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 Integer

cpPoint

The CP point, specified as a residue index

protected 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

Integer

getCPPoint()

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

Boolean

isTryAllCPs()

void

reset()

Set the parameters to the default.

void

setCPPoint(Integer cpPoint)

void

setTryAllCPs(Boolean tryAllCPs)

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, isShowAFPRanges, setDistanceIncrement, setGapExtension, setGapOpen, setMaxGapSize, setMaxNrIterationsForOptimization, setMaxOptRMSD, 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 Details
- tryAllCPs
  
  protected Boolean tryAllCPs
  
  If true, ignores cpPoint and tries all possible cp points.
- cpPoint
  
  protected Integer cpPoint
  
  The CP point, specified as a residue index
  TODO make this a ResidueNumber
Constructor Details
- OptimalCECPParameters
  
  public OptimalCECPParameters()
Method Details
- 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
- isTryAllCPs
  
  public Boolean isTryAllCPs()
  
  Returns:
  
  Whether we should try all CP sites
- setTryAllCPs
  
  public void setTryAllCPs(Boolean tryAllCPs)
  
  Parameters:
  
  tryAllCPs - Set whether we should try all CP sites
- getCPPoint
  
  public Integer getCPPoint()
  
  Returns:
  
  the cpPoint
- setCPPoint
  
  public void setCPPoint(Integer cpPoint)
  
  Parameters:
  
  cpPoint - the cpPoint to set

Class OptimalCECPParameters

Nested Class Summary

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

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Details

tryAllCPs

cpPoint

Constructor Details

OptimalCECPParameters

Method Details

toString

reset

getUserConfigHelp

getUserConfigParameters

getUserConfigParameterNames

getUserConfigTypes

isTryAllCPs

setTryAllCPs

getCPPoint

setCPPoint