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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDio
public class CSDio
Class CSDio contains the I/O methods for the Composite Samples Database (CSD).
[TODO] Redo the paradigm to use CSDcache methods etc. Needs major refactoring to resolve old cgelp2 virtual paging of single page file with multiple paging files that are finally saved into the single CSD database.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/.
Field Summary | |
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int |
actualSubHeaders
actual# of CSD DB subheaders and it should be LEQ MAXSUBHEADERS. |
boolean |
corruptedFlag
normally set false. |
java.lang.String |
csdBINfile
full path CSD binary random access database file (.csd) |
java.io.RandomAccessFile |
csdFD
Random access file descriptor for the bindary CSD |
long |
csdLength
size of the file when opened |
java.lang.String |
csdRDBMSname
Name of the CSD RDBMS database |
java.lang.String |
csdURL
[FUTURE] optional URL path to relational database |
int |
firstERspot
Rspot index of first eRspot if not 0 |
int |
lastCacheBlock
last block in CSD cache file |
int |
maxSubHeaders
# of CSD DB subheaders and it should be equal to MAXSUBHEADERS |
int |
nbrRspotSets
# of R-spot sets (ie==> max file size) |
boolean |
readOnlyCSDflag
may not write CSD |
int |
rsetBlocks
# blocks/Rset - from nSamples, (multiple of #nodes/block). |
int |
rSpotBaseBlock
Base address of the Rspot Node part of the CSD DB |
static java.lang.String |
VERSION
Version for this module |
int |
zSpot
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Constructor Summary | |
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CSDio()
CSDio() - Constructor for new CSDio. |
Method Summary | |
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boolean |
closeCSD()
closeCSD() - flush the database and close it. |
boolean |
flushBinCSD()
flushBinCSD() - flush the CSD if it is open and clear the state. |
boolean |
openBinCSD(java.lang.String csdName,
java.lang.String csdBINfile,
boolean readOnlyFlag)
openBinCSD() - open a new CSD file. |
boolean |
setBinCSDfile(java.lang.String csdBINfile)
setBinCSDfile() - change the current CSD |
java.lang.String |
toString()
toString() - get a pretty-print string representation of this instance |
boolean |
writeCacheFiles(boolean useAnnotationFlag,
boolean useNormFlag)
writeCacheFiles() - Write out the CSD database as cache files into the csdCACHEfile file that should already be set up. |
boolean |
writeRDBMS(boolean useAnnotationFlag,
boolean useNormFlag)
writeRDBMS() - Write out the CSD database into the RDBMS using the the csdRDBMSfile file that should already be set up. |
java.lang.String[][] |
writeTabDelimitedFiles(boolean useAnnotationFlag,
boolean useNormFlag)
writeTabDelimitedFiles() - Write out the database as a set of tab-delimited files used the CSD database name as the prefix followed by the type of data followed by .txt. |
boolean |
writeXMLfile(boolean useAnnotationFlag,
boolean useNormFlag)
writeXMLfile() - Write out the CSD database as an XML file into the csdXMLfile file that should already be set up. |
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, wait, wait, wait |
Field Detail |
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public static final java.lang.String VERSION
public java.lang.String csdBINfile
public java.lang.String csdRDBMSname
public java.lang.String csdURL
public java.io.RandomAccessFile csdFD
public long csdLength
public boolean readOnlyCSDflag
public boolean corruptedFlag
public int zSpot
public int rsetBlocks
public int nbrRspotSets
public int firstERspot
public int lastCacheBlock
public int actualSubHeaders
public int maxSubHeaders
public int rSpotBaseBlock
Constructor Detail |
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public CSDio()
Method Detail |
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public boolean setBinCSDfile(java.lang.String csdBINfile)
csdBINfile
- is the full path name of the new CSD databasepublic boolean flushBinCSD()
public boolean closeCSD()
public boolean openBinCSD(java.lang.String csdName, java.lang.String csdBINfile, boolean readOnlyFlag)
csdName
- is the name of the new CSD databasecsdBINfile
- is the full path name of the new binary CSD databasereadOnlyFlag
- is true if read only, else read,write
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String[][] writeTabDelimitedFiles(boolean useAnnotationFlag, boolean useNormFlag)
useAnnotationFlag
- - to add annotation fieldsuseNormFlag
- - to add normalization fields
public boolean writeXMLfile(boolean useAnnotationFlag, boolean useNormFlag)
useAnnotationFlag
- - to add annotation fieldsuseNormFlag
- - to add normalization fields
public boolean writeCacheFiles(boolean useAnnotationFlag, boolean useNormFlag)
useAnnotationFlag
- - to add annotation fieldsuseNormFlag
- - to add normalization fields
public boolean writeRDBMS(boolean useAnnotationFlag, boolean useNormFlag)
useAnnotationFlag
- - to add annotation fieldsuseNormFlag
- - to add normalization fields
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