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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDRmap
public class CSDRmap
Class CSDRmap contains the state Rmap information on the Composite Samples Database (CSD). It can be used to map Rspots in the Rsample to foreign spot ids and annotation..
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/.
Field Summary | |
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java.lang.String[] |
foreignSpotName
[0:nRmapSize-1] list of foreign spot names mapped by rspotNbr |
java.util.Hashtable |
foreignSpotName2RpotNbrHT
map of foreign spot name to Rspot set # |
static int |
glbIdRmapCounter
Global Rmap ID counter |
int |
idRmap
Rmap id for this instance |
boolean |
mapRspotToStdSpotFlag
false is standard Rspot mapping, true is standard Foreign Fspot mapping |
int |
maxRmapSize
The maximum # of spots in the preallocated map lists |
java.lang.String |
name
Name of the condition |
int |
nRmapSize
The # of spots in the map |
int[] |
rSampleSpotNbr2RspotNbr
[0:nRmapSize-1] map of Rsample spot number to the Rspot set idNbr. |
CSDannotation[] |
rspotNbr2Annotation
[0:nRmapSize-1] list of Rspot annotation objects if any. |
CSDRspot[] |
rspotNbr2Rspot
[0:nRmapSize-1] map of a number Rspot id number to the Rspot set object. |
java.lang.String |
timeStamp
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java.lang.String |
title
title information of condition. |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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CSDRmap()
CSDRmap() - Constructor for new CSDRmap. |
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CSDRmap(java.lang.String name,
java.lang.String timeStamp,
java.lang.String title)
CSDRmap() - Constructor for new CSDRmap. |
Method Summary | |
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boolean |
add(int rspotNbr,
CSDRspot rSpot,
java.lang.String fSpotName)
add() - add entry to the Rmap |
void |
clear()
clear() - clear Rmap |
boolean |
create(int nRmapSize)
create() - create the empty Rmap lists and hash tables of size nRmapSize |
static java.lang.String |
getTabDelimitedFields()
getTabDelimitedFields() - get a string representation of the tab-delimited data fields |
java.lang.String |
getTabDelimitedFieldsAndData()
getTabDelimitedFieldsAndData() - get a string representation of this instance as tab-delimited data fields and values. |
void |
init(int maxRmapSize)
init() - initialize Rmap list to specified size if > 0. |
boolean |
regrow(int newRmapSize)
regrow() - regrow the Rmap |
boolean |
remove(CSDRspot rSpot)
remove() - remove entry to the Rmap [TODO] |
boolean |
remove(java.lang.String fSpotName)
remove() - remove entry to the Rmap |
boolean |
rightSize()
rightSize() - right-size the size of the Rmap list to the size actually used. |
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 |
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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 static int glbIdRmapCounter
public java.lang.String name
public java.lang.String timeStamp
public java.lang.String title
public int idRmap
public boolean mapRspotToStdSpotFlag
public int nRmapSize
public int maxRmapSize
public CSDRspot[] rspotNbr2Rspot
public int[] rSampleSpotNbr2RspotNbr
public java.util.Hashtable foreignSpotName2RpotNbrHT
public java.lang.String[] foreignSpotName
public CSDannotation[] rspotNbr2Annotation
Constructor Detail |
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public CSDRmap()
public CSDRmap(java.lang.String name, java.lang.String timeStamp, java.lang.String title)
name
- of the RmaptimeStamp
- when the Rmaptitle
- information of RmapMethod Detail |
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public void clear()
clear
in interface CSDlistInterface
public void init(int maxRmapSize)
init
in interface CSDlistInterface
size
- to initialize size of the maximum listpublic boolean rightSize()
rightSize
in interface CSDlistInterface
public boolean create(int nRmapSize)
nRmapSize
- is # of Rspot sets in database
public boolean regrow(int newRmapSize)
regrow
in interface CSDlistInterface
newRmapSize
- is new # of Rspot sets in database
public boolean add(int rspotNbr, CSDRspot rSpot, java.lang.String fSpotName)
nRmapSize
- is # of Rspot sets in databaserSpot
- is Rspot to addfSpotName
- is foreign name of the rSpot
public boolean remove(CSDRspot rSpot)
rSpot
- is Rspot to remove
public boolean remove(java.lang.String fSpotName)
fSpotName
- is foreign name of the rSpot to remove
public java.lang.String toString()
toString
in interface CSDlistInterface
toString
in class java.lang.Object
public java.lang.String getTabDelimitedFieldsAndData()
public static java.lang.String getTabDelimitedFields()
public java.lang.String toTabDelimitedData()
public java.lang.String toXML()
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