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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDcond
public class CSDcond
Class CSDcond contains a list of Samples for a condition set of samples for the Composite Samples Database (CSD).
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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static int |
glbIdCondCounter
Global Condition list ID counter |
int |
idCond
Condition list id for this instance |
int |
maxSamples
maximum # of samples in allocated condition list. |
java.lang.String |
name
Name of the condition |
int |
nSamples
# of samples in condition. |
DbSample[] |
sampleList
[0:nSamples-1] list of samples in condition. |
java.lang.String[] |
sampleNames
[0:nSamples-1] list of names of samples in condition. |
java.lang.String |
timeStamp
|
java.lang.String |
title
title information of condition. |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
---|---|
CSDcond()
CSDcond() - Constructor for new CSDcond with a cleared list. |
|
CSDcond(java.lang.String name,
java.lang.String timeStamp,
java.lang.String title)
CSDcond() - Constructor for new CSDcond with a cleared list. |
Method Summary | |
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boolean |
add(DbSample dbS)
add() - add sample to condition. |
boolean |
add(DbSample dbS,
java.lang.String sName)
add() - add sample to condition. |
boolean |
add(java.lang.String sName)
add() - add sample name to condition. |
void |
clear()
clear() - clear condition list |
CSDcond |
cloneIt()
cloneIt() - make a cloned copy of a condition. |
CSDcond |
difference(CSDcond r1,
CSDcond r2)
difference() - do the intersection of two condition lists r3= difference(r1,r2). |
java.lang.String[] |
getSampleNames()
getSampleNames() - get the list of sample namess |
DbSample[] |
getSamplesList()
getSampleList() - get the list of sample DbSample objects |
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 size)
init() - initialize Condition list to specified size if > 0. |
CSDcond |
intersection(CSDcond r1,
CSDcond r2)
intersection() - do the intersection of two condition lists r3= intersection(r1,r2). |
int |
lookupIdxBySample(DbSample dbS)
lookupIdxBySample() - lookup index of sample object in condition. |
int |
lookupIdxBySample(java.lang.String sName)
lookupIdxBySample() - lookup index of sample name in condition. |
boolean |
regrow(int newSize)
regrow() - grow the condition. |
boolean |
remove(DbSample dbS)
remove() - remove sample to condition. |
boolean |
remove(java.lang.String sName)
remove() - remove sample to condition. |
boolean |
rightSize()
rightSize() - right-size the size of the Condition list to the size actually used. |
void |
sort()
sort() - sort the condition set in ascending order by sample names |
java.lang.String |
toString()
toString() - print list of DbDsamples in the Condition list. |
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 |
CSDcond |
union(CSDcond r1,
CSDcond r2)
union() - do the union of two condition 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 glbIdCondCounter
public java.lang.String name
public java.lang.String timeStamp
public java.lang.String title
public int idCond
public int maxSamples
public int nSamples
public java.lang.String[] sampleNames
public DbSample[] sampleList
Constructor Detail |
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public CSDcond()
public CSDcond(java.lang.String name, java.lang.String timeStamp, java.lang.String title)
name
- of the condition list of SamplestimeStamp
- when the condition list of Samplestitle
- information of condition list of Samples.Method Detail |
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public void clear()
clear
in interface CSDlistInterface
public void init(int size)
init
in interface CSDlistInterface
maxSamples
- initialization sizepublic boolean rightSize()
rightSize
in interface CSDlistInterface
public boolean regrow(int newSize)
regrow
in interface CSDlistInterface
newSize
- of the condition list
public void sort()
public boolean add(DbSample dbS, java.lang.String sName)
dbS
- is sample objectsName
- is sample name
public boolean add(DbSample dbS)
dbS
- is sample object
public boolean add(java.lang.String sName)
sName
- is sample name
public int lookupIdxBySample(java.lang.String sName)
sName
- is sample name
public int lookupIdxBySample(DbSample dbS)
dbS
- is sample object
public boolean remove(java.lang.String sName)
sName
- is sample name
public boolean remove(DbSample dbS)
dbS
- is sample object
public CSDcond cloneIt()
dbR
- is Rspot object
public CSDcond intersection(CSDcond r1, CSDcond r2)
r1
- is conditionr2
- is condition
public CSDcond union(CSDcond r1, CSDcond r2)
r1
- is conditionr2
- is condition
public CSDcond difference(CSDcond r1, CSDcond r2)
r1
- is conditionr2
- is condition
public java.lang.String[] getSampleNames()
public DbSample[] getSamplesList()
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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