O2Plib.db.CSD
Class CSDRspot

java.lang.Object
  extended by O2Plib.db.CSD.CSDglb
      extended by O2Plib.db.CSD.CSDRspot
All Implemented Interfaces:
CSDlistInterface

public class CSDRspot
extends CSDglb
implements CSDlistInterface

Class CSDRspot is an ERspot for the Composite Samples Database (CSD).

An Rspot set is an ordered list of corrersponding DbPspots from the samples in the CSD. Spot labels may be SP, PP, AP, US from the DbPairSamples DbPspot data. Spots that are SP, PP or AP are assigned as Rspots. If the US is an Rsample spot, then it too is an Rspot. Subsequently, if the Rsample is an AP label and it is a Rspot then it will be upgraded to a SP or PP as subsequent spot pairs are read into the Rspot set.

In addition, if the spot pair is a US with the Sample (Rsample has no spot), then that spot is added as an extended Rspot or ERspot set. If it is within a small mapped distance threshold (eRspotDistThr) to an existing ERspot, it is added to that ERspot set - otherwise a new ERspot is created. If the Rspot set is an ERspot set, the eRspotFlag is set.

The (xRspot,yRspot) coordinates are the centroid values of the Rsample spot (if it exists) and the idRsampleSpot is set to the Rsample spot idNbr for that spot. If the Rspot set is an ERspot set, then the (xRspot,yRspot) is set to (xERspot, yERspot).

The ERspot is used when reading in US spots from SPF files in order to determine if the US spot (not in the Rsample) should join an existing eRspot or create a new one if it is too far away.


 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/.

Version:
$Date: 2005/12/09 15:04:26 $ $Revision: 1.14 $
Author:
P. Lemkin, NCI-Frederick, Frederick, MD, 21702

Field Summary
 CSDannotation annotation
          Spot annotation
static int ERSPOT_DIST_THR
          Default distance threshold for restricting adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.
static float eRspotDistThr
          Restrict adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.
 boolean eRspotFlag
          This Rspot is an eRspot (extrapolated Rspot)
static int globalRspotCtr
          global Rspot set counter to generate new Rspot set IDs in the init() method.
 int idNbr
          Rspot set number [1:max # of Rspots].
 int idRsampleSpot
          The DbPspot rSpotNbr idNbr from the Rsample spot if it exists (i.e.
 int[] idxCondList
          List of indices constituting the corresponding CSDcond for each entry in the Rspot set.
 int[] idxSampleList
          List of indices [0:nSpots-1] constituting the corresponding DbSamples for each entry in the Rspot set.
 int indexRsample
          Index of Rsample in this.idxSampleList[].
 int lmSetRsample
          LMset that the Rsample belongs to
 int maxSpots
          Maximum number of spots in the Rspot set
 float[] mnCarea
          Mean area for Rspots being analyzed for condition subsets.
 float[] mnCdPrime
          Mean D' for entire Rspot set for condition subsets.
 float[] mnCnormDensity
          mean normalized density for Rspots being analyzed for condition subsets.
 float mnCVdensity
          Mean Coef.
 float mnXcentroid
          Mean Xabs (Rsample space) for entire Rspot set in to the Rsample cartesian space.
 float mnYcentroid
          Mean Yabs (Rsample space) for entire Rspot set in to the Rsample cartesian space.
 int[] nCsample
          # of samples in the Condition subset of the Rspot set.
 CSDRspot nextRspot
          Next instance for list of Rspots linked list
 CSDnorm norm
          Rspot set normalization method
 int nSpots
          Number of spots in the Rspot set
 DbPspot rSamplePspot
          The DbSpot for the Rsample Rspot.
 float rspCV
          sum of coefficient of variation (COV) density for entire Rspot set.
 float rspCVsq
          Square of sum of COV Density.
static int RSPOT_DIST_THR
          Default distance threshold for restricting adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.
static float rSpotDistThr
          Restrict adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.
 float[] sdMnCarea
          S.D.
 float[] sdMnCdPrime
          S.D.
 float[] sdMnCnormDensity
          S.D.
 float sdMnXcentroid
          S.D.
 float sdMnYcentroid
          S.D.
 DbPspot[] spotList
          List of DbPspots constituting the Rspot set [0:nSpots-1].
 float sumCVdensitySq
          sum of squares of all rSpCV
static java.lang.String VERSION
          Version for this module
 float xERspot
          Estimated X centroid coordinate of ERspot mapped to the Rsample coordinate space.This is created only if the Rspot is an ERspot.
 float xRspot
          X coordinate of Rsample Rspot.
 float yERspot
          Estimated Y centroid coordinate of ERspot mapped to the Rsample coordinate space.
 float yRspot
          Y coordinate of Rsample Rspot.
 
Fields inherited from class O2Plib.db.CSD.CSDglb
allSetSamples, AP, batchDir, BF_IS_LMS_SPOT, BF_ISVALIDSPOT, cacheDir, cdbIsOpenFlag, condListDB, CONSOLE_FLAG, CP, CSD_DBTYPE_CACHE, CSD_DBTYPE_RDBMS, CSD_DBTYPE_TAB_DELIM, CSD_DBTYPE_UNKNOWN, CSD_DBTYPE_XML, csdAcc, csdCache, csdCacheFile, csdDatabaseFile, csdFormatMode, csdIO, csdLMS, csdName, csdRdbmsFile, csdSizes, csdTabDelimFile, csdTotals, CSDversion, csdXMLfile, dataFiltersListDB, dateCreation, dateLastSession, dbRsample, dbSample, dbSamplesListDB, dbSPFlistsDB, dBugLMsetNbr, dBugPspotNbr, dBugRspotNbr, dBugSampleNbr, EP, epSetSamples, exprListsDB, GS, LM, MAX_NODE_SAFTY_FACTOR, mrl, nbrTimesInitialized, nCondListDB, nDataFiltersDB, needToSaveCSDdataFlag, NEVER, nExprListsDB, nOclDB, nodeSaftyFactor, normListDB, nRmapsDB, nRspotListsDB, nSamplesDB, nSPFfilesUsedDB, nSPFlistsDB, oclListDB, oclNameDB, PP, ppxDir, projDir, rdbmsDir, rMapsListDB, RSAMPLE, rspotListsDB, SAMPLE, sampleNamesDB, sampleNamesUsedDB, SP, tmpDir, US, useInternalDTDflag, wrkAnotation, wrkCalib, wrkERspot, wrkExpr, wrkSetSamples, xmlDir, xSetSamples, ySetSamples
 
Constructor Summary
CSDRspot()
          CSDRspot() - Constructor for new CSDRspot.
CSDRspot(int maxSpots)
          CSDRspot() - Constructor for new CSDRspot.
 
Method Summary
 boolean add(DbPspot ps)
          add() - add DbPspot to the Rspot set spotList[] list if the pairing code is SP, PP, AP, or (US with (xRmom,yRmom) NEQ 0).
 boolean add2ERspot(DbPspot ps)
          add2ERspot() - add DbPspot to ERspot set.
 boolean calcXYeRspotCentroid()
          calcXYeRspotCentroid() - compute (xERspot,yERspot) estimated centroid of ERspot data using non-Rsample Pspots which must exist.
 void clear()
          clear() - clear CSDRspot.
 CSDRspot cloneIt()
          cloneIt() - clone the contents of this Rspot.
 void copy(CSDRspot r)
          copy() - copy the contents of Rspot r to this Rspot.
 CSDnorm getNormalization()
          getNormalization() - set normalization for Rspot set.
 float[] getNormalizedDprimeData()
          getNormalizedDprimeData() - get normalized D' spot intensity for Rspot set.
static java.lang.String getTabDelimitedFields(boolean useAnnotationFlag, boolean useNormFlag)
          getTabDelimitedFields() - get a string representation of the tab-delimited data fields
 float[] getUnNormalizedDprimeData()
          getUnNormalizedDprimeData() - get unnormalized D' spot intensity for Rspot set.
 void init(int maxSpots)
          init() - initialize CSDRspot structures.
 DbPspot lookupBestDbPspotBySampleIdx(int idxSample)
          lookupBestDbPspotBySampleIdx() - find best DbPspot from Rspot set by sample index.
 boolean regrow(int newSize)
          regrow() - increase the size of the Rspot set
 boolean remove(DbPspot ps)
          remove() - remove DbPspot from Rspot set.
 boolean remove(int idxSample)
          remove() - remove DbPspot from Rspot set by sample index.
 boolean rightSize()
          rightSize() - right-size the size of the Rspot set to nSpots.
 CSDannotation setAnnotation()
          getAnnotation() - set annotation for Rspot set.
 void setAnnotation(CSDannotation annotation)
          setAnnotation() - set annotation to Rspot set.
static void setERspotDistanceThr(float eRspotDistanceThr)
          setERspotDistanceThr() - set threshold to restrict adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.
 void setERspotFlag(boolean eRspotFlag)
          setERspotFlag() - set the eRspot flag
 void setLMsetRsample(int lmSetRsample)
          setLMsetRsample() - set the LMset number associated with this spot for the Rsample
 void setNormalization(CSDnorm norm)
          setNormalization() - set annotation to Rspot set.
static void setRspotDistanceThr(float rSpotDistanceThr)
          setRspotDistanceThr() - set threshold to restrict adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.
 void setXYeRspotCoords(float xERspot, float yERspot)
          setXYeRspotCoords() - set the (xERspot,yERspot) for this eRspot set
 void setXYrspotCoords(float xRspot, float yRspot)
          setXYrspotCoords() - set the (xRspot,yRspot) for this Rspot set
 boolean sort(int sortByType)
          sort() - sort the Rspot set in ascending order by the feature specified by sortByType.
 java.lang.String toBriefXML()
          toBriefXML() - get a brief string representation of this instance as XML.
 java.lang.String toFullXML()
          toFullXML() - get a full string representation of this instance as XML.
 java.lang.String toString()
          toString() - print DbRspot features of the spot.
 java.lang.String toStringFull()
          toStringFull() - print DbRspot full features of the spot.
 java.lang.String toStringPointers()
          toStringPointers() - print DbRspot pointers of the spot.
 java.lang.String toStringStatistics()
          toStringStatistics() - print DbRspot statistics of the Rspot set.
 java.lang.String toTabDelimitedData(java.lang.String rowPrefix, boolean useAnnotationFlag, boolean useNormFlag)
          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 useFullRspotFlag)
          toXML() - get a string representation of this instance as XML
 
Methods inherited from class O2Plib.db.CSD.CSDglb
initGlb
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

VERSION

public static final java.lang.String VERSION
Version for this module

See Also:
Constant Field Values

RSPOT_DIST_THR

public static int RSPOT_DIST_THR
Default distance threshold for restricting adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.


ERSPOT_DIST_THR

public static int ERSPOT_DIST_THR
Default distance threshold for restricting adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.


globalRspotCtr

public static int globalRspotCtr
global Rspot set counter to generate new Rspot set IDs in the init() method.


idNbr

public int idNbr
Rspot set number [1:max # of Rspots].


idRsampleSpot

public int idRsampleSpot
The DbPspot rSpotNbr idNbr from the Rsample spot if it exists (i.e. the Rsample spot is not an US spot). This assumes that all samples are paired with the same Rsample. This may not always be the case - so use this with care! If this an ERspot set, then idRsampleSpot is 0. [TODO] could use an alternate coding...


rSamplePspot

public DbPspot rSamplePspot
The DbSpot for the Rsample Rspot. If Rsample is an EP spot, then this is set to a synthetic DbPspot in the Reference sample cartesian space with 0 density, 0 area, etc.


xRspot

public float xRspot
X coordinate of Rsample Rspot. If Rsample is an EP spot, then this is set to xERspotCentroid. -1 means undefined.


yRspot

public float yRspot
Y coordinate of Rsample Rspot. If Rsample is an EP spot, then this is set to yERspotCentroid. -1 means undefined.


lmSetRsample

public int lmSetRsample
LMset that the Rsample belongs to


rSpotDistThr

public static float rSpotDistThr
Restrict adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.


eRspotDistThr

public static float eRspotDistThr
Restrict adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.


eRspotFlag

public boolean eRspotFlag
This Rspot is an eRspot (extrapolated Rspot)


xERspot

public float xERspot
Estimated X centroid coordinate of ERspot mapped to the Rsample coordinate space.This is created only if the Rspot is an ERspot. -1 means undefined.


yERspot

public float yERspot
Estimated Y centroid coordinate of ERspot mapped to the Rsample coordinate space. This is created only if the Rspot is an ERspot. -1 means undefined.


nSpots

public int nSpots
Number of spots in the Rspot set


maxSpots

public int maxSpots
Maximum number of spots in the Rspot set


spotList

public DbPspot[] spotList
List of DbPspots constituting the Rspot set [0:nSpots-1]. Note: sync with idxSampleList[].


idxSampleList

public int[] idxSampleList
List of indices [0:nSpots-1] constituting the corresponding DbSamples for each entry in the Rspot set. Note: sync with spotList[]. The values for this array index the dbSamplesListDB[0:nSamplesDB-1].


indexRsample

public int indexRsample
Index of Rsample in this.idxSampleList[]. Note if we sort the Rspot, (i.e., spotList[] and idxSampleList[]), then we have to adjust the indexRsample to reflect the new position.


annotation

public CSDannotation annotation
Spot annotation


norm

public CSDnorm norm
Rspot set normalization method


idxCondList

public int[] idxCondList
List of indices constituting the corresponding CSDcond for each entry in the Rspot set. If the value is -1, then there are no condition sets and idx value of 0 is for the entire Rspot set


nCsample

public int[] nCsample
# of samples in the Condition subset of the Rspot set. If this is null, there are no condition subsets.


mnCdPrime

public float[] mnCdPrime
Mean D' for entire Rspot set for condition subsets. If this is null, there are no condition subsets.


mnCnormDensity

public float[] mnCnormDensity
mean normalized density for Rspots being analyzed for condition subsets. If this is null, there are no condition subsets.


mnCarea

public float[] mnCarea
Mean area for Rspots being analyzed for condition subsets. If this is null, there are no condition subsets.


sdMnCdPrime

public float[] sdMnCdPrime
S.D. of Mean D' for Rspot set for condition subsets. If this is null, there are no condition subsets.


sdMnCnormDensity

public float[] sdMnCnormDensity
S.D. of normalized density for Rspot set for condition subsets. If this is null, there are no condition subsets.


sdMnCarea

public float[] sdMnCarea
S.D. of area for Rspot set for condition subsets. If this is null, there are no condition subsets.


mnXcentroid

public float mnXcentroid
Mean Xabs (Rsample space) for entire Rspot set in to the Rsample cartesian space.


mnYcentroid

public float mnYcentroid
Mean Yabs (Rsample space) for entire Rspot set in to the Rsample cartesian space.


sdMnXcentroid

public float sdMnXcentroid
S.D. of X centroid for entire Rspot set


sdMnYcentroid

public float sdMnYcentroid
S.D. of Y centroid for entire Rspot set


rspCV

public float rspCV
sum of coefficient of variation (COV) density for entire Rspot set. [TODO] was computed in ck_limits_rspot()


rspCVsq

public float rspCVsq
Square of sum of COV Density. [TODO] was computed in ck_limits_rspot()


mnCVdensity

public float mnCVdensity
Mean Coef. Var. Density (COV) of entire Rspot set


sumCVdensitySq

public float sumCVdensitySq
sum of squares of all rSpCV


nextRspot

public CSDRspot nextRspot
Next instance for list of Rspots linked list

Constructor Detail

CSDRspot

public CSDRspot()
CSDRspot() - Constructor for new CSDRspot.


CSDRspot

public CSDRspot(int maxSpots)
CSDRspot() - Constructor for new CSDRspot.

Parameters:
maxSpots - is the maximum number of spots preallocated for this Rspot set.
Method Detail

clear

public void clear()
clear() - clear CSDRspot.

Specified by:
clear in interface CSDlistInterface

setERspotFlag

public void setERspotFlag(boolean eRspotFlag)
setERspotFlag() - set the eRspot flag

Parameters:
eRspotFlag - is flag value to set

setLMsetRsample

public void setLMsetRsample(int lmSetRsample)
setLMsetRsample() - set the LMset number associated with this spot for the Rsample

Parameters:
lmSetRsample - is the landmark set number if not -1

setXYrspotCoords

public void setXYrspotCoords(float xRspot,
                             float yRspot)
setXYrspotCoords() - set the (xRspot,yRspot) for this Rspot set

Parameters:
xRspot - is value to set
yRspot - is value to set

setXYeRspotCoords

public void setXYeRspotCoords(float xERspot,
                              float yERspot)
setXYeRspotCoords() - set the (xERspot,yERspot) for this eRspot set

Parameters:
xERspot - is value to set
yERspot - is value to set

setRspotDistanceThr

public static void setRspotDistanceThr(float rSpotDistanceThr)
setRspotDistanceThr() - set threshold to restrict adding spots to Rspot sets if the distance to a potential spot to be added with the (xRspot,yRspot) distance is LEQ this distance.

Parameters:
rSpotDistanceThr - distance to use. If it is <= 0, use RSPOT_DIST_THR

setERspotDistanceThr

public static void setERspotDistanceThr(float eRspotDistanceThr)
setERspotDistanceThr() - set threshold to restrict adding spots to ERspot sets if the distance to a potential spot to be added with the (xERspot,yERspot) distance is LEQ this distance.

Parameters:
eRspotDistanceThr - distance to use. If it is <= 0, use ERSPOT_DIST_THR

init

public void init(int maxSpots)
init() - initialize CSDRspot structures.

Specified by:
init in interface CSDlistInterface
Parameters:
maxSpots - is the maximum number of spots preallocated for this Rspot set.

copy

public void copy(CSDRspot r)
copy() - copy the contents of Rspot r to this Rspot. Copy the spotList[] and idxSampleList[] by value so can change them without changing Rspot r.

Parameters:
r - is Rspot to copy

cloneIt

public CSDRspot cloneIt()
cloneIt() - clone the contents of this Rspot. Copy the spotList[] and idxSampleList[] by value so can change them without changing Rspot r.

Returns:
the cloned Rspot.

sort

public boolean sort(int sortByType)
sort() - sort the Rspot set in ascending order by the feature specified by sortByType.
[TODO]

Parameters:
sortByType - - (will be feature type)
Returns:
true if succeed

regrow

public boolean regrow(int newSize)
regrow() - increase the size of the Rspot set

Specified by:
regrow in interface CSDlistInterface
Parameters:
newSize - is new size of Rspot set
Returns:
true if succeed

rightSize

public boolean rightSize()
rightSize() - right-size the size of the Rspot set to nSpots.

Specified by:
rightSize in interface CSDlistInterface
Returns:
true if succeed

add

public boolean add(DbPspot ps)
add() - add DbPspot to the Rspot set spotList[] list if the pairing code is SP, PP, AP, or (US with (xRmom,yRmom) NEQ 0). Put the sample index in a parallel idxSampleList[]. If there is no Rsample spot yet in the sampleList[], then add a clone copy of the ps but indicate this is for the Rsample in the idxSampleList[] array by setting the idxSampleList[0] entry to ps.idxRsample. Also copy the 'Rsample' data to the 'Sample' data for this cloned copy. Otherwise the idxSampleList[] entry is set to the Sample index sp.idxSample.

Parameters:
ps - is the DbPspot to add
Returns:
true if succeed

add2ERspot

public boolean add2ERspot(DbPspot ps)
add2ERspot() - add DbPspot to ERspot set. Note that there is no idRsampleSpot and that the centroid of the ERspot set is not determined at this point as it must be extrapolated after the ERspot set is completed. Note the Sample index is sp.idxSample.

Parameters:
ps - is the DbPspot to add. It must be a US spot with (xRmom,yRmom) EQ 0.
Returns:
true if succeed

calcXYeRspotCentroid

public boolean calcXYeRspotCentroid()
calcXYeRspotCentroid() - compute (xERspot,yERspot) estimated centroid of ERspot data using non-Rsample Pspots which must exist. For each Pspot in the Rspot set, it maps its coordinates to the Rsample space and then computes a mean virtual coordinat from these (nSpots-1) Pspots - the Rsample virtual Pspot is not counted. It also sets these values to (xERspot,yERspot) and updates spotList[0].(xRmom,yRmom,xSmom,ySmom) to these values so they can be used as an Rsample spot with zero density and area but with a virtual position in the Rsample map.

Returns:
true if succeed, false if failed (no Pspots in Rspot set).

remove

public boolean remove(DbPspot ps)
remove() - remove DbPspot from Rspot set. Note the Sample index is sp.idxSample.

Parameters:
ps - is the DbPspot to remove
Returns:
true if succeed, false if spot not found

remove

public boolean remove(int idxSample)
remove() - remove DbPspot from Rspot set by sample index. Note the Sample index is sp.idxSample. If there are several AP spots in the Rspot set for the same sample, it will remove them all.

Parameters:
idxSample - is the index of the spots for the Sample to remove
Returns:
true if succeed, false if spot not found

lookupBestDbPspotBySampleIdx

public DbPspot lookupBestDbPspotBySampleIdx(int idxSample)
lookupBestDbPspotBySampleIdx() - find best DbPspot from Rspot set by sample index. Note the Sample index is sp.idxSample. If there are several AP spots and a SP or PP in the Rspot set for the same sample, it will find the best (i.e. with SP or PP spot if there is one.

Parameters:
idxSample - is the index of the spots for the Sample
Returns:
DbPspot if succeed, null if spot not found

setAnnotation

public void setAnnotation(CSDannotation annotation)
setAnnotation() - set annotation to Rspot set.

Parameters:
annotation - to assign to the Rspot set

setAnnotation

public CSDannotation setAnnotation()
getAnnotation() - set annotation for Rspot set.


setNormalization

public void setNormalization(CSDnorm norm)
setNormalization() - set annotation to Rspot set.

Parameters:
norm - to assign to the Rspot set

getNormalization

public CSDnorm getNormalization()
getNormalization() - set normalization for Rspot set.


getNormalizedDprimeData

public float[] getNormalizedDprimeData()
getNormalizedDprimeData() - get normalized D' spot intensity for Rspot set.

Returns:
array of normalized D' data, else null if no spots or normalization

getUnNormalizedDprimeData

public float[] getUnNormalizedDprimeData()
getUnNormalizedDprimeData() - get unnormalized D' spot intensity for Rspot set.

Returns:
array of unnormalized D' data, else null if no spots or normalization

toString

public java.lang.String toString()
toString() - print DbRspot features of the spot.

Specified by:
toString in interface CSDlistInterface
Overrides:
toString in class java.lang.Object
Returns:
prettyprint spot string
See Also:
DpSpot#toStringSampleOnly

toStringFull

public java.lang.String toStringFull()
toStringFull() - print DbRspot full features of the spot.

Returns:
prettyprint spot string

toStringPointers

public java.lang.String toStringPointers()
toStringPointers() - print DbRspot pointers of the spot.

Returns:
prettyprint spot string

toStringStatistics

public java.lang.String toStringStatistics()
toStringStatistics() - print DbRspot statistics of the Rspot set.

Returns:
prettyprint spot string

getTabDelimitedFields

public static java.lang.String getTabDelimitedFields(boolean useAnnotationFlag,
                                                     boolean useNormFlag)
getTabDelimitedFields() - get a string representation of the tab-delimited data fields

Parameters:
useAnnotationFlag - - to add annotation fields
useNormFlag - - to add normalization fields
Returns:
string representation of the fields, with no "\n"

toTabDelimitedData

public java.lang.String toTabDelimitedData(java.lang.String rowPrefix,
                                           boolean useAnnotationFlag,
                                           boolean useNormFlag)
toTabDelimitedData() - get a string representation of this instance as tab-delimited data values. It will append the rowPrefix if not null before each generated row. It then makes a row for each pSpot in the Rspot set.

Parameters:
rowPrefix - to add to each row if not null
useAnnotationFlag - - to add annotation fields
useNormFlag - - to add normalization fields
Returns:
string representation of this instance, WITH "\n"

toBriefXML

public java.lang.String toBriefXML()
toBriefXML() - get a brief string representation of this instance as XML. Just ID list values. Do Not include details.

Returns:
string representation of this instance

toFullXML

public java.lang.String toFullXML()
toFullXML() - get a full string representation of this instance as XML. Use full representation.

Returns:
string representation of this instance

toXML

public java.lang.String toXML()
toXML() - get a full string representation of this instance as XML. Use full representation.

Returns:
string representation of this instance

toXML

public java.lang.String toXML(boolean useFullRspotFlag)
toXML() - get a string representation of this instance as XML

Parameters:
useFullFlag - add full details else just brief summary
Returns:
string representation of this instance