O2Plib.db.CSD
Class CSDannotation

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

public class CSDannotation
extends CSDglb

Class CSDannotation defines protein/peptide spot identification and annotation for an Rspot set in the Composite Samples Database (CSD).


 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: 1.10 $
Author:
P. Lemkin, NCI-Frederick, Frederick, MD, 21702

Field Summary
 int nbr
          Annotation ID number
 java.lang.String spID
          Swiss-Prot ID
 java.lang.String spName
          Swiss-Prot Name
 java.lang.String uniprotID
          UniProt ID
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
CSDannotation()
          CSDannotation() - Constructor for new CSDannotation.
 
Method Summary
 void clear()
          clear() - clear instance.
static java.lang.String getTabDelimitedFields()
          getTabDelimitedFields() - get a string representation of the tab-delimited data fields
 java.lang.String toString()
          toString() - get a pretty-print string representation of this instance
 java.lang.String toTabDelimitedData()
          toTabDelimitedData() - get a string representation of this instance as tab-delimited data values
 java.lang.String toXML()
          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

nbr

public int nbr
Annotation ID number


uniprotID

public java.lang.String uniprotID
UniProt ID


spID

public java.lang.String spID
Swiss-Prot ID


spName

public java.lang.String spName
Swiss-Prot Name

Constructor Detail

CSDannotation

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

Method Detail

clear

public void clear()
clear() - clear instance.


toString

public java.lang.String toString()
toString() - get a pretty-print string representation of this instance

Overrides:
toString in class java.lang.Object
Returns:
string representation of this instance

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"

toXML

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

Returns:
string representation of this instance