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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDexpr
public class CSDexpr
Class CSDexpr contains an expression profile vector data for the Composite Samples Database (CSD).
The mapping of samples to columns in the vector is by idxSampleList[0:nSamples-1]. There are 2 variants: raw data in expRawValues[0:nSamples-1] normalized data in expValues[0:nSamples-1]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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float[] |
expRawValues
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float[] |
expValues
|
int[] |
idxSampleList
|
int |
maxSamples
maximum size of the preallocated arrays |
CSDnorm |
normMethod
Normalization method used to compute the expValues[] |
int |
normMode
Normalization method which is CSDnorm.NORM_PCT_xxxx |
int |
nSamples
size of the dbSamples |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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CSDexpr()
CSDexpr() - Constructor for new CSDexpr. |
Method Summary | |
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void |
clear()
clear() - clear object list |
static java.lang.String |
getTabDelimitedFields()
getTabDelimitedFields() - get a string representation of the tab-delimited data fields |
void |
init(int size)
init() - initialize expression list to specified size if > 0. |
boolean |
regrow(int newSize)
regrow() - increase the size of the expression list |
boolean |
rightSize()
rightSize() - right-size the size of the expression list to the size actually used. |
java.lang.String |
toBriefXML()
toBriefXML() - get a brief string representation of this instance as XML. |
java.lang.String |
toFullXML()
toFullXML() - get a full string representation of this instance as XML. |
java.lang.String |
toString()
toString() - print normalized values for the expression list. |
java.lang.String |
toString(boolean useRawExprValuesFlag)
toString() - print values for the expression list - either raw or normalized values. |
java.lang.String |
toTabDelimitedData()
toTabDelimitedData() - get a string representation of this instance as tab-delimited data values |
java.lang.String |
toXML()
toXML() - get a full string representation of this instance as XML. |
java.lang.String |
toXML(boolean useFullFlag)
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 int maxSamples
public int nSamples
public int[] idxSampleList
public int normMode
public CSDnorm normMethod
public float[] expRawValues
public float[] expValues
Constructor Detail |
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public CSDexpr()
Method Detail |
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public void clear()
clear
in interface CSDlistInterface
public void init(int size)
init
in interface CSDlistInterface
size
- 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 java.lang.String toString()
toString
in interface CSDlistInterface
toString
in class java.lang.Object
public java.lang.String toString(boolean useRawExprValuesFlag)
useRawExprValuesFlag
- to print raw values else normalized values
public static java.lang.String getTabDelimitedFields()
public java.lang.String toTabDelimitedData()
public java.lang.String toBriefXML()
public java.lang.String toFullXML()
public java.lang.String toXML()
public java.lang.String toXML(boolean useFullFlag)
useFullFlag
- add full details else just brief summary
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