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java.lang.Objectorg.biojava.bio.structure.align.ce.CeParameters
org.biojava.bio.structure.align.ce.OptimalCECPParameters
public class OptimalCECPParameters
Contains the parameters that can be sent to CE
Field Summary | |
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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 |
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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 | |
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OptimalCECPParameters()
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Method Summary | |
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected Boolean tryAllCPs
cpPoint
and tries all possible cp points.
protected Integer cpPoint
TODO make this a ResidueNumber
protected OptimalCECPParameters params
Constructor Detail |
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public OptimalCECPParameters()
Method Detail |
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public String toString()
toString
in class CeParameters
public void reset()
ConfigStrucAligParams
reset
in interface ConfigStrucAligParams
reset
in class CeParameters
public List<String> getUserConfigHelp()
ConfigStrucAligParams
getUserConfigHelp
in interface ConfigStrucAligParams
getUserConfigHelp
in class CeParameters
public List<String> getUserConfigParameters()
ConfigStrucAligParams
getUserConfigParameters
in interface ConfigStrucAligParams
getUserConfigParameters
in class CeParameters
public List<String> getUserConfigParameterNames()
ConfigStrucAligParams
getUserConfigParameterNames
in interface ConfigStrucAligParams
getUserConfigParameterNames
in class CeParameters
public List<Class> getUserConfigTypes()
ConfigStrucAligParams
getUserConfigTypes
in interface ConfigStrucAligParams
getUserConfigTypes
in class CeParameters
public Boolean isTryAllCPs()
public void setTryAllCPs(Boolean tryAllCPs)
tryAllCPs
- Set whether we should try all CP sitespublic Integer getCPPoint()
public void setCPPoint(Integer cpPoint)
cpPoint
- the cpPoint to set
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