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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDfilterState
public class CSDfilterState
Class CSDfilterState contains the state for a named data filter parameter subset. This is a data-mining filter state search of the Composite Samples Database (CSD).
[TODO] make dynamic using hash tables instead of fixed index values. [TODO] add capability for dynamic Java plugins and RLO R-plugins to do the data filtering. Use CSDlimits stats.
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 java.util.Hashtable |
filterHash
hashTable for filter lookup |
static int |
LB
Lower bound index constant |
CSDlimits |
limits
|
boolean |
mappingModeFlag
using Rspot name mapping to foreign Fspot mapping |
java.lang.String |
name
Name of the data-mining filter state |
CSDnorm |
norm
current density normalization mode |
static int |
PAIRBIT_AP
Pairing-bit Sure-Pair AP |
static int |
PAIRBIT_CP
Pairing-bit Sure-Pair CP |
static int |
PAIRBIT_EP
Pairing-bit Sure-Pair EP |
static int |
PAIRBIT_GS
Pairing-bit Sure-Pair GS |
static int |
PAIRBIT_LM
Pairing-bit Sure-Pair LM |
static int |
PAIRBIT_PP
Pairing-bit Sure-Pair PP |
static int |
PAIRBIT_SP
Pairing-bit Sure-Pair SP |
static int |
PAIRBIT_US
Pairing-bit Sure-Pair US |
int |
pairingBits
spot pair label bits: from DbLM.PAIRBIT_xx where xx is US, SP, PP, AP, EP, CP, GS, LM. |
java.lang.String |
timeStamp
|
java.lang.String |
title
title information of data-mining filter state. |
static int |
UB
Upper bound index constant |
static java.lang.String |
VERSION
Version for this module |
CSDcond |
wrkSamples
list of samples in the working set of samples |
Constructor Summary | |
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CSDfilterState()
CSDfilterState() - Constructor for new CSDfilterState. |
Method Summary | |
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boolean |
chkPairingBits(CSDRspot r)
chkPairingBits() - test the pairing bits agains the Rspot. |
boolean |
chkPairingBits(CSDRspotList rsl)
chkPairingBits() - test the pairing bits agains the list of Rspots. |
int |
clearPairingBit(int pairCode)
clearPairingBit() - clear the search pairing bit |
int |
cvPairCode2PairingBit(int pairCode)
cvPairCode2PairingBit() - set the search pairing bit |
int |
getPairingBit()
getPairingBit() - get the search pairing bits |
static java.lang.String |
getPairingBitStr(int pairingBits)
getPairingBitStr() - get the search pairing bits as a string |
int |
setPairingBit(int pairCode)
setPairingBit() - set the search pairing bit |
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 |
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 |
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 final int LB
public static final int UB
public static final int PAIRBIT_SP
public static final int PAIRBIT_PP
public static final int PAIRBIT_AP
public static final int PAIRBIT_US
public static final int PAIRBIT_EP
public static final int PAIRBIT_CP
public static final int PAIRBIT_GS
public static final int PAIRBIT_LM
public java.lang.String name
public java.lang.String timeStamp
public java.lang.String title
public static java.util.Hashtable filterHash
public boolean mappingModeFlag
public int pairingBits
public CSDlimits limits
public CSDcond wrkSamples
public CSDnorm norm
Constructor Detail |
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public CSDfilterState()
Method Detail |
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public int setPairingBit(int pairCode)
pairCode
- to use in setting the pairing bit
public int clearPairingBit(int pairCode)
pairCode
- to use in clearing the pairing bit
public int cvPairCode2PairingBit(int pairCode)
pairCode
- to use in clearing the pairing bit
public int getPairingBit()
public boolean chkPairingBits(CSDRspot r)
r
- is CSDRspot to test
public boolean chkPairingBits(CSDRspotList rsl)
r
- is CSDRspotList to test
public static java.lang.String getPairingBitStr(int pairingBits)
paringBits
- to convert
public java.lang.String toString()
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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