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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDexprList
public class CSDexprList
Class CSDexprListList contains a list of expression profiles (vectors) data for the Composite Samples Database (CSD).
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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CSDexpr[] |
epList
[0:nEPlist-1] list of expression profiles |
static int |
glbIdExprListCounter
Global expression list ID counter |
int |
idExprList
Expression list id for this instance |
int[] |
idxSampleList
List of indices [0:nEPlist-1] constituting the corresponding DbSamples for each entry in the Rspot set. |
int |
maxEPlist
the maximum number of expression profiles in list if any. |
java.lang.String |
name
Name of expression profile list |
int |
nEPlist
the actual number of expression profiles in list if any. |
int |
nSamples
# of samples in condition. |
java.lang.String |
timeStamp
|
java.lang.String |
title
title information of expression profile. |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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CSDexprList()
CSDexprList() - Constructor for new CSDexprList. |
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CSDexprList(java.lang.String name,
java.lang.String timeStamp,
java.lang.String title)
CSDexprList() - Constructor for new CSDexprList. |
Method Summary | |
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boolean |
addExpr(CSDexpr dbE)
addExpr() - add Expr to ExprList. |
void |
clear()
clear() - clear the expression list |
CSDexprList |
cloneExprList()
cloneExprList() - make a cloned copy of an ExprList. |
CSDexprList |
difference(CSDexprList r1,
CSDexprList r2)
difference() - do the intersection of two ExprList lists r3= difference(r1,r2). |
CSDexpr[] |
getExprList()
getExprList() - get the list of Expression listS |
void |
init(int maxEPlist)
init() - initialize list of expression lists to specified size if > 0. |
CSDexprList |
intersection(CSDexprList r1,
CSDexprList r2)
intersection() - do the intersection of two ExprList lists r3= intersection(r1,r2). |
int |
lookupIdxByRspot(CSDexpr dbE)
lookupIdxByRspot() - lookup index of Rspot object in ExprList. |
boolean |
regrow(int newSize)
regrow() - increase the size of the expression lists |
boolean |
regrowExprList(int newSize)
regrowExprList() - grow the ExprList. |
boolean |
rightSize()
rightSize() - right-size the size of the list of expression lists to the size actually used. |
boolean |
rmvExpr(CSDexpr dbE)
rmvExpr() - remove Rspot from ExprList. |
java.lang.String |
toString()
toString() - print the list of expressions values in the list of expression lists. |
java.lang.String |
toTabDelimitedData()
toTabDelimitedData() - get a string representation of this instance as tab-delimited data values |
java.lang.String |
toTabDelimitedFields()
toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields |
java.lang.String |
toXML()
toXML() - get a string representation of this instance as XML |
CSDexprList |
union(CSDexprList r1,
CSDexprList r2)
union() - do the union of two ExprList lists r3= union(r1,r2). |
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 glbIdExprListCounter
public java.lang.String name
public java.lang.String timeStamp
public java.lang.String title
public int idExprList
public int nSamples
public int[] idxSampleList
public int nEPlist
public int maxEPlist
public CSDexpr[] epList
Constructor Detail |
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public CSDexprList()
public CSDexprList(java.lang.String name, java.lang.String timeStamp, java.lang.String title)
name
- of the expression listtimeStamp
- when the expression listtitle
- information of expression list .Method Detail |
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public void clear()
clear
in interface CSDlistInterface
public void init(int maxEPlist)
init
in interface CSDlistInterface
maxEPlist
- to initialize size of the maximum listpublic boolean regrow(int newSize)
regrow
in interface CSDlistInterface
newSize
- is new size of the list
public boolean rightSize()
rightSize
in interface CSDlistInterface
public boolean regrowExprList(int newSize)
newSize
- of the ExprList list
public boolean addExpr(CSDexpr dbE)
dbE
- is Expr object (may be null)
public int lookupIdxByRspot(CSDexpr dbE)
dbE
- is Expr object
public boolean rmvExpr(CSDexpr dbE)
dbE
- is Expr object
public CSDexprList cloneExprList()
dbR
- is Rspot object
public CSDexprList intersection(CSDexprList r1, CSDexprList r2)
r1
- is ExprListr2
- is ExprList
public CSDexprList union(CSDexprList r1, CSDexprList r2)
r1
- is ExprListr2
- is ExprList
public CSDexprList difference(CSDexprList r1, CSDexprList r2)
r1
- is ExprListr2
- is ExprList
public CSDexpr[] getExprList()
public java.lang.String toString()
toString
in interface CSDlistInterface
toString
in class java.lang.Object
public java.lang.String toTabDelimitedFields()
public java.lang.String toTabDelimitedData()
public java.lang.String toXML()
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