O2Plib.db.CSD
Class CSDexprList

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

public class CSDexprList
extends CSDglb
implements CSDlistInterface

Class CSDexprListList contains a list of expression profiles (vectors) data for the Composite Samples Database (CSD).


 This file is derived from Open2Dprot, MAExplorer and GELLAB-II cgelp2 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: 1.11 $
Author:
P. Lemkin, NCI-Frederick, Frederick, MD, 21702

Field Summary
 CSDexpr[] epList
          [0:nEPlist-1] list of expression profiles
static int glbIdExprListCounter
          Global expression list ID counter
 int idExprList
          Expression list id for this instance
 int[] idxSampleList
          List of indices [0:nEPlist-1] constituting the corresponding DbSamples for each entry in the Rspot set.
 int maxEPlist
          the maximum number of expression profiles in list if any.
 java.lang.String name
          Name of expression profile list
 int nEPlist
          the actual number of expression profiles in list if any.
 int nSamples
          # of samples in condition.
 java.lang.String timeStamp
           
 java.lang.String title
          title information of expression profile.
static java.lang.String VERSION
          Version for this module
 
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
CSDexprList()
          CSDexprList() - Constructor for new CSDexprList.
CSDexprList(java.lang.String name, java.lang.String timeStamp, java.lang.String title)
          CSDexprList() - Constructor for new CSDexprList.
 
Method Summary
 boolean addExpr(CSDexpr dbE)
          addExpr() - add Expr to ExprList.
 void clear()
          clear() - clear the expression list
 CSDexprList cloneExprList()
          cloneExprList() - make a cloned copy of an ExprList.
 CSDexprList difference(CSDexprList r1, CSDexprList r2)
          difference() - do the intersection of two ExprList lists r3= difference(r1,r2).
 CSDexpr[] getExprList()
          getExprList() - get the list of Expression listS
 void init(int maxEPlist)
          init() - initialize list of expression lists to specified size if > 0.
 CSDexprList intersection(CSDexprList r1, CSDexprList r2)
          intersection() - do the intersection of two ExprList lists r3= intersection(r1,r2).
 int lookupIdxByRspot(CSDexpr dbE)
          lookupIdxByRspot() - lookup index of Rspot object in ExprList.
 boolean regrow(int newSize)
          regrow() - increase the size of the expression lists
 boolean regrowExprList(int newSize)
          regrowExprList() - grow the ExprList.
 boolean rightSize()
          rightSize() - right-size the size of the list of expression lists to the size actually used.
 boolean rmvExpr(CSDexpr dbE)
          rmvExpr() - remove Rspot from ExprList.
 java.lang.String toString()
          toString() - print the list of expressions values in the list of expression lists.
 java.lang.String toTabDelimitedData()
          toTabDelimitedData() - get a string representation of this instance as tab-delimited data values
 java.lang.String toTabDelimitedFields()
          toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields
 java.lang.String toXML()
          toXML() - get a string representation of this instance as XML
 CSDexprList union(CSDexprList r1, CSDexprList r2)
          union() - do the union of two ExprList lists r3= union(r1,r2).
 
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

glbIdExprListCounter

public static int glbIdExprListCounter
Global expression list ID counter


name

public java.lang.String name
Name of expression profile list


timeStamp

public java.lang.String timeStamp

title

public java.lang.String title
title information of expression profile.


idExprList

public int idExprList
Expression list id for this instance


nSamples

public int nSamples
# of samples in condition.


idxSampleList

public int[] idxSampleList
List of indices [0:nEPlist-1] constituting the corresponding DbSamples for each entry in the Rspot set.


nEPlist

public int nEPlist
the actual number of expression profiles in list if any.


maxEPlist

public int maxEPlist
the maximum number of expression profiles in list if any.


epList

public CSDexpr[] epList
[0:nEPlist-1] list of expression profiles

Constructor Detail

CSDexprList

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


CSDexprList

public CSDexprList(java.lang.String name,
                   java.lang.String timeStamp,
                   java.lang.String title)
CSDexprList() - Constructor for new CSDexprList.

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

clear

public void clear()
clear() - clear the expression list

Specified by:
clear in interface CSDlistInterface

init

public void init(int maxEPlist)
init() - initialize list of expression lists to specified size if > 0.

Specified by:
init in interface CSDlistInterface
Parameters:
maxEPlist - to initialize size of the maximum list

regrow

public boolean regrow(int newSize)
regrow() - increase the size of the expression lists

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

rightSize

public boolean rightSize()
rightSize() - right-size the size of the list of expression lists to the size actually used.

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

regrowExprList

public boolean regrowExprList(int newSize)
regrowExprList() - grow the ExprList. If the size is LEQ 0, then clear the list (set it to null).

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

addExpr

public boolean addExpr(CSDexpr dbE)
addExpr() - add Expr to ExprList.

Parameters:
dbE - is Expr object (may be null)
Returns:
true if succeed

lookupIdxByRspot

public int lookupIdxByRspot(CSDexpr dbE)
lookupIdxByRspot() - lookup index of Rspot object in ExprList.

Parameters:
dbE - is Expr object
Returns:
-1 if failed, else the index if succeed

rmvExpr

public boolean rmvExpr(CSDexpr dbE)
rmvExpr() - remove Rspot from ExprList.

Parameters:
dbE - is Expr object
Returns:
true if succeed

cloneExprList

public CSDexprList cloneExprList()
cloneExprList() - make a cloned copy of an ExprList.

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

intersection

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

Parameters:
r1 - is ExprList
r2 - is ExprList
Returns:
CSDexprList r3 of new ExprList if succeed, else null

union

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

Parameters:
r1 - is ExprList
r2 - is ExprList
Returns:
CSDexprList r3 of new ExprList if succeed, else null

difference

public CSDexprList difference(CSDexprList r1,
                              CSDexprList r2)
difference() - do the intersection of two ExprList 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 ExprList
r2 - is ExprList
Returns:
CSDexprList r3 of new ExprList if succeed, else null

getExprList

public CSDexpr[] getExprList()
getExprList() - get the list of Expression listS

Returns:
list if succeed else null

toString

public java.lang.String toString()
toString() - print the list of expressions values in the list of expression lists.

Specified by:
toString in interface CSDlistInterface
Overrides:
toString in class java.lang.Object
Returns:
prettyprint list of expression list values string

toTabDelimitedFields

public java.lang.String toTabDelimitedFields()
toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields

Returns:
string representation of this instance

toTabDelimitedData

public java.lang.String toTabDelimitedData()
toTabDelimitedData() - get a string representation of this instance as tab-delimited data values

Returns:
string representation of this instance

toXML

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

Returns:
string representation of this instance