de.bioforscher.singa.structure.algorithms.superimposition.fit3d

Interface Fit3DBuilder.SiteParameterConfigurationStep

All Superinterfaces:

Fit3DBuilder.SiteConfigurationStep

All Known Implementing Classes:

Fit3DBuilder.Builder

Enclosing class:

Fit3DBuilder

public static interface Fit3DBuilder.SiteParameterConfigurationStep
extends Fit3DBuilder.SiteConfigurationStep

Method Summary

Modifier and Type	Method and Description
Fit3DBuilder.SiteParameterConfigurationStep	cutoffScore(double cutoffScore) The cutoff score that should be used when extending the site alignment.
Fit3DBuilder.SiteParameterConfigurationStep	substitutionMatrix(SubstitutionMatrix substitutionMatrix) The SubstitutionMatrix to be used to calculate the Xie score.

Methods inherited from interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DBuilder.SiteConfigurationStep

exhaustive, ignoreSpecifiedExchanges, kuhnMunkres, restrictToSpecifiedExchanges

Method Detail

cutoffScore

Fit3DBuilder.SiteParameterConfigurationStep cutoffScore(double cutoffScore)

The cutoff score that should be used when extending the site alignment.

Parameters:

cutoffScore - The cutoff score.

Returns:

The Fit3DBuilder.SiteParameterConfigurationStep to configure other parameters.

substitutionMatrix

Fit3DBuilder.SiteParameterConfigurationStep substitutionMatrix(SubstitutionMatrix substitutionMatrix)

The SubstitutionMatrix to be used to calculate the Xie score.

Parameters:

substitutionMatrix - The substitution matrix.

Returns:

The Fit3DBuilder.SiteParameterConfigurationStep to configure other parameters.