Uses of Class
org.strbio.mol.Alignment

Packages that use Alignment

org.strbio.local	These classes are for running or exchanging data with local programs (other programs installed on your computer).
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 Alignment in org.strbio.local

Methods in org.strbio.local with parameters of type Alignment

Protein

Modeller.model(Alignment al) Make a model for a given alignment

Uses of Alignment in org.strbio.mol

Fields in org.strbio.mol declared as Alignment

Alignment	AlignmentSet.calculated A vector containing the last alignment calculated with Align.
Alignment	AlignmentSet.correct A vector of correct sequence-fold monomer pairs.
Alignment	AlignmentSet.nail A vector of 'nailed down' seq-fold monomer pairs.

Methods in org.strbio.mol that return Alignment

Alignment	Polymer.getGlobalAlignment(Polymer y, AlignmentParameters ap, Alignment nail) This does the above, but without actually storing the alignment as gaps in the polymers.
Alignment	Alignment.inverse() invert alignment, returning fold->seq alignment
static Alignment	Alignment.makeFromSuperposition(Protein seq, Protein fold) Make from 2 superimposed proteins, using JDB's method. 1) Make table of everything in (fold) which is <= CUTOFF angstroms from each residue in (seq). 2) Get longest consecutive stretch, and set them as aligned; remove these residues from future consideration. 3) Repeat until nothing is left that has any matches.
static Alignment	Alignment.makeFromSuperpositionDP(Protein seq, Protein fold) Make from a superposition, using dynamic programming.

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

double[]	Alignment.ASns(Alignment correct, int tolerance) calculate alignment sensitivity, as in CASP2.
double[]	Alignment.ASpc(Alignment correct, int tolerance) calculate alignment specificity, as in CASP2.
void	AlignmentStats.calculate(Alignment correct, Alignment calculated, MinareaResults ma) Calculate all results (that can be), given correct and calculated alignments, and minarea results (for RMS only; can be null to ignore).
void	AlignmentStats.calculateCorrect(Alignment correct) Only calculate the stats that depend on correct alignment
void	AlignmentStats.calculateEstimated(Alignment calculated) Only calculate the estimated stats.
void	AlignmentStats.calculateScores(Alignment al, ScoreList sc) Calculate scores, given a score list.
double[]	Alignment.compare(Alignment av, int tolerance) compares two alignments.
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, 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.
void	Alignment.printRelative(Alignment b, Printf outfile) prints out both sequences with alternating seq and fold lines, and also shows relation relative to another alignment (i.e. the correct alignment)
double[]	Alignment.shift(Alignment av) calculate average alignment shift, as in CASP2.

Constructors in org.strbio.mol with parameters of type Alignment

Alignment(Alignment av)
make a new alignment from another one.

Uses of Alignment in org.strbio.mol.lib

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

Alignment

MinareaResults.alignment

Methods in org.strbio.mol.lib that return Alignment

Alignment	ThreadResults.getAlignment(int i) get an alignment, or null if it hasn't been done.
Alignment	ThreadResults.getAlignmentRank(int n) get an alignment for a given rank, or null if it hasn't been done.

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

void	ScoreUFSippl90.setAlignment(Alignment a)
void	AlignmentDependent.setAlignment(Alignment al) This function is called to provide the alignment.
void	ScoreList.setAlignment(Alignment al) Set up scoring functions with a given Alignment functions that implement AlignmentDependent
void	AlignmentParameters.setAlignment(Alignment al) Set the alignment for scoring functions that require it.