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

Class CECPParameters

java.lang.Object

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

org.biojava.nbio.structure.align.ce.CECPParameters

All Implemented Interfaces:

ConfigStrucAligParams

public class CECPParameters
extends CeParameters

Provides parameters to CeCPMain

Author:

Spencer Bliven

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CECPParameters.DuplicationHint

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

CeParameters.ScoringStrategy

Field Summary

Fields

Modifier and Type	Field	Description
static int	DEFAULT_MIN_CP_LENGTH
protected CECPParameters.DuplicationHint	duplicationHint
protected Integer	minCPLength

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
CECPParameters()

Method Summary

Modifier and Type	Method	Description
CECPParameters.DuplicationHint	getDuplicationHint()
Integer	getMinCPLength()
List<String>	getUserConfigHelp()	The help text for each of these parameters.
List<String>	getUserConfigParameterNames()	The labels to be displayed to the user for each parameter
List<String>	getUserConfigParameters()	get the list of parameters that the user can change through the user interface.
List<Class>	getUserConfigTypes()	Get the data types of the parameters
void	reset()	Set the parameters to the default.
void	setDuplicationHint(CECPParameters.DuplicationHint duplicationHint)
void	setMinCPLength(Integer minCPLength)
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

DEFAULT_MIN_CP_LENGTH

public static final int DEFAULT_MIN_CP_LENGTH

See Also:

Constant Field Values

duplicationHint

protected CECPParameters.DuplicationHint duplicationHint

minCPLength

protected Integer minCPLength

Constructor Detail

CECPParameters

public CECPParameters()

Method Detail

toString

public 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 List<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 List<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 List<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 List<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

getDuplicationHint

public CECPParameters.DuplicationHint getDuplicationHint()

setDuplicationHint

public void setDuplicationHint(CECPParameters.DuplicationHint duplicationHint)

getMinCPLength

public Integer getMinCPLength()

setMinCPLength

public void setMinCPLength(Integer minCPLength)