starfish.chemistry
Class Noe

java.lang.Object
  starfish.chemistry.Noe

All Implemented Interfaces:

java.io.Serializable, Constraint

public class Noe
extends java.lang.Object
implements Constraint, java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface starfish.chemistry.Constraint

Constraint.GenTypes

Field Summary

double	atomScale
double	contribution
int	dcClass
double	disContrib
DistanceStat	disStat
DistanceStat	disStatAvg
DistanceRange	dRange
double	intensity
double	lower
double	netWorkValue
int	nPossible
starfish.datasets.peaks.Peak	peak
double	ppmError
java.util.Map	resMap
double	scale
SpatialSetGroup	spg1
SpatialSetGroup	spg2
boolean	symmetrical
double	upper
double	volume

Constructor Summary

Noe(starfish.datasets.peaks.Peak p, SpatialSetGroup spg1, SpatialSetGroup spg2, double newScale)

Noe(starfish.datasets.peaks.Peak p, SpatialSet sp1, SpatialSet sp2, double newScale)

Method Summary

void	activate(starfish.chemistry.Flags enumVal)
static double	avgDistance(java.util.ArrayList<java.lang.Double> dArray, double expValue, int nMonomers)
static java.util.HashMap<starfish.datasets.peaks.PeakList,java.lang.Double>	calcMedian(java.lang.String mMode, starfish.datasets.peaks.PeakList whichList)
static void	calculateContributions(boolean useDistances)
static void	calibrateExp(starfish.datasets.peaks.PeakList whichList)
static void	clearLimitToAssigned()
static void	clearScaleMap()
static NoeCalibration	defaultCal(starfish.datasets.peaks.PeakList peakList)
static void	findNetworks(boolean useContrib)
static void	findRedundant()
static void	findSymmetrical()
static Noe	get(int i)
int	getActive()
static NoeSet	getActiveSet()
java.lang.String	getActivityFlags()
static java.util.ArrayList<Noe>	getConstraints(boolean requireActive)
static java.util.ArrayList<Noe>	getConstraints(java.lang.String filter, boolean requireActive)
double	getDistance()
void	getElem(tcl.lang.Interp interp, java.lang.String elemName, tcl.lang.TclObject arg)
java.lang.String	getEntity(SpatialSetGroup spg)
Constraint.GenTypes	getGenType()
int	getID()
static int	getNStructures()
static java.util.ArrayList	getPeakList(starfish.datasets.peaks.Peak peak)
java.lang.String	getPeakListName()
int	getPeakNum()
static int	getSize()
SpatialSetGroup	getSPG(int setNum, boolean getSwapped, boolean filterMode)
DistanceStat	getStat()
double	getValue()
java.lang.String	getViolChars(DistanceStat dStat)
void	inactivate(starfish.chemistry.Flags enumVal)
static void	inactivateDiagonal()
boolean	isActive()
static boolean	isCalibratable()
static boolean	isDirty()
boolean	isUserActive()
static void	limitToAssigned(tcl.lang.Interp interp)
static void	limitToMaxAmbig(int maxVal)
static void	limitToMaxViol(double maxViol)
static void	limitToMinContrib(double minContrib)
static void	limitToMinPPMError(double minPPM)
static void	resetConstraints()
void	setActive(int newState)
static void	setActive(NoeSet noeSet)
static void	setCalibratable(boolean state)
static void	setDirty()
void	setGenType(Constraint.GenTypes genType)
static void	setScale(starfish.datasets.peaks.PeakList peakList, NoeCalibration noeCal)
java.lang.String	toSTARString()
static void	updateContributions(boolean useDistances)
static void	updateDistanceContribs()
static void	updateDistances()
static void	updateDistancesIndividual()
void	updateGenType(tcl.lang.Interp interp, java.util.Map<java.lang.String,starfish.chemistry.NoeCmd.NoeMatch> map, MatchCriteria[] matchCriteria)
static void	updateGenTypes(tcl.lang.Interp interp)
static void	updateNPossible(starfish.datasets.peaks.PeakList whichList)
void	updatePPMError(tcl.lang.Interp interp, MatchCriteria[] matchCriteria)
static void	updatePPMErrors(tcl.lang.Interp interp)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

spg1

public SpatialSetGroup spg1

spg2

public SpatialSetGroup spg2

peak

public starfish.datasets.peaks.Peak peak

intensity

public double intensity

volume

public double volume

scale

public double scale

atomScale

public double atomScale

disStat

public DistanceStat disStat

disStatAvg

public DistanceStat disStatAvg

lower

public double lower

upper

public double upper

dcClass

public int dcClass

ppmError

public double ppmError

symmetrical

public boolean symmetrical

contribution

public double contribution

disContrib

public double disContrib

dRange

public DistanceRange dRange

nPossible

public int nPossible

netWorkValue

public double netWorkValue

resMap

public java.util.Map resMap

Constructor Detail

Noe

public Noe(starfish.datasets.peaks.Peak p,
           SpatialSet sp1,
           SpatialSet sp2,
           double newScale)

Noe

public Noe(starfish.datasets.peaks.Peak p,
           SpatialSetGroup spg1,
           SpatialSetGroup spg2,
           double newScale)

Method Detail

getPeakList

public static java.util.ArrayList getPeakList(starfish.datasets.peaks.Peak peak)

getID

public int getID()

Specified by:

getID in interface Constraint

updatePPMError

public void updatePPMError(tcl.lang.Interp interp,
                           MatchCriteria[] matchCriteria)
                    throws tcl.lang.TclException

Throws:

tcl.lang.TclException

updatePPMErrors

public static void updatePPMErrors(tcl.lang.Interp interp)
                            throws tcl.lang.TclException

Throws:

tcl.lang.TclException

updateGenTypes

public static void updateGenTypes(tcl.lang.Interp interp)
                           throws tcl.lang.TclException

Throws:

tcl.lang.TclException

updateGenType

public void updateGenType(tcl.lang.Interp interp,
                          java.util.Map<java.lang.String,starfish.chemistry.NoeCmd.NoeMatch> map,
                          MatchCriteria[] matchCriteria)
                   throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getSPG

public SpatialSetGroup getSPG(int setNum,
                              boolean getSwapped,
                              boolean filterMode)

getNStructures

public static int getNStructures()

getViolChars

public java.lang.String getViolChars(DistanceStat dStat)

getStat

public DistanceStat getStat()

Specified by:

getStat in interface Constraint

setActive

public static void setActive(NoeSet noeSet)

getActiveSet

public static NoeSet getActiveSet()

getSize

public static int getSize()

resetConstraints

public static void resetConstraints()

isCalibratable

public static boolean isCalibratable()

setCalibratable

public static void setCalibratable(boolean state)

setDirty

public static void setDirty()

isDirty

public static boolean isDirty()

getConstraints

public static java.util.ArrayList<Noe> getConstraints(boolean requireActive)

getConstraints

public static java.util.ArrayList<Noe> getConstraints(java.lang.String filter,
                                                      boolean requireActive)

getPeakListName

public java.lang.String getPeakListName()

getPeakNum

public int getPeakNum()

updateContributions

public static void updateContributions(boolean useDistances)

get

public static Noe get(int i)

getElem

public void getElem(tcl.lang.Interp interp,
                    java.lang.String elemName,
                    tcl.lang.TclObject arg)
             throws tcl.lang.TclException

Throws:

tcl.lang.TclException

getEntity

public java.lang.String getEntity(SpatialSetGroup spg)

inactivateDiagonal

public static void inactivateDiagonal()

updateDistancesIndividual

public static void updateDistancesIndividual()

avgDistance

public static double avgDistance(java.util.ArrayList<java.lang.Double> dArray,
                                 double expValue,
                                 int nMonomers)

updateDistances

public static void updateDistances()

updateDistanceContribs

public static void updateDistanceContribs()

limitToAssigned

public static void limitToAssigned(tcl.lang.Interp interp)
                            throws tcl.lang.TclException

Throws:

tcl.lang.TclException

clearLimitToAssigned

public static void clearLimitToAssigned()

limitToMaxAmbig

public static void limitToMaxAmbig(int maxVal)

limitToMinContrib

public static void limitToMinContrib(double minContrib)

limitToMinPPMError

public static void limitToMinPPMError(double minPPM)

limitToMaxViol

public static void limitToMaxViol(double maxViol)

calcMedian

public static java.util.HashMap<starfish.datasets.peaks.PeakList,java.lang.Double> calcMedian(java.lang.String mMode,
                                                                                              starfish.datasets.peaks.PeakList whichList)

clearScaleMap

public static void clearScaleMap()

setScale

public static void setScale(starfish.datasets.peaks.PeakList peakList,
                            NoeCalibration noeCal)

defaultCal

public static NoeCalibration defaultCal(starfish.datasets.peaks.PeakList peakList)

calibrateExp

public static void calibrateExp(starfish.datasets.peaks.PeakList whichList)

updateNPossible

public static void updateNPossible(starfish.datasets.peaks.PeakList whichList)

findSymmetrical

public static void findSymmetrical()

calculateContributions

public static void calculateContributions(boolean useDistances)

findNetworks

public static void findNetworks(boolean useContrib)

findRedundant

public static void findRedundant()

isActive

public boolean isActive()

isUserActive

public boolean isUserActive()

Specified by:

isUserActive in interface Constraint

getActive

public int getActive()

setActive

public void setActive(int newState)

getActivityFlags

public java.lang.String getActivityFlags()

inactivate

public void inactivate(starfish.chemistry.Flags enumVal)

activate

public void activate(starfish.chemistry.Flags enumVal)

getDistance

public double getDistance()

Returns:

the distance

getValue

public double getValue()

Specified by:

getValue in interface Constraint

toSTARString

public java.lang.String toSTARString()

Specified by:

toSTARString in interface Constraint

getGenType

public Constraint.GenTypes getGenType()

Returns:

the genType

setGenType

public void setGenType(Constraint.GenTypes genType)

Parameters:

genType - the genType to set