Uses of Class
gata.aligner.LocalAlignment

Packages that use LocalAlignment

gata.aligner	For aligning and post processing DNA sequences using BLAST for subsequent import into GATAPlotter.
gata.main	Main app, utility, and params for GATAPlotter.

Uses of LocalAlignment in gata.aligner

Methods in gata.aligner that return LocalAlignment

LocalAlignment[]

Seqs.makeLocalAlignments(java.util.ArrayList data)

Constructors in gata.aligner with parameters of type LocalAlignment

Alignment(java.lang.String s1, int start1, int stop1, java.lang.String s2, int start2, int stop2, int aScore, int ori, AlignParams ap, LocalAlignment la)

Uses of LocalAlignment in gata.main

Methods in gata.main that return LocalAlignment

static LocalAlignment[]

GATAUtil.mergeLAArrays(LocalAlignment[] a, LocalAlignment[] b)

Methods in gata.main with parameters of type LocalAlignment

static Alignment[]	GATAUtil.makeSubAligns(LocalAlignment[] locs)
static LocalAlignment[]	GATAUtil.mergeLAArrays(LocalAlignment[] a, LocalAlignment[] b)