Uses of Class
org.biojava.nbio.structure.align.ce.StartupParameters

Packages that use StartupParameters

Package	Description
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.fatcat	Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.align.util

Uses of StartupParameters in org.biojava.nbio.structure.align.ce

Subclasses of StartupParameters in org.biojava.nbio.structure.align.ce

Modifier and Type	Class	Description
protected class	CeCPUserArgumentProcessor.CeCPStartupParams
protected static class	CeUserArgumentProcessor.CeStartupParams

Fields in org.biojava.nbio.structure.align.ce declared as StartupParameters

Modifier and Type	Field	Description
protected StartupParameters	AbstractUserArgumentProcessor.params

Methods in org.biojava.nbio.structure.align.ce that return StartupParameters

Modifier and Type	Method	Description
protected abstract StartupParameters	AbstractUserArgumentProcessor.getStartupParametersInstance()	StartupParameters is a bean to store all the possible command line parameters.
protected StartupParameters	CeCPUserArgumentProcessor.getStartupParametersInstance()
protected StartupParameters	CeUserArgumentProcessor.getStartupParametersInstance()

Uses of StartupParameters in org.biojava.nbio.structure.align.fatcat

Subclasses of StartupParameters in org.biojava.nbio.structure.align.fatcat

Modifier and Type	Class	Description
protected class	FatCatUserArgumentProcessor.FatCatStartupParams

Methods in org.biojava.nbio.structure.align.fatcat that return StartupParameters

Modifier and Type	Method	Description
protected StartupParameters	FatCatUserArgumentProcessor.getStartupParametersInstance()

Uses of StartupParameters in org.biojava.nbio.structure.align.seq

Subclasses of StartupParameters in org.biojava.nbio.structure.align.seq

Modifier and Type	Class	Description
protected static class	SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

Methods in org.biojava.nbio.structure.align.seq that return StartupParameters

Modifier and Type	Method	Description
protected StartupParameters	SmithWatermanUserArgumentProcessor.getStartupParametersInstance()

Uses of StartupParameters in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util with parameters of type StartupParameters

Modifier and Type	Method	Description
static UserConfiguration	UserConfiguration.fromStartupParams(StartupParameters params)