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 enum

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 final 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, 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
- 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 Details
- CECPParameters
  
  public CECPParameters()
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
- getDuplicationHint
  
  public CECPParameters.DuplicationHint getDuplicationHint()
- setDuplicationHint
  
  public void setDuplicationHint(CECPParameters.DuplicationHint duplicationHint)
- getMinCPLength
  
  public Integer getMinCPLength()
- setMinCPLength
  
  public void setMinCPLength(Integer minCPLength)

Class CECPParameters

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

DEFAULT_MIN_CP_LENGTH

duplicationHint

minCPLength

Constructor Details

CECPParameters

Method Details

toString

reset

getUserConfigHelp

getUserConfigParameters

getUserConfigParameterNames

getUserConfigTypes

getDuplicationHint

setDuplicationHint

getMinCPLength

setMinCPLength