Uses of Class
org.dishevelled.bio.assembly.gfa.Reference

Packages that use Reference

Package	Description
org.dishevelled.bio.assembly.gfa	Graphical Fragment Assembly (GFA) support common to 1.0 and 2.0 versions.
org.dishevelled.bio.assembly.gfa1	Graphical Fragment Assembly (GFA) 1.0 support.
org.dishevelled.bio.assembly.gfa2	Graphical Fragment Assembly (GFA) 2.0 support.

Uses of Reference in org.dishevelled.bio.assembly.gfa

Methods in org.dishevelled.bio.assembly.gfa that return Reference

Modifier and Type	Method and Description
static Reference	Reference.splitValueOf(String id, String orientation) Parse a reference from the specified values.
static Reference	Reference.valueOf(String value) Parse a reference from the specified value.

Uses of Reference in org.dishevelled.bio.assembly.gfa1

Methods in org.dishevelled.bio.assembly.gfa1 that return Reference

Modifier and Type	Method and Description
Reference	Containment.getContained() Return the contained reference for this containment.
Reference	Containment.getContainer() Return the container reference for this containment.
Reference	Link.getSource() Return the source reference for this link.
Reference	Traversal.getSource() Return the source reference for this traversal.
Reference	Link.getTarget() Return the target reference for this link.
Reference	Traversal.getTarget() Return the target reference for this traversal.

Methods in org.dishevelled.bio.assembly.gfa1 that return types with arguments of type Reference

Modifier and Type	Method and Description
List<Reference>	Path.getSegments() Return an immutable list of segment references for this path.

Constructors in org.dishevelled.bio.assembly.gfa1 with parameters of type Reference

Constructor and Description
Containment(Reference container, Reference contained, int position, String overlap, Map<String,Tag> tags) Create a new containment GFA 1.0 record.
Link(Reference source, Reference target, String overlap, Map<String,Tag> tags) Create a new link GFA 1.0 record.
Traversal(String pathName, int ordinal, Reference source, Reference target, String overlap, Map<String,Tag> tags) Create a new traversal GFA 1.0 record.

Constructor parameters in org.dishevelled.bio.assembly.gfa1 with type arguments of type Reference

Constructor and Description
Path(String name, List<Reference> segments, List<String> overlaps, Map<String,Tag> tags) Create a new path GFA 1.0 record.

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

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

Modifier and Type	Method and Description
Reference	Fragment.getExternal() Return the external reference for this fragment.
Reference	Edge.getSource() Return the source reference for this edge.
Reference	Gap.getSource() Return the source reference for this gap.
Reference	Edge.getTarget() Return the target reference for this edge.
Reference	Gap.getTarget() Return the target reference for this gap.

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

Modifier and Type	Method and Description
List<Reference>	Path.getReferences() Return an immutable list of references for this path.

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

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.
Gap(String id, Reference source, Reference target, int distance, Integer variance, Map<String,Tag> tags) Create a new gap GFA 2.0 record.

Constructor parameters in org.dishevelled.bio.assembly.gfa2 with type arguments of type Reference

Constructor and Description
Path(String id, List<Reference> references, Map<String,Tag> tags) Create a new path GFA 2.0 record.