CeParameters (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.align.ce.CeParameters

All Implemented Interfaces:

ConfigStrucAligParams

Direct Known Subclasses:

CECPParameters, CESymmParameters, OptimalCECPParameters
```
public class CeParameters
extends Object
implements ConfigStrucAligParams
```
Contains the parameters that can be sent to CE

Author:

Andreas Prlic

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class CeParameters.ScoringStrategy

Nested Classes
Modifier and Type	Class and Description
`static class`	`CeParameters.ScoringStrategy`

Field Summary

Fields
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 String`	`DEFAULT_SUBSTITUTION_MATRIX`
`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 Summary

Constructors
Constructor and Description

CeParameters()

Constructors
Constructor and Description
`CeParameters()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Double`	`getDistanceIncrement()`
`Double`	`getGapExtension()`
`Double`	`getGapOpen()`
`Integer`	`getMaxGapSize()` the Max gap size parameter G . default is 30, which was described to obtained empirically in the CE paper.
`int`	`getMaxNrIterationsForOptimization()` Get the maximum nr of times the (slow) optimiziation of alignment should iterate.
`Double`	`getMaxOptRMSD()` Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
`Double`	`getORmsdThr()` Get the Original RMSD threshold from which the alignment optimization is started
`Double`	`getRmsdThr()` RMSD Threshold
`Double`	`getRmsdThrJoin()` RMSD threshold for joining of AFPs
`CeParameters.ScoringStrategy`	`getScoringStrategy()`
`double`	`getSeqWeight()` Should sequence conservation be considered as part of the alignment?
`SubstitutionMatrix<AminoAcidCompound>`	`getSubstitutionMatrix()` Sets the substitution matrix to be used for influencing the alignment with sequence conservation information.
`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
`Integer`	`getWinSize()` The window size to look at
`boolean`	`isOptimizeAlignment()` Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.
`boolean`	`isShowAFPRanges()`
`void`	`reset()` Set the parameters to the default.
`void`	`setDistanceIncrement(Double distanceIncrement)`
`void`	`setGapExtension(Double gapExtension)`
`void`	`setGapOpen(Double gapOpen)`
`void`	`setMaxGapSize(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(Double param)` set the maximum RMSD cutoff to be applied during alignment optimization.
`void`	`setOptimizeAlignment(boolean optimizeAlignment)` Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level.
`void`	`setORmsdThr(Double oRmsdThr)` Set the Original RMSD threshold from which the alignment optimization is started
`void`	`setRmsdThr(Double rmsdThr)`
`void`	`setRmsdThrJoin(Double rmsdThrJoin)`
`void`	`setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)` Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.
`void`	`setSeqWeight(double seqWeight)` Should sequence conservation be considered as part of the alignment?
`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(Integer winSize)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - winSize
```
protected int winSize
```
  - rmsdThr
```
protected double rmsdThr
```
  - rmsdThrJoin
```
protected double rmsdThrJoin
```
  - maxOptRMSD
```
protected double maxOptRMSD
```
  - scoringStrategy
```
protected CeParameters.ScoringStrategy scoringStrategy
```
  - maxGapSize
```
protected int maxGapSize
```
  - showAFPRanges
```
protected boolean showAFPRanges
```
  - sideChainScoringType
```
protected int sideChainScoringType
```
  - DEFAULT_GAP_OPEN
```
protected static final double DEFAULT_GAP_OPEN
```
    See Also:
    
    Constant Field Values
  - DEFAULT_GAP_EXTENSION
```
protected static final double DEFAULT_GAP_EXTENSION
```
    See Also:
    
    Constant Field Values
  - DISTANCE_INCREMENT
```
protected static final double DISTANCE_INCREMENT
```
    See Also:
    
    Constant Field Values
  - DEFAULT_oRmsdThr
```
protected static final double DEFAULT_oRmsdThr
```
    See Also:
    
    Constant Field Values
  - DEFAULT_SUBSTITUTION_MATRIX
```
protected static final String DEFAULT_SUBSTITUTION_MATRIX
```
    See Also:
    
    Constant Field Values
  - gapOpen
```
protected double gapOpen
```
  - gapExtension
```
protected double gapExtension
```
  - distanceIncrement
```
protected double distanceIncrement
```
  - oRmsdThr
```
protected double oRmsdThr
```
  - maxNrIterationsForOptimization
```
protected int maxNrIterationsForOptimization
```
  - substitutionMatrix
```
protected SubstitutionMatrix<AminoAcidCompound> substitutionMatrix
```
  - seqWeight
```
protected double seqWeight
```
- Constructor Detail
  - CeParameters
```
public CeParameters()
```
- Method Detail
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - reset
```
public void reset()
```
    Description copied from interface: ConfigStrucAligParams
    
    Set the parameters to the default.
    
    Specified by:
    
    reset in interface ConfigStrucAligParams
  - getWinSize
```
public Integer getWinSize()
```
    The window size to look at
    
    Returns:
    
    window size
  - setWinSize
```
public void setWinSize(Integer winSize)
```
  - getRmsdThr
```
public Double getRmsdThr()
```
    RMSD Threshold
    
    Returns:
    
    RMSD threshold
  - setRmsdThr
```
public void setRmsdThr(Double rmsdThr)
```
  - getRmsdThrJoin
```
public Double getRmsdThrJoin()
```
    RMSD threshold for joining of AFPs
    
    Returns:
    
    rmsd threshold
  - setRmsdThrJoin
```
public void setRmsdThrJoin(Double rmsdThrJoin)
```
  - getScoringStrategy
```
public CeParameters.ScoringStrategy getScoringStrategy()
```
  - setScoringStrategy
```
public void setScoringStrategy(CeParameters.ScoringStrategy scoringStrategy)
```
    Set the scoring strategy to use. 0 is default CE scoring scheme. 1 uses Side chain orientation.
    
    Parameters:
    
    scoringStrategy -
  - setMaxGapSize
```
public void setMaxGapSize(Integer maxGapSize)
```
    Set the Max gap size parameter. Default 30. For unlimited gaps set to -1
    
    Parameters:
    
    maxGapSize -
  - getMaxGapSize
```
public Integer getMaxGapSize()
```
    the Max gap size parameter G . default is 30, which was described to obtained empirically in the CE paper. the larger the max gap size, the longer the compute time, but in same cases drastically improved results. Set to -1 for unlimited gap size.
    
    Returns:
    
    max gap size parameter
  - getUserConfigHelp
```
public List<String> getUserConfigHelp()
```
    Description copied from interface: ConfigStrucAligParams
    
    The help text for each of these parameters.
    
    Specified by:
    
    getUserConfigHelp in interface ConfigStrucAligParams
    
    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
    
    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
    
    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
    
    Returns:
    
    list of parameter classes
  - isShowAFPRanges
```
public boolean isShowAFPRanges()
```
    Returns:
    
    whether information about AFPs should be printed
  - setShowAFPRanges
```
public void setShowAFPRanges(boolean showAFPRanges)
```
  - setMaxOptRMSD
```
public void setMaxOptRMSD(Double param)
```
    set the maximum RMSD cutoff to be applied during alignment optimization. (default: 99 = unlimited)
    
    Parameters:
    
    param - maxOptRMSD
  - getMaxOptRMSD
```
public Double getMaxOptRMSD()
```
    Returns the maximum RMSD cutoff to be applied during alignment optimization (default: 99 = unlimited)
    
    Returns:
    
    maxOptRMSD
  - getGapOpen
```
public Double getGapOpen()
```
  - setGapOpen
```
public void setGapOpen(Double gapOpen)
```
  - getGapExtension
```
public Double getGapExtension()
```
  - setGapExtension
```
public void setGapExtension(Double gapExtension)
```
  - getDistanceIncrement
```
public Double getDistanceIncrement()
```
  - setDistanceIncrement
```
public void setDistanceIncrement(Double distanceIncrement)
```
  - getORmsdThr
```
public Double getORmsdThr()
```
    Get the Original RMSD threshold from which the alignment optimization is started
    
    Returns:
    
    oRMSDThreshold
  - setORmsdThr
```
public void setORmsdThr(Double oRmsdThr)
```
    Set the Original RMSD threshold from which the alignment optimization is started
    
    Parameters:
    
    oRmsdThr - the threshold
  - getMaxNrIterationsForOptimization
```
public int getMaxNrIterationsForOptimization()
```
    Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
    
    Parameters:
    
    maxNrIterationsForOptimization -
  - setMaxNrIterationsForOptimization
```
public void setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization)
```
    Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
    
    Parameters:
    
    maxNrIterationsForOptimization -
  - getSeqWeight
```
public double getSeqWeight()
```
    Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.
    
    Returns:
    
    seqWeight the weight factor (default 0)
  - setSeqWeight
```
public void setSeqWeight(double seqWeight)
```
    Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much. By default this is set to 0, meaning no contribution of the sequence alignment score.
    
    Parameters:
    
    seqWeight - the weight factor (default 0)
  - getSubstitutionMatrix
```
public SubstitutionMatrix<AminoAcidCompound> getSubstitutionMatrix()
```
    Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)
    
    Returns:
    
    substitutionMatrix
  - setSubstitutionMatrix
```
public void setSubstitutionMatrix(SubstitutionMatrix<AminoAcidCompound> substitutionMatrix)
```
    Sets the substitution matrix to be used for influencing the alignment with sequence conservation information. Default: SDM matrix (Prlic et al 2000)
    
    Parameters:
    
    substitutionMatrix -
  - isOptimizeAlignment
```
public boolean isOptimizeAlignment()
```
    Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level. This is useful for edge cases with remote homology, but can be slow for large structures.
    
    Returns:
    
    optimizeAlignment
  - setOptimizeAlignment
```
public void setOptimizeAlignment(boolean optimizeAlignment)
```
    Whether the CE algorithm should extend the best found trace with dynamic programming, while keeping RMSD at about the same level. This is useful for edge cases with remote homology, but can be slow for large structures.
    
    Parameters:
    
    optimizeAlignment -

Class CeParameters

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

winSize

rmsdThr

rmsdThrJoin

maxOptRMSD

scoringStrategy

maxGapSize

showAFPRanges

sideChainScoringType

DEFAULT_GAP_OPEN

DEFAULT_GAP_EXTENSION

DISTANCE_INCREMENT

DEFAULT_oRmsdThr

DEFAULT_SUBSTITUTION_MATRIX

gapOpen

gapExtension

distanceIncrement

oRmsdThr

maxNrIterationsForOptimization

substitutionMatrix

seqWeight

Constructor Detail

CeParameters

Method Detail

toString

reset

getWinSize

setWinSize

getRmsdThr

setRmsdThr

getRmsdThrJoin

setRmsdThrJoin

getScoringStrategy

setScoringStrategy

setMaxGapSize

getMaxGapSize

getUserConfigHelp

getUserConfigParameters

getUserConfigParameterNames

getUserConfigTypes

isShowAFPRanges

setShowAFPRanges

setMaxOptRMSD

getMaxOptRMSD

getGapOpen

setGapOpen

getGapExtension

setGapExtension

getDistanceIncrement

setDistanceIncrement

getORmsdThr

setORmsdThr

getMaxNrIterationsForOptimization

setMaxNrIterationsForOptimization

getSeqWeight

setSeqWeight

getSubstitutionMatrix

setSubstitutionMatrix

isOptimizeAlignment

setOptimizeAlignment