org.biojava.bio.structure.align.ce
public class CeParameters extends java.lang.Object implements ConfigStrucAligParams
Modifier and Type | Field and Description |
---|---|
static int |
CA_AND_SIDE_CHAIN_ANGLE_SCORING |
protected static double |
DEFAULT_GAP_EXTENSION |
protected static double |
DEFAULT_GAP_OPEN |
protected static double |
DEFAULT_oRmsdThr |
static int |
DEFAULT_SCORING_STRATEGY |
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 |
static java.lang.String |
SCORING_STRATEGY |
protected int |
scoringStrategy |
static int |
SEQUENCE_CONSERVATION |
protected double |
seqWeight |
protected boolean |
showAFPRanges |
static int |
SIDE_CHAIN_ANGLE_SCORING |
static int |
SIDE_CHAIN_SCORING |
protected int |
sideChainScoringType |
protected SubstitutionMatrix<AminoAcidCompound> |
substitutionMatrix |
protected int |
winSize |
Constructor and Description |
---|
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
|
java.lang.Integer |
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(java.lang.Integer 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
public static final int DEFAULT_SCORING_STRATEGY
public static final int SIDE_CHAIN_SCORING
public static final int SIDE_CHAIN_ANGLE_SCORING
public static final int CA_AND_SIDE_CHAIN_ANGLE_SCORING
public static final int SEQUENCE_CONSERVATION
public static final java.lang.String SCORING_STRATEGY
protected int 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 java.lang.Integer getScoringStrategy()
public void setScoringStrategy(java.lang.Integer 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
-