSample dbSample,
DbLM dbLM)
DbPairSamples() - setup DbPairSamples instance of the database |
|
DbPspot(DbSample dbSample)
DbPspot() - Constructor for new DbPspot. |
|
DbPspot(DbSample dbRsample,
DbSample dbSample)
DbPspot() - Constructor for new DbPspot. |
|
DbSpot(DbSample dbSample)
DbSpot() - Constructor for new DbSpot. |
|
DbSpot(DbSample dbRsample,
DbSample dbSample)
DbSpot() - Constructor for new DbSpot. |
|
DbSpot(DbSample dbRsample,
DbSample dbSample,
int maxNbrAltLandmark)
DbSpot() - Constructor for new DbSpot. |
|
DbSpot(DbSample dbSample,
int maxNbrAltLandmark)
DbSpot() - Constructor for new DbSpot. |
|
| Uses of DbSample in O2Plib.db.CSD |
|---|
| Fields in O2Plib.db.CSD declared as DbSample | |
|---|---|
static DbSample |
CSDglb.dbRsample
|
static DbSample |
CSDglb.dbSample
|
DbSample |
CSDnorm.dbSample
|
static DbSample[] |
CSDglb.dbSamplesListDB
|
DbSample[] |
CSDcond.sampleList
[0:nSamples-1] list of samples in condition. |
| Methods in O2Plib.db.CSD that return DbSample | |
|---|---|
DbSample[] |
CSDcond.getSamplesList()
getSampleList() - get the list of sample DbSample objects |
| Methods in O2Plib.db.CSD with parameters of type DbSample | |
|---|---|
boolean |
CSDcond.add(DbSample dbS)
add() - add sample to condition. |
boolean |
CSDcond.add(DbSample dbS,
java.lang.String sName)
add() - add sample to condition. |
int |
CSDcond.lookupIdxBySample(DbSample dbS)
lookupIdxBySample() - lookup index of sample object in condition. |
boolean |
CSDcond.remove(DbSample dbS)
remove() - remove sample to condition. |
void |
CSD.setDbSampleList(DbSample[] aDbSamplesListDB)
setDbSamples() - set the list of samples for the CSD. |
void |
CSD.setDbSampleList(DbSample[] aDbSamplesListDB,
java.lang.String[] aSampleNamesDB)
setDbSamples() - set the list of samples for the CSD. |
void |
CSD.setDbSamples(DbSample aDbRsample,
DbSample aDbSample)
setDbSamples() - set the dbRsample and dbSample objects for this spot. |
| Uses of DbSample in O2Plib.image |
|---|
| Methods in O2Plib.image with parameters of type DbSample | |
|---|---|
int[] |
PixFunctions.calcHistogram(DbSample dbS,
int x1,
int y1,
int x2,
int y2)
calcHistogram() - compute grayscale histogram from image pixel data for sample dbS. |
int[] |
PixFunctions.calcHistogram(DbSample dbS,
Roi roi)
calcHistogram() - compute grayscale histogram from image pixel data for sample dbS. |
static DbSpot |
PixFunctions.calcMeanGrayValue(DbSample dbS,
int xC,
int yC,
int size,
DbSpot bkgrdSpot)
calcMeanGrayValue() - compute mean gray value of spot and return the values in a DbSpot instance for sample dbS with (sp.area, sp.density, sp.xMom, sp.yMom, sp.density, sp.mnDensity, sp.dMax, sp.dMin, sp.sxy) Note: the std-deviation of sp.density is saved in sp.sxy. |
static void |
DrawPix.drawBoundariesForSpots(DbSample dbSample,
char[] pix,
int pixWidth,
int color)
drawBoundariesForSpots() - If generating the segmented spot image in pix5, and the -DRAWSPOTS:B<'O'riginal or 'Z'image> was set, draw a white boundary around each spot in the 'O'riginal or segmented 'Z' image (-DRAWSPOTS:BO default). |
static void |
DrawPix.drawBoundariesForSpots(DbSample dbSample,
int[] pix,
int pixWidth,
int color)
drawBoundariesForSpots() - If generating the segmented spot image in pix5, and the -DRAWSPOTS:B<'O'riginal or 'Z'image> was set, draw a white boundary around each spot in the 'O'riginal or segmented 'Z' image (-DRAWSPOTS:BO default). |
static void |
DrawPix.drawDotsInSpots(DbSample dbSample,
char[] pix,
int color,
int pixWidth,
boolean drawPlusFlag,
boolean drawMinEnclRectFlag,
boolean drawSxSyEllipseFlag)
drawDotsInSpots() - draw symbol indicating the spots in the spot list in the pix. |
static void |
DrawPix.drawDotsInSpots(DbSample dbSample,
int[] pix,
int color,
int pixWidth,
boolean drawPlusFlag,
boolean drawMinEnclRectFlag,
boolean drawSxSyEllipseFlag)
drawDotsInSpots() - draw symbol indicating the spots in the spot list in the pix. |
| Uses of DbSample in O2Plib.misc |
|---|
| Fields in O2Plib.misc declared as DbSample | |
|---|---|
private DbSample |
CalibrateOD.dbSample
Global instances |
| Methods in O2Plib.misc with parameters of type DbSample | |
|---|---|
void |
CalibrateOD.setDbSample(DbSample dbSample)
setDbSample() - set the database sample object on this calibration instance. |
| Constructors in O2Plib.misc with parameters of type DbSample | |
|---|---|
CalibrateOD(DbSample dbSample,
int maxGray)
CalibrateOD() - constructor to set up the initial map. |
|
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