public class CeParameters extends java.lang.Object implements ConfigStrucAligParams
Modifier and Type | Class and Description |
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static class |
CeParameters.ScoringStrategy |
Modifier and Type | Field and Description |
---|---|
protected static double |
DEFAULT_GAP_EXTENSION |
protected static double |
DEFAULT_GAP_OPEN |
protected static double |
DEFAULT_oRmsdThr |
protected static double |
DISTANCE_INCREMENT |
protected double |
distanceIncrement |
protected double |
gapExtension |
protected double |
gapOpen |
protected int |
maxGapSize |
protected int |
maxNrIterationsForOptimization |
protected double |
maxOptRMSD |
protected double |
oRmsdThr |
protected double |
rmsdThr |
protected double |
rmsdThrJoin |
protected CeParameters.ScoringStrategy |
scoringStrategy |
protected double |
seqWeight |
protected boolean |
showAFPRanges |
protected int |
sideChainScoringType |
protected SubstitutionMatrix<AminoAcidCompound> |
substitutionMatrix |
protected int |
winSize |
Constructor and Description |
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CeParameters() |
Modifier and Type | Method and Description |
---|---|
java.lang.Double |
getDistanceIncrement() |
java.lang.Double |
getGapExtension() |
java.lang.Double |
getGapOpen() |
java.lang.Integer |
getMaxGapSize()
the Max gap size parameter G .
|
int |
getMaxNrIterationsForOptimization()
Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
|
java.lang.Double |
getMaxOptRMSD()
Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
|
java.lang.Double |
getORmsdThr()
Get the Original RMSD threshold from which the alignment optimization is started
|
java.lang.Double |
getRmsdThr()
RMSD Threshold
|
java.lang.Double |
getRmsdThrJoin()
RMSD threshold for joining of AFPs
|
CeParameters.ScoringStrategy |
getScoringStrategy() |
double |
getSeqWeight()
Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
|
SubstitutionMatrix<AminoAcidCompound> |
getSubstitutionMatrix()
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
|
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.Integer |
getWinSize()
The window size to look at
|
boolean |
isShowAFPRanges() |
void |
reset()
Set the parameters to the default.
|
void |
setDistanceIncrement(java.lang.Double distanceIncrement) |
void |
setGapExtension(java.lang.Double gapExtension) |
void |
setGapOpen(java.lang.Double gapOpen) |
void |
setMaxGapSize(java.lang.Integer maxGapSize)
Set the Max gap size parameter.
|
void |
setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization)
Set the maximum nr of times the (slow) optimiziation of alignment should iterate.
|
void |
setMaxOptRMSD(java.lang.Double param)
set the maximum RMSD cutoff to be applied during alignment optimization.
|
void |
setORmsdThr(java.lang.Double oRmsdThr)
Set the Original RMSD threshold from which the alignment optimization is started
|
void |
setRmsdThr(java.lang.Double rmsdThr) |
void |
setRmsdThrJoin(java.lang.Double rmsdThrJoin) |
void |
setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)
Set the scoring strategy to use.
|
void |
setSeqWeight(double seqWeight)
Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
|
void |
setShowAFPRanges(boolean showAFPRanges) |
void |
setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)
Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
|
void |
setWinSize(java.lang.Integer winSize) |
java.lang.String |
toString() |
protected int winSize
protected double rmsdThr
protected double rmsdThrJoin
protected double maxOptRMSD
protected CeParameters.ScoringStrategy scoringStrategy
protected int maxGapSize
protected boolean showAFPRanges
protected int sideChainScoringType
protected static final double DEFAULT_GAP_OPEN
protected static final double DEFAULT_GAP_EXTENSION
protected static final double DISTANCE_INCREMENT
protected static final double DEFAULT_oRmsdThr
protected double gapOpen
protected double gapExtension
protected double distanceIncrement
protected double oRmsdThr
protected int maxNrIterationsForOptimization
protected SubstitutionMatrix<AminoAcidCompound> substitutionMatrix
protected double seqWeight
public java.lang.String toString()
toString
in class java.lang.Object
public void reset()
ConfigStrucAligParams
reset
in interface ConfigStrucAligParams
public java.lang.Integer getWinSize()
public void setWinSize(java.lang.Integer winSize)
public java.lang.Double getRmsdThr()
public void setRmsdThr(java.lang.Double rmsdThr)
public java.lang.Double getRmsdThrJoin()
public void setRmsdThrJoin(java.lang.Double rmsdThrJoin)
public CeParameters.ScoringStrategy getScoringStrategy()
public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)
scoringStrategy
- public void setMaxGapSize(java.lang.Integer maxGapSize)
maxGapSize
- public java.lang.Integer getMaxGapSize()
public java.util.List<java.lang.String> getUserConfigHelp()
ConfigStrucAligParams
getUserConfigHelp
in interface ConfigStrucAligParams
public java.util.List<java.lang.String> getUserConfigParameters()
ConfigStrucAligParams
getUserConfigParameters
in interface ConfigStrucAligParams
public java.util.List<java.lang.String> getUserConfigParameterNames()
ConfigStrucAligParams
getUserConfigParameterNames
in interface ConfigStrucAligParams
public java.util.List<java.lang.Class> getUserConfigTypes()
ConfigStrucAligParams
getUserConfigTypes
in interface ConfigStrucAligParams
public boolean isShowAFPRanges()
public void setShowAFPRanges(boolean showAFPRanges)
public void setMaxOptRMSD(java.lang.Double param)
param
- maxOptRMSDpublic java.lang.Double getMaxOptRMSD()
public java.lang.Double getGapOpen()
public void setGapOpen(java.lang.Double gapOpen)
public java.lang.Double getGapExtension()
public void setGapExtension(java.lang.Double gapExtension)
public java.lang.Double getDistanceIncrement()
public void setDistanceIncrement(java.lang.Double distanceIncrement)
public java.lang.Double getORmsdThr()
public void setORmsdThr(java.lang.Double oRmsdThr)
oRmsdThr
- the thresholdpublic int getMaxNrIterationsForOptimization()
maxNrIterationsForOptimization
- public void setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization)
maxNrIterationsForOptimization
- public double getSeqWeight()
public void setSeqWeight(double seqWeight)
seqWeight
- the weight factor (default 0)public SubstitutionMatrix<AminoAcidCompound> getSubstitutionMatrix()
public void setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)
substitutionMatrix
-