Uses of Class
org.strbio.mol.lib.AlignmentParametersEA

Packages that use AlignmentParametersEA

org.strbio.app	These classes are stand-alone applications.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.

Uses of AlignmentParametersEA in org.strbio.app

Fields in org.strbio.app declared as AlignmentParametersEA

static AlignmentParametersEA

JThreadServer.alAP

Uses of AlignmentParametersEA in org.strbio.mol.lib

Subclasses of AlignmentParametersEA in org.strbio.mol.lib

class	OptimalAAParameters The optimal alignment parameters for maximizing alignment accuracy.
class	OptimalAAParametersFR The optimal fold recognition parameters.

Methods in org.strbio.mol.lib with parameters of type AlignmentParametersEA

void	ThreadResults.printAlignment(Printf outfile, AlignmentParametersEA ap, int i) print one alignment in a standard format.
void	ThreadResults.printAlignments(Printf outfile, AlignmentParametersEA ap, double cutoff) print alignments in a standard format.
void	ThreadResults.saveResultAS(Printf outfile, AlignmentParametersEA ap, int i) save one alignment in AS-readable format.
void	ThreadResults.saveResultModeller(Printf outfile, AlignmentParametersEA ap, int i) save one result in AlignmentSet-readable format to a file.
void	ThreadResults.saveResultsAS(Printf outfile, AlignmentParametersEA ap, double cutoff) save results in AlignmentSet-readable format to a file.
void	ThreadResults.saveResultsEnglish(Printf outfile, AlignmentParametersEA ap, double cutoff) save results in english to a file.
void	ThreadResults.saveResultsModeller(Printf outfile, AlignmentParametersEA ap, double cutoff) save results in AlignmentSet-readable format to a file.