org.biojava.bio.structure.align.ce
Class OptimalCECPParameters

java.lang.Object
  extended by org.biojava.bio.structure.align.ce.CeParameters
      extended by org.biojava.bio.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

Field Summary
protected  Integer cpPoint
          The CP point, specified as a residue index
protected  OptimalCECPParameters params
           
protected  Boolean tryAllCPs
          If true, ignores cpPoint and tries all possible cp points.
 
Fields inherited from class org.biojava.bio.structure.align.ce.CeParameters
CA_AND_SIDE_CHAIN_ANGLE_SCORING, DEFAULT_GAP_EXTENSION, DEFAULT_GAP_OPEN, DEFAULT_oRmsdThr, DEFAULT_SCORING_STRATEGY, DISTANCE_INCREMENT, distanceIncrement, gapExtension, gapOpen, maxGapSize, maxNrIterationsForOptimization, maxOptRMSD, oRmsdThr, rmsdThr, rmsdThrJoin, SCORING_STRATEGY, scoringStrategy, SEQUENCE_CONSERVATION, seqWeight, showAFPRanges, SIDE_CHAIN_ANGLE_SCORING, SIDE_CHAIN_SCORING, sideChainScoringType, substitutionMatrix, winSize
 
Constructor Summary
OptimalCECPParameters()
           
 
Method Summary
 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.bio.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 Detail

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


params

protected OptimalCECPParameters params
Constructor Detail

OptimalCECPParameters

public OptimalCECPParameters()
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

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