org.biojava.bio.structure.align.ce
Class CeParameters

java.lang.Object
  extended by org.biojava.bio.structure.align.ce.CeParameters
All Implemented Interfaces:
ConfigStrucAligParams
Direct Known Subclasses:
OptimalCECPParameters

public class CeParameters
extends Object
implements ConfigStrucAligParams

Contains the parameters that can be sent to CE

Author:
Andreas Prlic

Field Summary
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 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 Summary
CeParameters()
           
 
Method Summary
 Double getDistanceIncrement()
           
 Double getGapExtension()
           
 Double getGapOpen()
           
 Integer getMaxGapSize()
          the Max gap size parameter G .
 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
 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.
 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 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 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(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(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

DEFAULT_SCORING_STRATEGY

public static final int DEFAULT_SCORING_STRATEGY
See Also:
Constant Field Values

SIDE_CHAIN_SCORING

public static final int SIDE_CHAIN_SCORING
See Also:
Constant Field Values

SIDE_CHAIN_ANGLE_SCORING

public static final int SIDE_CHAIN_ANGLE_SCORING
See Also:
Constant Field Values

CA_AND_SIDE_CHAIN_ANGLE_SCORING

public static final int CA_AND_SIDE_CHAIN_ANGLE_SCORING
See Also:
Constant Field Values

SEQUENCE_CONSERVATION

public static final int SEQUENCE_CONSERVATION
See Also:
Constant Field Values

SCORING_STRATEGY

public static final String SCORING_STRATEGY
See Also:
Constant Field Values

scoringStrategy

protected int 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

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 Integer getScoringStrategy()

setScoringStrategy

public void setScoringStrategy(Integer 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 -