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java.lang.Object O2Plib.db.CSD.CSDglb
public class CSDglb
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/.
Field Summary | |
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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 | |
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CSDglb()
|
Method Summary | |
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int |
initGlb()
initGlb() - reset all variables to initial state. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String VERSION
public static boolean NEVER
public static boolean CONSOLE_FLAG
public static final int RSAMPLE
public static final int SAMPLE
public static final int BF_ISVALIDSPOT
public static final int BF_IS_LMS_SPOT
public static final int US
public static final int SP
public static final int PP
public static final int AP
public static final int EP
public static final int CP
public static final int GS
public static final int LM
public static final int CSD_DBTYPE_UNKNOWN
public static final int CSD_DBTYPE_XML
public static final int CSD_DBTYPE_CACHE
public static final int CSD_DBTYPE_RDBMS
public static final int CSD_DBTYPE_TAB_DELIM
public static final float MAX_NODE_SAFTY_FACTOR
public static int nbrTimesInitialized
public static java.lang.String csdName
public static java.lang.String csdDatabaseFile
public static java.lang.String projDir
public static java.lang.String batchDir
public static java.lang.String cacheDir
public static java.lang.String ppxDir
public static java.lang.String rdbmsDir
public static java.lang.String tmpDir
public static java.lang.String xmlDir
public static int csdFormatMode
public static java.lang.String csdXMLfile
public static java.lang.String csdCacheFile
public static java.lang.String csdRdbmsFile
public static java.lang.String csdTabDelimFile
public static boolean useInternalDTDflag
public static boolean cdbIsOpenFlag
public static boolean needToSaveCSDdataFlag
public static float nodeSaftyFactor
public static java.lang.String dateCreation
public static java.lang.String dateLastSession
public static java.lang.String CSDversion
public static CSDacc csdAcc
public static CSDio csdIO
public static CSDcache csdCache
public static DbSample dbRsample
public static DbSample dbSample
public static DbPairSamples[] dbSPFlistsDB
public static int nSPFlistsDB
public static DbSample[] dbSamplesListDB
public static java.lang.String[] sampleNamesDB
public static int nSamplesDB
public static java.lang.String[] sampleNamesUsedDB
public static int nSPFfilesUsedDB
public static CSDlms csdLMS
public static CSDcal wrkCalib
public static CSDexprList[] exprListsDB
public static int nExprListsDB
public static CSDexpr wrkExpr
public static CSDRspot wrkERspot
public static CSDRspotList mrl
public static CSDRspotList[] rspotListsDB
public static int nRspotListsDB
public static CSDannotation wrkAnotation
public static CSDRmap[] rMapsListDB
public static int nRmapsDB
public static CSDcond[] condListDB
public static int nCondListDB
public static CSDcond allSetSamples
public static CSDcond wrkSetSamples
public static CSDcond xSetSamples
public static CSDcond ySetSamples
public static CSDcond epSetSamples
public static CSDcond[][] oclListDB
public static java.lang.String[] oclNameDB
public static int nOclDB
public static CSDfilterState[] dataFiltersListDB
public static int nDataFiltersDB
public static CSDnorm[] normListDB
public static CSDsizes csdSizes
public static CSDtotals csdTotals
public static int dBugLMsetNbr
public static int dBugRspotNbr
public static int dBugPspotNbr
public static int dBugSampleNbr
Constructor Detail |
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public CSDglb()
Method Detail |
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public int initGlb()
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