O2Plib.db.CSD
Class CSDRspotList

java.lang.Object
  extended by O2Plib.db.CSD.CSDglb
      extended by O2Plib.db.CSD.CSDRspotList

public class CSDRspotList
extends CSDglb

Class CSDRspotList contains a Rspot List or (RSL). This consists of a subset of Rspots in the Composite Samples Database (CSD).

The list maintains both a number list of Rspot numbers and a list of the Rspot objects.


 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: 1.12 $
Author:
P. Lemkin, NCI-Frederick, Frederick, MD, 21702

Field Summary
static float DEF_MIN_ACCEPTABLE_DIST
          Default value of minimum distance for a best fit search by (x,y) coordinates to be valid.
 float defMinAcceptableDist
          Default minimum acceptable (x,y) search distance.
static int glbIdRSLcounter
          Global RSL ID counter
 int idRSL
          RSL id for this Rspot set list instance
static int maxRspots
          Maximum total number of Rspots in the rspotList[0:maxRspots-1].
 float minBestFitXYdistance
          Distance of minimum nearest best-fit XY coordinate search set by last lookupRspotByBestFitRspotXYcoordSearch() call.
 int minBestFitXYIdx
          Index in rspotsList[] of minimum nearest best-fit XY coordinate search set by last lookupRspotByBestFitRspotXYcoordSearch() call.
 java.lang.String name
          Name of the list of Rspots
static int nbrERspots
          Number of ERspots in the send part of the rspotList[nbrERspots:totRspots-1].
static int nbrRspots
          Number of non-EP Rspots in the first part of the [0:nbrRspots-1].
 CSDRspot[] rspotsList
          [0:totRspots-1] list of Rspot objects
 int[] rspotsNbrs
          [0:totRspots-1] list of Rspot numbers
 java.lang.String timeStamp
           
 java.lang.String title
          title information of list of Rspots.
static int totRspots
          Total number of Rspots in the rspotList[0:totRspots-1].
 boolean useXYhashFlag
          Flag to use xyHashtable for lookup of Rspots by CSDRspot.(xRspot,yRspot).
static java.lang.String VERSION
          Version for this module
 java.util.Hashtable xyHash
          hashTable for xy coordinate lookup.
 
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
CSDRspotList()
          CSDRspotList() - Constructor for new CSDRspotList with a cleared list.
CSDRspotList(java.lang.String name, java.lang.String timeStamp, java.lang.String title)
          CSDRspotList() - Constructor for new CSDRspotList with a cleared list.
 
Method Summary
 boolean add(CSDRspot dbR)
          add() - add Rspot to RSL.
 boolean add(CSDRspot dbR, int rNbr)
          add() - add Rspot to RSL.
 boolean add(int idNbr)
          add() - add Rspot number to RSL.
 boolean addDbug(CSDRspot dbR, int rNbr, int pSpotNbr)
          addDbug() - DBUG version.
 CSDRspot addRspotToHashtable(CSDRspot r)
          addRspotToHashtable() - Add Rspot to Rspot list hashtable.
 CSDRspot addRspotToHashtableDbug(CSDRspot r, int pSpotNbr)
          addRspotToHashtableDbug() - DBUG version.
 void clear()
          clear() - clear the RSL.
 CSDRspotList cloneIt()
          cloneIt() - make a cloned copy of a RSL.
 CSDRspotList difference(CSDRspotList r1, CSDRspotList r2)
          difference() - do the intersection of two RSL lists r3= difference(r1,r2).
 CSDRspot[] getRspotsList()
          getRspotsList() - get the list of Rspot CSDRspot objects
 int[] getRspotsNbrs()
          getRspotsNbrs() - get the list of Rspot numbers
 java.lang.String getTabDelimitedFieldsAndData(boolean useAnnotationFlag, boolean useNormFlag)
          getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values.
 void init(int maxRspots)
          init() - initialize Rspot list list to specified size if > 0.
 CSDRspotList intersection(CSDRspotList r1, CSDRspotList r2)
          intersection() - do the intersection of two RSL lists r3= intersection(r1,r2).
 int lookupIdxByRspot(CSDRspot dbR)
          lookupIdxByRspot() - lookup index of Rspot object in RSL.
 int lookupIdxByRspot(int rNbr)
          lookupIdxByRspot() - lookup index of Rspot number in RSL.
 CSDRspot lookupRspotByExactRspotXYcoord(float x, float y)
          lookupRspotByExactRspotXYcoord() - lookup Rspot set by exact Rspot set (xRspot,yRspot) coordinates.
 CSDRspot lookupRspotByExactRspotXYcoordDbug(float x, float y, int lmSetRsample, int pSpotNbr)
          lookupRspotByExactRspotXYcoordDbug() - DBUG version.
 CSDRspot lookupRspotByNearestERspotXYcoord(float x, float y, float minAcceptableDist)
          lookupRspotByNearestERspotXYcoord() - lookup nearest ERspot set by (xERspot,yERspot) coordinates.
 CSDRspot lookupRspotByNearestRspotXYcoord(float x, float y, float minAcceptableDist)
          lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates.
 CSDRspot lookupRspotByNearestRspotXYcoord(float x, float y, float minAcceptableDist, boolean onlyERspotsFlag)
          lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates.
 CSDRspot lookupRspotByNearestRspotXYcoord(int x, int y, float minAcceptableDist)
          lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates.
 CSDRspot lookupRspotByRspotIDnbr(int rNbr)
          lookupRspotByRspotIDnbr() - lookup Rspot set by ID number
 boolean regrow(int newSize)
          regrow() - grow the RSL.
 boolean remove(CSDRspot dbR)
          remove() - remove Rspot from RSL.
 boolean remove(int rNbr)
          remove() - remove Rspot from RSL.
 boolean rightSize()
          rightSize() - right-size the size of the RspotList to totRspots.
 boolean rightSize(boolean alsoRightSizeRpotsFlag)
          rightSize() - right-size the size of the RspotList to totRspots.
 CSDRspot rmvFromHashtable(CSDRspot r)
          rmvFromHashtable() - Remove Rspot from Rspot set hashtable.
 void setDefMinAcceptableDist(float defMinAcceptableDist)
          setDefMinAcceptableDist() - set defMinAcceptableDist
 boolean setRspotsList(CSDRspot[] rspotsListData)
          setRspotsList() - set the list of Rspot CSDRspot objects This makes a copy of the Rspots not of the rspotsListData array and assigned the rspotsNbrs[], sets up maxRspots, totRspots, nbrRspots, nbrERspots.
 void setUseXYhashFlag(boolean useXYhashFlag)
          setUseXYhashFlag() - set useXYhashFlag to enable use of xyHash table.
 void sort()
          sort() - sort the list of Rspot sets in ascending order by Rspot numbers
 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() - return a list of Rspot data for the List of Rspots.
 java.lang.String toStringFull()
          toStringFull() - return a list of Rspot data for the List of Rspots.
 java.lang.String toStringIDs()
          toStringIDs() - return a list of Rspot ID numbers for the list of Rspots.
 java.lang.String toXML(boolean useFullRspotFlag)
          toXML() - get a string representation of this instance as XML
 CSDRspotList union(CSDRspotList r1, CSDRspotList r2)
          union() - do the union of two RSL lists r3= union(r1,r2).
 boolean writeBriefXML(java.io.BufferedWriter bw)
          writeBriefXML() - write a brief representation of this instance as XML.
 boolean writeFullXML(java.io.BufferedWriter bw)
          writeFullXML() - get a full string representation of this instance as XML.
 boolean writeXML(java.io.BufferedWriter bw, boolean useFullRspotFlag)
          writeXML() - 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

DEF_MIN_ACCEPTABLE_DIST

public static final float DEF_MIN_ACCEPTABLE_DIST
Default value of minimum distance for a best fit search by (x,y) coordinates to be valid. See defMinAcceptableDist.

See Also:
Constant Field Values

glbIdRSLcounter

public static int glbIdRSLcounter
Global RSL ID counter


name

public java.lang.String name
Name of the list of Rspots


timeStamp

public java.lang.String timeStamp

title

public java.lang.String title
title information of list of Rspots.


idRSL

public int idRSL
RSL id for this Rspot set list instance


maxRspots

public static int maxRspots
Maximum total number of Rspots in the rspotList[0:maxRspots-1]. for a preallocated list.


totRspots

public static int totRspots
Total number of Rspots in the rspotList[0:totRspots-1]. totRspots= nbrRspots+nbrERspots


nbrRspots

public static int nbrRspots
Number of non-EP Rspots in the first part of the [0:nbrRspots-1].


nbrERspots

public static int nbrERspots
Number of ERspots in the send part of the rspotList[nbrERspots:totRspots-1].


rspotsNbrs

public int[] rspotsNbrs
[0:totRspots-1] list of Rspot numbers


rspotsList

public CSDRspot[] rspotsList
[0:totRspots-1] list of Rspot objects


useXYhashFlag

public boolean useXYhashFlag
Flag to use xyHashtable for lookup of Rspots by CSDRspot.(xRspot,yRspot). If the flag is not set, it will do a nearest neighbor search.


xyHash

public java.util.Hashtable xyHash
hashTable for xy coordinate lookup. The key is the Rsample (x,y) coordinates in the CSD reference map that the Rspot is mapped. Note: only SP, PP, and AP Pspots, and US Pspots in the Sample (not in the Rsample) are stored in this hash table since ERspots will not have an estimated (x,y) centroid until after the ERspot set is fully computed. The key is computed as:
   ((int)xRmom & 0xFFFF) << 16 | ((int)yRmom) & 0xFFFF)


minBestFitXYdistance

public float minBestFitXYdistance
Distance of minimum nearest best-fit XY coordinate search set by last lookupRspotByBestFitRspotXYcoordSearch() call. If the distance is -1, there was no best fit.


minBestFitXYIdx

public int minBestFitXYIdx
Index in rspotsList[] of minimum nearest best-fit XY coordinate search set by last lookupRspotByBestFitRspotXYcoordSearch() call. If the index is -1, there was no best fit.


defMinAcceptableDist

public float defMinAcceptableDist
Default minimum acceptable (x,y) search distance.

Constructor Detail

CSDRspotList

public CSDRspotList()
CSDRspotList() - Constructor for new CSDRspotList with a cleared list.


CSDRspotList

public CSDRspotList(java.lang.String name,
                    java.lang.String timeStamp,
                    java.lang.String title)
CSDRspotList() - Constructor for new CSDRspotList with a cleared list.

Parameters:
name - of the list of Rspots
timeStamp - when the list of Rspots
title - information of list of Rspots.
Method Detail

clear

public void clear()
clear() - clear the RSL.


setDefMinAcceptableDist

public void setDefMinAcceptableDist(float defMinAcceptableDist)
setDefMinAcceptableDist() - set defMinAcceptableDist

Parameters:
defMinAcceptableDist - - value to set

setUseXYhashFlag

public void setUseXYhashFlag(boolean useXYhashFlag)
setUseXYhashFlag() - set useXYhashFlag to enable use of xyHash table. If the table is enabled and there is no hash table, then create one.

Parameters:
useXYhashFlag - - value to set

init

public void init(int maxRspots)
init() - initialize Rspot list list to specified size if > 0.

Parameters:
maxRspots - to initialize size of the maximum list

regrow

public boolean regrow(int newSize)
regrow() - grow the RSL. If the size is LEQ 0, then clear the list (set it to null). If the newSize is less than the actual size, then grow it.

Parameters:
newSize - of the RSL list
Returns:
true if succeed

rightSize

public boolean rightSize()
rightSize() - right-size the size of the RspotList to totRspots.

Returns:
true if succeed

rightSize

public boolean rightSize(boolean alsoRightSizeRpotsFlag)
rightSize() - right-size the size of the RspotList to totRspots.

Parameters:
alsoRightSizeRpotsFlag - also rightSize each of the Rspot sets.
Returns:
true if succeed

sort

public void sort()
sort() - sort the list of Rspot sets in ascending order by Rspot numbers


addRspotToHashtable

public CSDRspot addRspotToHashtable(CSDRspot r)
addRspotToHashtable() - Add Rspot to Rspot list hashtable. The xyHash is for Rspot xy coordinate lookup (r.xRspot,r.yRspot). If there are coordinates defined i.e., set to (-1,-1), then no hash entry is allowed. It can be added at a later time when the coordinates are defined. The key is the Rsample (x,y) coordinates in the CSD reference map to which the Rspot is mapped. Note: only SP, PP, and AP Pspots, and US Pspots in the Sample (not in the Rsample) are stored in this hash table since ERspots will not have an estimated (x,y) centroid until after the ERspot set is fully computed. The key is computed as:
   ((int)xRmom & 0xFFFF) << 16 | ((int)yRmom) & 0xFFFF)

Parameters:
r - is Rspot set to add to the list of Rspots

addRspotToHashtableDbug

public CSDRspot addRspotToHashtableDbug(CSDRspot r,
                                        int pSpotNbr)
addRspotToHashtableDbug() - DBUG version. Add Rspot to Rspot list hashtable. The xyHash is for Rspot xy coordinate lookup (r.xRspot,r.yRspot). If there are coordinates defined i.e., set to (-1,-1), then no hash entry is allowed. It can be added at a later time when the coordinates are defined. The key is the Rsample (x,y) coordinates in the CSD reference map to which the Rspot is mapped. Note: only SP, PP, and AP Pspots, and US Pspots in the Sample (not in the Rsample) are stored in this hash table since ERspots will not have an estimated (x,y) centroid until after the ERspot set is fully computed. The key is computed as:
   ((int)xRmom & 0xFFFF) << 16 | ((int)yRmom) & 0xFFFF)

Parameters:
r - is Rspot set to add to the list of Rspots
pSpotNbr - is Rsample Pspot number being debugged

rmvFromHashtable

public CSDRspot rmvFromHashtable(CSDRspot r)
rmvFromHashtable() - Remove Rspot from Rspot set hashtable.

Parameters:
r - is Rspot set to remove

lookupRspotByExactRspotXYcoord

public CSDRspot lookupRspotByExactRspotXYcoord(float x,
                                               float y)
lookupRspotByExactRspotXYcoord() - lookup Rspot set by exact Rspot set (xRspot,yRspot) coordinates. If useXYhashFlag is not set, then do a nearest neighbor search using defMinAcceptableDist.

Parameters:
x - is Rspot set X coordinate
y - is Rspot set Y coordinate
Returns:
Rspot set if found, else null

lookupRspotByExactRspotXYcoordDbug

public CSDRspot lookupRspotByExactRspotXYcoordDbug(float x,
                                                   float y,
                                                   int lmSetRsample,
                                                   int pSpotNbr)
lookupRspotByExactRspotXYcoordDbug() - DBUG version. Lookup Rspot set by exact Rspot set (xRspot,yRspot) coordinates. If useXYhashFlag is not set, then do a nearest neighbor search using defMinAcceptableDist.

Parameters:
x - is Rspot set X coordinate
y - is Rspot set Y coordinate
lmSetRsample - is the LMset number of spot being debugged
pSpotNbr - is the Pspot number of spot being debugged
Returns:
Rspot set if found, else null

lookupRspotByRspotIDnbr

public CSDRspot lookupRspotByRspotIDnbr(int rNbr)
lookupRspotByRspotIDnbr() - lookup Rspot set by ID number

Parameters:
rNbr - is Rspot number to lookup
Returns:
Rspot set if found, else null

lookupRspotByNearestRspotXYcoord

public CSDRspot lookupRspotByNearestRspotXYcoord(int x,
                                                 int y,
                                                 float minAcceptableDist)
lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates. If the best fit is found, then set minBestFitXYdistance and minBestFitXYIdx.

Parameters:
x - is Rspot set X coordinate
y - is Rspot set Y coordinate
minAcceptableDist - is minimal acceptable distance.
Returns:
Rspot set if found, else null and minBestFitXYdistance and minBestFitXYIdx are set to -1.

lookupRspotByNearestRspotXYcoord

public CSDRspot lookupRspotByNearestRspotXYcoord(float x,
                                                 float y,
                                                 float minAcceptableDist)
lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates. If the best fit is found, then set minBestFitXYdistance and minBestFitXYIdx.

Parameters:
x - is Rspot set X coordinate
y - is Rspot set Y coordinate
minAcceptableDist - is minimal acceptable distance.
Returns:
Rspot set if found, else null and minBestFitXYdistance and minBestFitXYIdx are set to -1.

lookupRspotByNearestERspotXYcoord

public CSDRspot lookupRspotByNearestERspotXYcoord(float x,
                                                  float y,
                                                  float minAcceptableDist)
lookupRspotByNearestERspotXYcoord() - lookup nearest ERspot set by (xERspot,yERspot) coordinates. If the best fit is found, then set minBestFitXYdistance and minBestFitXYIdx.

Parameters:
x - is ERspot set X coordinate
y - is ERspot set Y coordinate
minAcceptableDist - is minimal acceptable distance.
Returns:
ERspot set if found, else null and minBestFitXYdistance and minBestFitXYIdx are set to -1.

lookupRspotByNearestRspotXYcoord

public CSDRspot lookupRspotByNearestRspotXYcoord(float x,
                                                 float y,
                                                 float minAcceptableDist,
                                                 boolean onlyERspotsFlag)
lookupRspotByNearestRspotXYcoord() - lookup nearest Rspot set by (xRspot,yRspot) coordinates. If the best fit is found, then set minBestFitXYdistance and minBestFitXYIdx.

Parameters:
x - is Rspot set X coordinate
y - is Rspot set Y coordinate
minAcceptableDist - is minimal acceptable distance.
onlyERspotsFlag - to only search ERspots in Rspot list.
Returns:
Rspot set if found, else null and minBestFitXYdistance and minBestFitXYIdx are set to -1.

addDbug

public boolean addDbug(CSDRspot dbR,
                       int rNbr,
                       int pSpotNbr)
addDbug() - DBUG version. add Rspot to RSL.

Parameters:
dbR - is Rspot object (may be null)
rNbr - is Rspot number (MUST NOT be 0)
pSpotNbr - is Rsample Pspot number being debugged in addRspotToHashtable(dbR,pSpotNbr) call.
Returns:
true if succeed

add

public boolean add(CSDRspot dbR,
                   int rNbr)
add() - add Rspot to RSL.

Parameters:
dbR - is Rspot object (may be null)
rNbr - is Rspot number (MUST NOT be 0)
Returns:
true if succeed

add

public boolean add(CSDRspot dbR)
add() - add Rspot to RSL. Use the Rspot dbR.nbr for the rspotNbr

Parameters:
dbR - is Rspot object
Returns:
true if succeed

add

public boolean add(int idNbr)
add() - add Rspot number to RSL. Do not save the Rspot object, just use Rspot numbers.

Parameters:
rNbr - is Rspot idNbr number value
Returns:
true if succeed

lookupIdxByRspot

public int lookupIdxByRspot(int rNbr)
lookupIdxByRspot() - lookup index of Rspot number in RSL.

Parameters:
rNbr - is Rspot number
Returns:
-1 if failed, else the index if succeed

lookupIdxByRspot

public int lookupIdxByRspot(CSDRspot dbR)
lookupIdxByRspot() - lookup index of Rspot object in RSL.

Parameters:
dbR - is Rspot object
Returns:
-1 if failed, else the index if succeed

remove

public boolean remove(int rNbr)
remove() - remove Rspot from RSL.

Parameters:
rNbr - is Rspot number
Returns:
true if succeed

remove

public boolean remove(CSDRspot dbR)
remove() - remove Rspot from RSL.

Parameters:
dbR - is Rspot object
Returns:
true if succeed

cloneIt

public CSDRspotList cloneIt()
cloneIt() - make a cloned copy of a RSL. NOTE: do NOT clone the idRSL. Each new RSL gets a new idRSL.

Parameters:
dbR - is Rspot object
Returns:
-1 if failed, else the index if succeed

intersection

public CSDRspotList intersection(CSDRspotList r1,
                                 CSDRspotList r2)
intersection() - do the intersection of two RSL lists r3= intersection(r1,r2). I.e., Rspots in r1 must also be in r2 else it is not in r3.

Parameters:
r1 - is RSL
r2 - is RSL
Returns:
CSDRspotList r3 of new RSL if succeed, else null

union

public CSDRspotList union(CSDRspotList r1,
                          CSDRspotList r2)
union() - do the union of two RSL lists r3= union(r1,r2).

Parameters:
r1 - is RSL
r2 - is RSL
Returns:
CSDRspotList r3 of new RSL if succeed, else null

difference

public CSDRspotList difference(CSDRspotList r1,
                               CSDRspotList r2)
difference() - do the intersection of two RSL lists r3= difference(r1,r2). That is (r1 less r2). If a spot in r2 i s in r2, then it is removed from r3. If the spot is in r2 but not in r1, it is ignored.

Parameters:
r1 - is RSL
r2 - is RSL
Returns:
CSDRspotList r3 of new RSL if succeed, else null

getRspotsNbrs

public int[] getRspotsNbrs()
getRspotsNbrs() - get the list of Rspot numbers

Returns:
list if succeed else null

getRspotsList

public CSDRspot[] getRspotsList()
getRspotsList() - get the list of Rspot CSDRspot objects

Returns:
list if succeed else null

setRspotsList

public boolean setRspotsList(CSDRspot[] rspotsListData)
setRspotsList() - set the list of Rspot CSDRspot objects This makes a copy of the Rspots not of the rspotsListData array and assigned the rspotsNbrs[], sets up maxRspots, totRspots, nbrRspots, nbrERspots.

Parameters:
rspotsListData - is new list to use
Returns:
list if succeed else null

toStringIDs

public java.lang.String toStringIDs()
toStringIDs() - return a list of Rspot ID numbers for the list of Rspots.

Returns:
"" if fail, else list of space separated Rspot numbers

toStringFull

public java.lang.String toStringFull()
toStringFull() - return a list of Rspot data for the List of Rspots.

Returns:
"" if fail, else list of space separated Rspot data

toString

public java.lang.String toString()
toString() - return a list of Rspot data for the List of Rspots.

Overrides:
toString in class java.lang.Object
Returns:
"" if fail, else list of space separated Rspot data

getTabDelimitedFieldsAndData

public java.lang.String getTabDelimitedFieldsAndData(boolean useAnnotationFlag,
                                                     boolean useNormFlag)
getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values. This includes the Rspot list data, the Rspot set data and the individual Pspot data. Data is repeated on each line as horizontally stacked data - suitable for reading into R.

Parameters:
useAnnotationFlag - - to add annotation fields
useNormFlag - - to add normalization fields
Returns:
string representation of this full instance

toBriefXML

public java.lang.String toBriefXML()
toBriefXML() - get a brief string representation of this instance as XML. Just list Rspot numbers

Returns:
string representation of this instance

writeBriefXML

public boolean writeBriefXML(java.io.BufferedWriter bw)
writeBriefXML() - write a brief representation of this instance as XML. Just list Rspot numbers

Parameters:
bw - is BufferedWriter to use
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 Rspot representation.

Returns:
string representation of this instance

writeFullXML

public boolean writeFullXML(java.io.BufferedWriter bw)
writeFullXML() - get a full string representation of this instance as XML. Use full Rspot representation.

Parameters:
bw - is BufferedWriter to use
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:
useFullRspotFlag - add full Rspot else just Rspot number
Returns:
string representation of this instance

writeXML

public boolean writeXML(java.io.BufferedWriter bw,
                        boolean useFullRspotFlag)
writeXML() - get a string representation of this instance as XML

Parameters:
bw - is BufferedWriter to use
useFullRspotFlag - add full Rspot else just Rspot number
Returns:
string representation of this instance