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

Packages that use ScoreList

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.

Uses of ScoreList in org.strbio.mol

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

double	Alignment.averageScore(ScoreList sl) Returns average score of all pairs of aligned monomers.
double	AlignmentSet.averageScore(ScoreList sl) Returns average score of all pairs of aligned monomers.
void	AlignmentStats.calculateScores(Alignment al, ScoreList sc) Calculate scores, given a score list.
double	Polymer.globalAlign(Polymer y, GapModel gm, ScoreList sl, int[] nail) Deprecated. use AlignmentParameters
double	Polymer.globalCompare(Polymer y, GapModel gm, ScoreList sl) Deprecated. use AlignmentParameters

Uses of ScoreList in org.strbio.mol.lib

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

ScoreList	ScoreList.next The next in the list, or null if there are no more scoring functions.
ScoreList	AlignmentParameters.scoreList The scoring functions used.

Constructors in org.strbio.mol.lib with parameters of type ScoreList

AlignmentParameters(GapModel gm, ScoreList sl)
Provide an initial gap model and score list.

AlignmentParametersEA(GapModel gm, ScoreList sl)