Package org.biojava.nbio.structure.align.ce

Class OptimalCECPParameters

java.lang.Object

org.biojava.nbio.structure.align.ce.CeParameters

org.biojava.nbio.structure.align.ce.OptimalCECPParameters

All Implemented Interfaces:

ConfigStrucAligParams

public class OptimalCECPParameters
extends CeParameters

Contains the parameters that can be sent to CE

Author:

Andreas Prlic

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.align.ce.CeParameters

CeParameters.ScoringStrategy

Field Summary

Fields

Modifier and Type	Field	Description
protected java.lang.Integer	cpPoint	The CP point, specified as a residue index
protected java.lang.Boolean	tryAllCPs	If true, ignores cpPoint and tries all possible cp points.

Fields inherited from class org.biojava.nbio.structure.align.ce.CeParameters

DEFAULT_GAP_EXTENSION, DEFAULT_GAP_OPEN, DEFAULT_oRmsdThr, DEFAULT_SUBSTITUTION_MATRIX, DISTANCE_INCREMENT, distanceIncrement, gapExtension, gapOpen, maxGapSize, maxNrIterationsForOptimization, maxOptRMSD, oRmsdThr, rmsdThr, rmsdThrJoin, scoringStrategy, seqWeight, showAFPRanges, sideChainScoringType, substitutionMatrix, winSize

Constructor Summary

Constructors

Constructor	Description
OptimalCECPParameters()

Method Summary

Modifier and Type	Method	Description
java.lang.Integer	getCPPoint()
java.util.List<java.lang.String>	getUserConfigHelp()	The help text for each of these parameters.
java.util.List<java.lang.String>	getUserConfigParameterNames()	The labels to be displayed to the user for each parameter
java.util.List<java.lang.String>	getUserConfigParameters()	get the list of parameters that the user can change through the user interface.
java.util.List<java.lang.Class>	getUserConfigTypes()	Get the data types of the parameters
java.lang.Boolean	isTryAllCPs()
void	reset()	Set the parameters to the default.
void	setCPPoint(java.lang.Integer cpPoint)
void	setTryAllCPs(java.lang.Boolean tryAllCPs)
java.lang.String	toString()

Methods inherited from class org.biojava.nbio.structure.align.ce.CeParameters

getDistanceIncrement, getGapExtension, getGapOpen, getMaxGapSize, getMaxNrIterationsForOptimization, getMaxOptRMSD, getORmsdThr, getRmsdThr, getRmsdThrJoin, getScoringStrategy, getSeqWeight, getSubstitutionMatrix, getWinSize, isOptimizeAlignment, isShowAFPRanges, setDistanceIncrement, setGapExtension, setGapOpen, setMaxGapSize, setMaxNrIterationsForOptimization, setMaxOptRMSD, setOptimizeAlignment, setORmsdThr, setRmsdThr, setRmsdThrJoin, setScoringStrategy, setSeqWeight, setShowAFPRanges, setSubstitutionMatrix, setWinSize

Methods inherited from class java.lang.Object

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

Field Detail

tryAllCPs

protected java.lang.Boolean tryAllCPs

If true, ignores cpPoint and tries all possible cp points.

cpPoint

protected java.lang.Integer cpPoint

The CP point, specified as a residue index

TODO make this a ResidueNumber

Constructor Detail

OptimalCECPParameters

public OptimalCECPParameters()

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class CeParameters

reset

public void reset()

Description copied from interface: ConfigStrucAligParams

Set the parameters to the default.

Specified by:

reset in interface ConfigStrucAligParams

Overrides:

reset in class CeParameters

getUserConfigHelp

public java.util.List<java.lang.String> getUserConfigHelp()

Description copied from interface: ConfigStrucAligParams

The help text for each of these parameters.

Specified by:

getUserConfigHelp in interface ConfigStrucAligParams

Overrides:

getUserConfigHelp in class CeParameters

Returns:

help strings

getUserConfigParameters

public java.util.List<java.lang.String> getUserConfigParameters()

Description copied from interface: ConfigStrucAligParams

get the list of parameters that the user can change through the user interface. Parameter names are the same names as the corresponding Get/Set methods.

Specified by:

getUserConfigParameters in interface ConfigStrucAligParams

Overrides:

getUserConfigParameters in class CeParameters

Returns:

list of parameters

getUserConfigParameterNames

public java.util.List<java.lang.String> getUserConfigParameterNames()

Description copied from interface: ConfigStrucAligParams

The labels to be displayed to the user for each parameter

Specified by:

getUserConfigParameterNames in interface ConfigStrucAligParams

Overrides:

getUserConfigParameterNames in class CeParameters

Returns:

list of parameter names

getUserConfigTypes

public java.util.List<java.lang.Class> getUserConfigTypes()

Description copied from interface: ConfigStrucAligParams

Get the data types of the parameters

Specified by:

getUserConfigTypes in interface ConfigStrucAligParams

Overrides:

getUserConfigTypes in class CeParameters

Returns:

list of parameter classes

isTryAllCPs

public java.lang.Boolean isTryAllCPs()

Returns:

Whether we should try all CP sites

setTryAllCPs

public void setTryAllCPs(java.lang.Boolean tryAllCPs)

Parameters:

tryAllCPs - Set whether we should try all CP sites

getCPPoint

public java.lang.Integer getCPPoint()

Returns:

the cpPoint

setCPPoint

public void setCPPoint(java.lang.Integer cpPoint)

Parameters:

cpPoint - the cpPoint to set