O2Plib.db.CSD
Class CSDglb

java.lang.Object
  extended by O2Plib.db.CSD.CSDglb
Direct Known Subclasses:
CSD, CSDacc, CSDannotation, CSDcache, CSDcal, CSDcond, CSDexpr, CSDexprList, CSDfilterState, CSDio, CSDlimits, CSDlms, CSDnorm, CSDRmap, CSDRspot, CSDRspotList, CSDsizes, CSDtotals

public class CSDglb
extends java.lang.Object

Class CSDglb contains global variables for the support of the Composite Samples Database data structure for Open2Dprot programs. It contains data for a single DB.

 Notation for object arrays with:
 1. 'wrk'XXX prefix are working instances of CSD object types.
 2. 'csd'XXX prefaix are the primary instance of that CSD object. Multiple
    instances are not used.
 3. xxx'DB' are list of these database objects.

This file is derived from Open2Dprot, MAExplorer, and GELLAB-II C 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
static CSDcond allSetSamples
          SEt of all samples.
static int AP
          Ambiguous Pair - pairing program generated label
static java.lang.String batchDir
          Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/
static int BF_IS_LMS_SPOT
          Bit feature of a spot.
static int BF_ISVALIDSPOT
          Bit feature of a spot.
static java.lang.String cacheDir
          Cache database directory {projDir}/cache/
static boolean cdbIsOpenFlag
          Flag indicates CSD DB is opened
static CSDcond[] condListDB
          Database of list of condition lists of samples in the CSD either by data filtering or by computation (e.g., boolean computation of conditions from other condition sets).
static boolean CONSOLE_FLAG
           
static int CP
          Composite Sample Database spot pair.
static int CSD_DBTYPE_CACHE
          CSD database type is cache data
static int CSD_DBTYPE_RDBMS
          CSD database type is RDBMS data
static int CSD_DBTYPE_TAB_DELIM
          CSD database type is Tab-delimited data
static int CSD_DBTYPE_UNKNOWN
          CSD database type is unknown data
static int CSD_DBTYPE_XML
          CSD database type is XML data
static CSDacc csdAcc
          Accession/MAIPE sample information related data
static CSDcache csdCache
          This supports multiple memory and multiple disk caches for a single Composite Sample Database (CSD).
static java.lang.String csdCacheFile
          Full path binary cache file for the CSD without the path.
static java.lang.String csdDatabaseFile
          Composite Sample Database file (CSD) without the path.
static int csdFormatMode
          CSD database type is CSD_DBTYPE_UNKNOWN, CSD_DBTYPE_XML, CSD_DBTYPE_CACHE, or CSD_DBTYPE_RDBMS
static CSDio csdIO
          Name of the CSD I/O database
static CSDlms csdLMS
          Landmark database for all of the CSD samples database if landmarks are used.
static java.lang.String csdName
          Name of the CSD database
static java.lang.String csdRdbmsFile
          Full path RDBMS file for the CSD without the path.
static CSDsizes csdSizes
          CSD sizes related data
static java.lang.String csdTabDelimFile
          Full path Tab-Delim file for the CSD without the path.
static CSDtotals csdTotals
          CSD totals statistics and SSF and SFP statistics related data
static java.lang.String CSDversion
          contains the version of the CSD.
static java.lang.String csdXMLfile
          Full path XML file for the CSD without the path.
static CSDfilterState[] dataFiltersListDB
          Database list of data filter parameter subset.
static java.lang.String dateCreation
          Date at time of initial creation
static java.lang.String dateLastSession
          Date of last session
static DbSample dbRsample
           
static DbSample dbSample
           
static DbSample[] dbSamplesListDB
           
static DbPairSamples[] dbSPFlistsDB
          List of SPF pairs read from SPF files [0:nSPFlist-1].
static int dBugLMsetNbr
          The LMset number to be debugged.
static int dBugPspotNbr
          The Pspot number to be debugged.
static int dBugRspotNbr
          The Rspot number to be debugged.
static int dBugSampleNbr
          The Sample number to be debugged.
static int EP
          Extrapolated Pair - by CSD database program
static CSDcond epSetSamples
          Expression Profile set of samples.
static CSDexprList[] exprListsDB
          Database list of expression profile lists [0:nExprListsDB-1] if not null.
static int GS
          Garbage Spot - generated by CSD database or editing programs
static int LM
          LandMark spot [could be virtual landmark] - by CSD database program
static float MAX_NODE_SAFTY_FACTOR
           
static CSDRspotList mrl
          Master database list of all Rspots sets.
static int nbrTimesInitialized
          Count # times initialized
static int nCondListDB
          size of condList
static int nDataFiltersDB
          size of dataFilterList
static boolean needToSaveCSDdataFlag
          Flag indicates need to save the CSD DB data
static boolean NEVER
          NEVER and CONSOLE_FLAG - debugging variables - must not be final!
static int nExprListsDB
          The size of exprListsDB[] expression profile lists.
static int nOclDB
          the number of Ordered condition lists
static float nodeSaftyFactor
          default to MAX_NODE_SAFTY_FACTOR - free space in the spot node
static CSDnorm[] normListDB
          [0:nSamplesDB-1] lists of sample normalizations for CSD database
static int nRmapsDB
          Database number of Rmap entries in the rMapList[0:nRmaps-1].
static int nRspotListsDB
          size of rspotListsDB
static int nSamplesDB
          size of the dbSampleList
static int nSPFfilesUsedDB
          # of SPF files actual PSL used to create DB
static int nSPFlistsDB
          size of the dbSPFlist
static CSDcond[][] oclListDB
          Database meta-list of ordered lists of sample conditions each of which contains lists of samples.
static java.lang.String[] oclNameDB
          [0:nOclDB-1] is list of names of ordered lists of sample conditions
static int PP
          Possible Pair - pairing program generated label
static java.lang.String ppxDir
          Original sample images directory {projDir}/ppx/
static java.lang.String projDir
          Project directory path
static java.lang.String rdbmsDir
          RDBMS database directory {projDir}/rdbms/
static CSDRmap[] rMapsListDB
          Database list of Rmaps of the Rspot indices to foreign spot indices to/from spot annotation IDs and info.
static int RSAMPLE
          The index for the Rsample (Reference Sample)
static CSDRspotList[] rspotListsDB
          Database of all RspotLists' objects of size [0:nRrspotListDB-1].
static int SAMPLE
          The index for the Sample to be paired with the Rsample
static java.lang.String[] sampleNamesDB
           
static java.lang.String[] sampleNamesUsedDB
          PSL samples used to create DB.
static int SP
          Sure Pair - pairing program generated label
static java.lang.String tmpDir
          Tmp images directory {projDir}/tmp/
static int US
          Unresolved Spot - pairing program generated label
static boolean useInternalDTDflag
          Use internal "Open2Dprot-CSD.dtd" file in CSD XML output file.
static java.lang.String VERSION
          Version for this module
static CSDannotation wrkAnotation
          Working Annotation related data instance.
static CSDcal wrkCalib
          Working calibration related data
static CSDRspot wrkERspot
          Working Rspot related data.
static CSDexpr wrkExpr
          Working expression profile related data.
static CSDcond wrkSetSamples
          Working set of samples.
static java.lang.String xmlDir
          Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files.
static CSDcond xSetSamples
          X set of samples.
static CSDcond ySetSamples
          Y set of samples.
 
Constructor Summary
CSDglb()
           
 
Method Summary
 int initGlb()
          initGlb() - reset all variables to initial state.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

VERSION

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

See Also:
Constant Field Values

NEVER

public static boolean NEVER
NEVER and CONSOLE_FLAG - debugging variables - must not be final!


CONSOLE_FLAG

public static boolean CONSOLE_FLAG

RSAMPLE

public static final int RSAMPLE
The index for the Rsample (Reference Sample)

See Also:
Constant Field Values

SAMPLE

public static final int SAMPLE
The index for the Sample to be paired with the Rsample

See Also:
Constant Field Values

BF_ISVALIDSPOT

public static final int BF_ISVALIDSPOT
Bit feature of a spot. Is a valid spot

See Also:
Constant Field Values

BF_IS_LMS_SPOT

public static final int BF_IS_LMS_SPOT
Bit feature of a spot. Spot is a landmark spot

See Also:
Constant Field Values

US

public static final int US
Unresolved Spot - pairing program generated label

See Also:
Constant Field Values

SP

public static final int SP
Sure Pair - pairing program generated label

See Also:
Constant Field Values

PP

public static final int PP
Possible Pair - pairing program generated label

See Also:
Constant Field Values

AP

public static final int AP
Ambiguous Pair - pairing program generated label

See Also:
Constant Field Values

EP

public static final int EP
Extrapolated Pair - by CSD database program

See Also:
Constant Field Values

CP

public static final int CP
Composite Sample Database spot pair. The CSD' is a statistical representation of a set of effective sample replicates generated by the database program.

See Also:
Constant Field Values

GS

public static final int GS
Garbage Spot - generated by CSD database or editing programs

See Also:
Constant Field Values

LM

public static final int LM
LandMark spot [could be virtual landmark] - by CSD database program

See Also:
Constant Field Values

CSD_DBTYPE_UNKNOWN

public static final int CSD_DBTYPE_UNKNOWN
CSD database type is unknown data

See Also:
Constant Field Values

CSD_DBTYPE_XML

public static final int CSD_DBTYPE_XML
CSD database type is XML data

See Also:
Constant Field Values

CSD_DBTYPE_CACHE

public static final int CSD_DBTYPE_CACHE
CSD database type is cache data

See Also:
Constant Field Values

CSD_DBTYPE_RDBMS

public static final int CSD_DBTYPE_RDBMS
CSD database type is RDBMS data

See Also:
Constant Field Values

CSD_DBTYPE_TAB_DELIM

public static final int CSD_DBTYPE_TAB_DELIM
CSD database type is Tab-delimited data

See Also:
Constant Field Values

MAX_NODE_SAFTY_FACTOR

public static final float MAX_NODE_SAFTY_FACTOR
See Also:
Constant Field Values

nbrTimesInitialized

public static int nbrTimesInitialized
Count # times initialized


csdName

public static java.lang.String csdName
Name of the CSD database


csdDatabaseFile

public static java.lang.String csdDatabaseFile
Composite Sample Database file (CSD) without the path. This will be saved in the xml/CSDxxx.xml or cache/CSDxxx.cache directories. From -csdFile:


projDir

public static java.lang.String projDir
Project directory path


batchDir

public static java.lang.String batchDir
Batch temporary data files used in exec'ing pipeline modules directory {projDir}/batch/


cacheDir

public static java.lang.String cacheDir
Cache database directory {projDir}/cache/


ppxDir

public static java.lang.String ppxDir
Original sample images directory {projDir}/ppx/


rdbmsDir

public static java.lang.String rdbmsDir
RDBMS database directory {projDir}/rdbms/


tmpDir

public static java.lang.String tmpDir
Tmp images directory {projDir}/tmp/


xmlDir

public static java.lang.String xmlDir
Directory {projDir}/xml/ use to accession, landmark, SSF, SPF, CSD and other database files.


csdFormatMode

public static int csdFormatMode
CSD database type is CSD_DBTYPE_UNKNOWN, CSD_DBTYPE_XML, CSD_DBTYPE_CACHE, or CSD_DBTYPE_RDBMS


csdXMLfile

public static java.lang.String csdXMLfile
Full path XML file for the CSD without the path. This has the same base file name as the csdDatabaseFile file, but with a .xml file extension. This will be saved in the projDir+"xml/"+csdDatabaseFile+".xml".


csdCacheFile

public static java.lang.String csdCacheFile
Full path binary cache file for the CSD without the path. This has the same base file name as the csdDatabaseFile file, but with a .cache file extension. This will be saved in the projDir+"cache/"+csdDatabaseFile+".cache".


csdRdbmsFile

public static java.lang.String csdRdbmsFile
Full path RDBMS file for the CSD without the path. This has the same base file name as the csdDatabaseFile file, but with a .rdbms file extension. This will be saved in the projDir+"rdbms/"+csdDatabaseFile+".rdbms".


csdTabDelimFile

public static java.lang.String csdTabDelimFile
Full path Tab-Delim file for the CSD without the path. This has the same base file name as the csdDatabaseFile file, but with a .rdbms file extension. This will be saved in the projDir+"xml/"+csdDatabaseFile+".txt".


useInternalDTDflag

public static boolean useInternalDTDflag
Use internal "Open2Dprot-CSD.dtd" file in CSD XML output file.


cdbIsOpenFlag

public static boolean cdbIsOpenFlag
Flag indicates CSD DB is opened


needToSaveCSDdataFlag

public static boolean needToSaveCSDdataFlag
Flag indicates need to save the CSD DB data


nodeSaftyFactor

public static float nodeSaftyFactor
default to MAX_NODE_SAFTY_FACTOR - free space in the spot node


dateCreation

public static java.lang.String dateCreation
Date at time of initial creation


dateLastSession

public static java.lang.String dateLastSession
Date of last session


CSDversion

public static java.lang.String CSDversion
contains the version of the CSD.


csdAcc

public static CSDacc csdAcc
Accession/MAIPE sample information related data


csdIO

public static CSDio csdIO
Name of the CSD I/O database


csdCache

public static CSDcache csdCache
This supports multiple memory and multiple disk caches for a single Composite Sample Database (CSD).


dbRsample

public static DbSample dbRsample

dbSample

public static DbSample dbSample

dbSPFlistsDB

public static DbPairSamples[] dbSPFlistsDB
List of SPF pairs read from SPF files [0:nSPFlist-1]. Note the size of the SPF list is 1 less than that of the dbSamplesListDB[] list.


nSPFlistsDB

public static int nSPFlistsDB
size of the dbSPFlist


dbSamplesListDB

public static DbSample[] dbSamplesListDB

sampleNamesDB

public static java.lang.String[] sampleNamesDB

nSamplesDB

public static int nSamplesDB
size of the dbSampleList


sampleNamesUsedDB

public static java.lang.String[] sampleNamesUsedDB
PSL samples used to create DB. This may be a subset of sampleName[] of size [0:nSPFfilesUsedDB-1]


nSPFfilesUsedDB

public static int nSPFfilesUsedDB
# of SPF files actual PSL used to create DB


csdLMS

public static CSDlms csdLMS
Landmark database for all of the CSD samples database if landmarks are used.


wrkCalib

public static CSDcal wrkCalib
Working calibration related data


exprListsDB

public static CSDexprList[] exprListsDB
Database list of expression profile lists [0:nExprListsDB-1] if not null.


nExprListsDB

public static int nExprListsDB
The size of exprListsDB[] expression profile lists.


wrkExpr

public static CSDexpr wrkExpr
Working expression profile related data. This instance may be used for static data initialization if required.


wrkERspot

public static CSDRspot wrkERspot
Working Rspot related data. This instance may be used for data initialization if required.


mrl

public static CSDRspotList mrl
Master database list of all Rspots sets. The first part of the list is nbrRspots non-EP spots (SP, PP or AP) labeled spots. The second part of the list is nbrERspots EP spots (EP, CP or GP) labeled spots.


rspotListsDB

public static CSDRspotList[] rspotListsDB
Database of all RspotLists' objects of size [0:nRrspotListDB-1].


nRspotListsDB

public static int nRspotListsDB
size of rspotListsDB


wrkAnotation

public static CSDannotation wrkAnotation
Working Annotation related data instance. Each Rspot set may have its own instance.


rMapsListDB

public static CSDRmap[] rMapsListDB
Database list of Rmaps of the Rspot indices to foreign spot indices to/from spot annotation IDs and info.


nRmapsDB

public static int nRmapsDB
Database number of Rmap entries in the rMapList[0:nRmaps-1].


condListDB

public static CSDcond[] condListDB
Database of list of condition lists of samples in the CSD either by data filtering or by computation (e.g., boolean computation of conditions from other condition sets).


nCondListDB

public static int nCondListDB
size of condList


allSetSamples

public static CSDcond allSetSamples
SEt of all samples.


wrkSetSamples

public static CSDcond wrkSetSamples
Working set of samples.


xSetSamples

public static CSDcond xSetSamples
X set of samples.


ySetSamples

public static CSDcond ySetSamples
Y set of samples.


epSetSamples

public static CSDcond epSetSamples
Expression Profile set of samples.


oclListDB

public static CSDcond[][] oclListDB
Database meta-list of ordered lists of sample conditions each of which contains lists of samples. Size [0:nOclDB-1][0:nConditions(variable)]


oclNameDB

public static java.lang.String[] oclNameDB
[0:nOclDB-1] is list of names of ordered lists of sample conditions


nOclDB

public static int nOclDB
the number of Ordered condition lists


dataFiltersListDB

public static CSDfilterState[] dataFiltersListDB
Database list of data filter parameter subset. This is a data filter state search of CSD. Size of [0:nDataFilters-1]


nDataFiltersDB

public static int nDataFiltersDB
size of dataFilterList


normListDB

public static CSDnorm[] normListDB
[0:nSamplesDB-1] lists of sample normalizations for CSD database


csdSizes

public static CSDsizes csdSizes
CSD sizes related data


csdTotals

public static CSDtotals csdTotals
CSD totals statistics and SSF and SFP statistics related data


dBugLMsetNbr

public static int dBugLMsetNbr
The LMset number to be debugged. It must be GEQ 0 since a value of -1 means no debugging.


dBugRspotNbr

public static int dBugRspotNbr
The Rspot number to be debugged. It must be GEQ 0 since a value of -1 means no debugging.


dBugPspotNbr

public static int dBugPspotNbr
The Pspot number to be debugged. It must be GEQ 0 since a value of -1 means no debugging.


dBugSampleNbr

public static int dBugSampleNbr
The Sample number to be debugged. It must be GEQ 0 since a value of -1 means no debugging.

Constructor Detail

CSDglb

public CSDglb()
Method Detail

initGlb

public int initGlb()
initGlb() - reset all variables to initial state. Test if re-init, and then return true if re-initialized.

Returns:
# times initialized.