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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDlimits
public class CSDlimits
Class CSDlimits contains the sizing spot/Rspot set feature limits for the Composite Samples Database (CSD).
[TODO] refactor.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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float[] |
covAreaLimits
[LB:UB] COV area limits |
float[] |
covDensLimits
[LB:UB] COV density limits |
float[] |
densRangeDiffLimits
[LB:UB] (maxDensity-mnBkground) diff calibrated density limits/pixel |
float[] |
dLlimits
[LB:UB] dL limits |
float |
dLthr
Maximum threshold distance from spot-pair center to their corresponding landmark. |
float[] |
dPlimits
[LB:UB] dP limits |
float |
dPthr
Maximum threshold distance between spots in a spot-pair |
static int |
LB
Lower bound index constant |
static int |
LIMITS_COV_AREA
Sizing limits: coefficient of variation of area |
static int |
LIMITS_COV_DENSITY
Sizing limits: coefficient of variation of density |
static int |
LIMITS_DL
Sizing limits: dL |
static int |
LIMITS_DP
Sizing limits: dP |
static int |
LIMITS_MN_AREA
Sizing limits: mean area |
static int |
LIMITS_MN_DENS_RANGE
Sizing limits: mean density range (maxdensity-bkgrd density)/pixel |
static int |
LIMITS_MN_DENSITY
Sizing limits: mean density |
static int |
LIMITS_MW
Sizing limits: MW |
static int |
LIMITS_MZ
Sizing limits: MZ (2D-LC-MS) |
static int |
LIMITS_N_SAMPLES_PER_COND
Sizing limits: # of samples/condition (minimum) |
static int |
LIMITS_P_VALUE
Sizing limits: pValue |
static int |
LIMITS_PIE
|
static int |
LIMITS_REL_DIST
Sizing limits: relative distance from the landmark indicating that the pairing has more certainty if closer. |
static int |
LIMITS_RT
Sizing limits: RT (retention time 2D LC-MS) |
float[] |
mnAreaLimits
[LB:UB] mean area limits |
float[] |
mnDensLimits
[LB:UB] mean density limits |
float[] |
mwLimits
[LB:UB] mw (y) region limits |
float[] |
mzLimits
[LB:UB] mz (2D LC-MS) (y) region limits |
float[] |
nSampleLimits
[LB:UB] # samples/class |
float[] |
pieLimits
[LB:UB] pIe (x) region limits |
float[] |
pValueLimit
PREFILTER: continus p-value limits |
float[] |
relDistLimits
[LB:UB] relative distance limits |
float[] |
rtLimits
[LB:UB] retention time (2D LC-MS) (x) region limits |
int |
sizingBits
|
static int |
UB
Upper bound index constant |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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CSDlimits()
CSDlimits() - Constructor for new CSDlimits. |
Method Summary | |
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boolean |
chkPspotLimits(DbPspot pSpot)
chkPspotLimits() - check a DbPspot's Sample values for MW, pIe, (or RT, MZ) area, density (D'), density range, dP and dL limits. |
boolean |
chkRspotLimits(CSDRspot rSpot)
chkRspotLimits() - check if all DbPspots in the Rspot set meet the Sample values for MW, pIe, area, density (D'), density range, dP and dL limits. |
int |
clearSizingBit(int sizingCode)
clearSizingBit() - clear the search sizing limits bit |
static java.lang.String |
getSizingBitStr(int sb)
getSizingBitStr() - get the search sizing limits bits as a string |
int |
setSizingBit(int sizingCode)
setSizingBit() - set the search sizing limits 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 LIMITS_PIE
public static final int LIMITS_MW
public static final int LIMITS_RT
public static final int LIMITS_MZ
public static final int LIMITS_DL
public static final int LIMITS_DP
public static final int LIMITS_REL_DIST
public static final int LIMITS_MN_AREA
public static final int LIMITS_MN_DENSITY
public static final int LIMITS_MN_DENS_RANGE
public static final int LIMITS_COV_AREA
public static final int LIMITS_COV_DENSITY
public static final int LIMITS_N_SAMPLES_PER_COND
public static final int LIMITS_P_VALUE
public int sizingBits
public float[] pieLimits
public float[] mwLimits
public float[] rtLimits
public float[] mzLimits
public float[] dLlimits
public float[] dPlimits
public float[] relDistLimits
public float[] mnAreaLimits
public float[] mnDensLimits
public float[] densRangeDiffLimits
public float[] covAreaLimits
public float[] covDensLimits
public float[] nSampleLimits
public float[] pValueLimit
public float dPthr
public float dLthr
Constructor Detail |
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public CSDlimits()
Method Detail |
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public boolean chkPspotLimits(DbPspot pSpot)
pSpot
- to check
public boolean chkRspotLimits(CSDRspot rSpot)
rSpot
- to check
public int setSizingBit(int sizingCode)
sizingCode
- to use in setting the sizing limits bit
public int clearSizingBit(int sizingCode)
sizingCode
- to use in clearing the sizing limits bit
public static java.lang.String getSizingBitStr(int sb)
sb
- is sizing bits 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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