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

Packages that use AlignmentParameters

org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.raf	These classes are related to the RAF file format used by the ASTRAL database.

Uses of AlignmentParameters in org.strbio.mol

Fields in org.strbio.mol declared as AlignmentParameters

AlignmentParameters	ThreadSet.alignmentParameters Alignment parameters
AlignmentParameters	ThreadSet.alignmentParameters2 Alignment parameters for evaluating alignment goodness in FR tests; Null means use same one as that used to generate the alignment.

Methods in org.strbio.mol with parameters of type AlignmentParameters

double	Alignment.avgScoreWithGaps(AlignmentParameters ap) Returns average score for all pairs of aligned monomers.
double	Alignment.avgScoreWithoutGaps(AlignmentParameters ap) Returns average score for all pairs of aligned monomers.
Alignment	Polymer.getGlobalAlignment(Polymer y, AlignmentParameters ap, Alignment nail) This does the above, but without actually storing the alignment as gaps in the polymers.
double	Alignment.globalAlign(AlignmentParameters ap) Do the global alignment, returning the score (which is also stored in lastScore)
double	AlignmentSet.globalAlign(AlignmentParameters ap) Do the global alignment, store in 'calculated', return comparison score.
double	Alignment.globalAlign(AlignmentParameters ap, Alignment nail) Do the global alignment, returning the score (which is also stored in lastScore)
double	Polymer.globalAlign(Polymer y, AlignmentParameters ap, Alignment nail) a mostly generic global alignment function.
double	AlignmentSet.globalCompare(AlignmentParameters ap) Find the global comparison score.
double	Polymer.globalCompare(Polymer y, AlignmentParameters ap) a mostly generic global comparison function.

Uses of AlignmentParameters in org.strbio.mol.lib

Subclasses of AlignmentParameters in org.strbio.mol.lib

class	AlignmentParametersEA Parameters, with some statistical functions to tell you how accurate they are at alignment and/or fold recognition.
class	OptimalAAParameters The optimal alignment parameters for maximizing alignment accuracy.
class	OptimalAAParametersFR The optimal fold recognition parameters.

Fields in org.strbio.mol.lib declared as AlignmentParameters

AlignmentParameters	FRParametersNode.creationAP Alignment parameters used to create the alignment.
AlignmentParameters	FRParametersNode.evaluationAP Alignment parameters used to evaluate the alignment.

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

void	ThreadResults.makeAlignment(Printf outfile, AlignmentParameters ap, int i) make one alignment to a given fold.
void	ThreadResults.makeAlignments(Printf outfile, AlignmentParameters ap, double cutoff) make alignments for all folds >= a certain pMatch value.

Uses of AlignmentParameters in org.strbio.raf

Fields in org.strbio.raf declared as AlignmentParameters

static AlignmentParameters

MakeRAF.ap