Uses of Class
O2Plib.db.DbSample

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.