Uses of Class
org.dishevelled.bio.assembly.gfa2.Alignment

Packages that use Alignment

Package	Description
org.dishevelled.bio.assembly.gfa2	Graphical Fragment Assembly (GFA) 2.0 support.

Uses of Alignment in org.dishevelled.bio.assembly.gfa2

Methods in org.dishevelled.bio.assembly.gfa2 that return Alignment

Modifier and Type	Method and Description
Alignment	Edge.getAlignment() Return the alignment for this edge, if any.
Alignment	Fragment.getAlignment() Return the alignment for this fragment, if any.
static Alignment	Alignment.valueOf(String value) Parse an alignment from the specified value.

Methods in org.dishevelled.bio.assembly.gfa2 that return types with arguments of type Alignment

Modifier and Type	Method and Description
Optional<Alignment>	Edge.getAlignmentOpt() Return an optional wrapping the alignment for this edge.
Optional<Alignment>	Fragment.getAlignmentOpt() Return an optional wrapping the alignment for this fragment.

Constructors in org.dishevelled.bio.assembly.gfa2 with parameters of type Alignment

Constructor and Description
Edge(String id, Reference source, Reference target, Position sourceStart, Position sourceEnd, Position targetStart, Position targetEnd, Alignment alignment, Map<String,Tag> tags) Create a new edge GFA 2.0 record.
Fragment(String segmentId, Reference external, Position segmentStart, Position segmentEnd, Position fragmentStart, Position fragmentEnd, Alignment alignment, Map<String,Tag> tags) Create a new fragment GFA 2.0 record.