public class OptimalCECPParameters extends CeParameters
CeParameters.ScoringStrategy
Modifier and Type | Field and 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. |
DEFAULT_GAP_EXTENSION, DEFAULT_GAP_OPEN, DEFAULT_oRmsdThr, DISTANCE_INCREMENT, distanceIncrement, gapExtension, gapOpen, maxGapSize, maxNrIterationsForOptimization, maxOptRMSD, oRmsdThr, rmsdThr, rmsdThrJoin, scoringStrategy, seqWeight, showAFPRanges, sideChainScoringType, substitutionMatrix, winSize
Constructor and Description |
---|
OptimalCECPParameters() |
Modifier and Type | Method and 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() |
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
protected java.lang.Boolean tryAllCPs
cpPoint
and tries all possible cp points.protected java.lang.Integer cpPoint
TODO make this a ResidueNumber
public java.lang.String toString()
toString
in class CeParameters
public void reset()
ConfigStrucAligParams
reset
in interface ConfigStrucAligParams
reset
in class CeParameters
public java.util.List<java.lang.String> getUserConfigHelp()
ConfigStrucAligParams
getUserConfigHelp
in interface ConfigStrucAligParams
getUserConfigHelp
in class CeParameters
public java.util.List<java.lang.String> getUserConfigParameters()
ConfigStrucAligParams
getUserConfigParameters
in interface ConfigStrucAligParams
getUserConfigParameters
in class CeParameters
public java.util.List<java.lang.String> getUserConfigParameterNames()
ConfigStrucAligParams
getUserConfigParameterNames
in interface ConfigStrucAligParams
getUserConfigParameterNames
in class CeParameters
public java.util.List<java.lang.Class> getUserConfigTypes()
ConfigStrucAligParams
getUserConfigTypes
in interface ConfigStrucAligParams
getUserConfigTypes
in class CeParameters
public java.lang.Boolean isTryAllCPs()
public void setTryAllCPs(java.lang.Boolean tryAllCPs)
tryAllCPs
- Set whether we should try all CP sitespublic java.lang.Integer getCPPoint()
public void setCPPoint(java.lang.Integer cpPoint)
cpPoint
- the cpPoint to set