O2Plib.db.CSD
Class CSDexpr

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

public class CSDexpr
extends CSDglb
implements CSDlistInterface

Class CSDexpr contains an expression profile vector data for the Composite Samples Database (CSD).

 The mapping of samples to columns in the vector is
 by idxSampleList[0:nSamples-1].
 There are 2 variants:
     raw data in         expRawValues[0:nSamples-1]
     normalized data in  expValues[0:nSamples-1]
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
 float[] expRawValues
           
 float[] expValues
           
 int[] idxSampleList
           
 int maxSamples
          maximum size of the preallocated arrays
 CSDnorm normMethod
          Normalization method used to compute the expValues[]
 int normMode
          Normalization method which is CSDnorm.NORM_PCT_xxxx
 int nSamples
          size of the dbSamples
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
CSDexpr()
          CSDexpr() - Constructor for new CSDexpr.
 
Method Summary
 void clear()
          clear() - clear object list
static java.lang.String getTabDelimitedFields()
          getTabDelimitedFields() - get a string representation of the tab-delimited data fields
 void init(int size)
          init() - initialize expression list to specified size if > 0.
 boolean regrow(int newSize)
          regrow() - increase the size of the expression list
 boolean rightSize()
          rightSize() - right-size the size of the expression list to the size actually used.
 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 normalized values for the expression list.
 java.lang.String toString(boolean useRawExprValuesFlag)
          toString() - print values for the expression list - either raw or normalized values.
 java.lang.String toTabDelimitedData()
          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 useFullFlag)
          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

maxSamples

public int maxSamples
maximum size of the preallocated arrays


nSamples

public int nSamples
size of the dbSamples


idxSampleList

public int[] idxSampleList

normMode

public int normMode
Normalization method which is CSDnorm.NORM_PCT_xxxx


normMethod

public CSDnorm normMethod
Normalization method used to compute the expValues[]


expRawValues

public float[] expRawValues

expValues

public float[] expValues
Constructor Detail

CSDexpr

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

Method Detail

clear

public void clear()
clear() - clear object list

Specified by:
clear in interface CSDlistInterface

init

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

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

regrow

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

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 expression list to the size actually used.

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

toString

public java.lang.String toString()
toString() - print normalized values for the expression list.

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

toString

public java.lang.String toString(boolean useRawExprValuesFlag)
toString() - print values for the expression list - either raw or normalized values.

Parameters:
useRawExprValuesFlag - to print raw values else normalized values
Returns:
prettyprint list of expression values string

getTabDelimitedFields

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

Returns:
string representation of this instance, no "\n"

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, no "\n"

toBriefXML

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

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 useFullFlag)
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