Uses of Class
statalign.base.AlignColumn

Packages that use AlignColumn

statalign.base

Uses of AlignColumn in statalign.base

Fields in statalign.base declared as AlignColumn

AlignColumn	Vertex.first
AlignColumn	AlignColumn.left This reference points to the left child of this AlignColumn
AlignColumn	AlignColumn.next This reference points to the next AlignColumn in the alignment
AlignColumn	AlignColumn.parent This reference points to the parent of this AlignColumn
AlignColumn	AlignColumn.prev This reference points to the previous AlignColumn in the alignment
AlignColumn	AlignColumn.right This reference points to the right child of this Aligncolumn

Methods in statalign.base that return AlignColumn

AlignColumn

AlignColumn.clone() Creates a new column as a clone of the this, copying (or cloning) all fields except prev and next.

Methods in statalign.base with parameters of type AlignColumn

double	Vertex.exciseSilentIndel(AlignColumn c)
double	Vertex.exciseSilentIndel(AlignColumn c, boolean remove)
double	Vertex.exciseSilentIndelBlock(AlignColumn insert, boolean remove)
double	Vertex.insertSilentIndel(AlignColumn c)
double	Vertex.insertSilentIndelBlock(AlignColumn c)

Constructors in statalign.base with parameters of type AlignColumn

AlignColumn(AlignColumn next)

AlignColumn(AlignColumn next, boolean newSeq)
It creates a new AlignColumn, chains it to the next column (namely, it is used to generate a new ancestral sequence built in a traceback phase of a dynamic programming).