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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSD
public class CSD
Class CSD supports a Composite Samples Database data structure for Open2Dprot programs. It contains data for a single DB.
******************************************************************** ****** NOT RELEASED - work in progress - THIS WILL CHANGE!!!! ***** 1. There are more fields and objects that will be added from refactored MAExplorer, Flicker, GELLAB-II, and other analysis methods to make invoking analysis methods and R easier. 2. JDBC related classed will be added. 3. After the initial brain-dump, need to GGGR this design. Remove old-paradigm code/objects; orient it towards use with XML and RDBMS databases. 4. Add classes: ********************************************************************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 java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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CSD()
CSD() - Constructor for new CSD. |
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CSD(java.lang.String csdName,
java.lang.String csdDatabaseFile,
java.lang.String projDir,
int csdFormatMode)
CSD() - Constructor for new CSD. |
Method Summary | |
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boolean |
clearCSD()
clearCSD() - clear the CSD [TODO] |
void |
init()
init() - setup the related sub class object instances |
boolean |
openCSDdbFile()
openCSDdbFile() - Open the CSD RDBMS, XML or cache file Don't open if it is already opened. |
boolean |
removeSPFandSSFSpotListsCSD()
removeSPFandSSFSpotListsCSD() - remove the non-Rsample spotlist[] and spotPairList[] . |
boolean |
renameCSD(java.lang.String newCSDname)
renameCSD() - rename the CSD [TODO] |
boolean |
rightSize()
rightSize() - "Right-size" all CSD lists if required. |
boolean |
saveCSD()
saveCSD() - save the CSD [TODO] |
boolean |
setCSDnameProj(java.lang.String aCsdName,
java.lang.String aCsdDatabaseFile,
java.lang.String aProjDir,
int aCsdFormatMode)
setCSDnameProj() - change the current CSD name and project directory |
void |
setDbPairSamples(DbPairSamples[] aDbSPFlistsDB)
setDbPairSamples() - set the dbSPFlist of pair-samples for the CSD. |
void |
setDbSampleList(DbSample[] aDbSamplesListDB)
setDbSamples() - set the list of samples for the CSD. |
void |
setDbSampleList(DbSample[] aDbSamplesListDB,
java.lang.String[] aSampleNamesDB)
setDbSamples() - set the list of samples for the CSD. |
void |
setDbSamples(DbSample aDbRsample,
DbSample aDbSample)
setDbSamples() - set the dbRsample and dbSample objects for this spot. |
void |
setLMsetDebugging(int dBugLMsetNumber)
setLMsetDebugging() - set the debug LMset number for the CSD. |
void |
setPspotDebugging(int dBugPspotNumber)
setPspotDebugging() - set the debug Pspot number for the CSD. |
void |
setRspotDebugging(int dBugRspotNumber)
setRspotDebugging() - set the debug Rspot number for the CSD. |
void |
setSampleDebugging(int dBugSampleNumber)
setSampleDebugging() - set the debug Sample number for the CSD. |
void |
setUseInternalDTDflag(boolean aUseInternalDTDflag)
setUseInternalDTDflag() - set the use internal DTD flag. |
java.lang.String |
toXML()
toXML() - convert database to XML string |
Methods inherited from class O2Plib.db.CSD.CSDglb |
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initGlb |
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
Constructor Detail |
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public CSD()
public CSD(java.lang.String csdName, java.lang.String csdDatabaseFile, java.lang.String projDir, int csdFormatMode)
csdName
- is the base name of the CSD databasecsdDatabaseFile
- is the name of the CSD database with a full
path and file extension.projDir
- is the project directory for the filecsdFormatMode
- is CSD_XML, CSD_CACHE, or CSD_RDBMSMethod Detail |
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public void init()
public boolean clearCSD()
public boolean saveCSD()
public boolean renameCSD(java.lang.String newCSDname)
newCSDname
- is new name for current CSD database
public boolean setCSDnameProj(java.lang.String aCsdName, java.lang.String aCsdDatabaseFile, java.lang.String aProjDir, int aCsdFormatMode)
aCsdName
- is the base name of the CSD databaseaCsdDatabaseFile
- is the name of the CSD database with a full
path and file extension.aProjDir
- is the project directory for the fileaCsdFormatMode
- is CSD_DBTYPE_XML, CSD_DBTYPE_CACHE,
or CSD_DBTYPE_RDBMS
public void setUseInternalDTDflag(boolean aUseInternalDTDflag)
useInternalDTDflag
- status to setpublic boolean openCSDdbFile()
public void setDbSamples(DbSample aDbRsample, DbSample aDbSample)
dbRsample
- is sample for pairing with this spotdbSample
- for this spotpublic void setDbPairSamples(DbPairSamples[] aDbSPFlistsDB)
dbSPFlists
- is the list of DbSamples if not null.public void setDbSampleList(DbSample[] aDbSamplesListDB, java.lang.String[] aSampleNamesDB)
dbSamplesList
- is the list of DbSamples if not null.sampleNames
- is the list of sample string names if not nullpublic void setDbSampleList(DbSample[] aDbSamplesListDB)
dbSamplesListDB
- is the list of DbSamples if not null.public void setLMsetDebugging(int dBugLMsetNumber)
dBugLMsetNumber
- is the debug LMset numberpublic void setRspotDebugging(int dBugRspotNumber)
dBugRspotNumber
- is the debug spot numberpublic void setPspotDebugging(int dBugPspotNumber)
dBugPspotNumber
- is the debug spot numberpublic void setSampleDebugging(int dBugSampleNumber)
dBugSampleNumber
- is the debug spot numberpublic boolean rightSize()
public boolean removeSPFandSSFSpotListsCSD()
public java.lang.String toXML()
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