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

Packages that use Tag

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 Tag in org.dishevelled.bio.assembly.gfa

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

Modifier and Type	Method and Description
static Tag	Tag.valueOf(String value) Parse a tag from the specified value.

Methods in org.dishevelled.bio.assembly.gfa that return types with arguments of type Tag

Modifier and Type	Method and Description
Map<String,Tag>	GfaRecord.getTags() Return an immutable map of tags keyed by tag name for this GFA record.

Constructor parameters in org.dishevelled.bio.assembly.gfa with type arguments of type Tag

Constructor and Description
GfaRecord(Map<String,Tag> tags) Create a new GFA record with the specified tags.

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

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

Constructor and Description
Containment(Reference container, Reference contained, int position, String overlap, Map<String,Tag> tags) Create a new containment GFA 1.0 record.
Gfa1Record(Map<String,Tag> tags) Create a new GFA 1.0 record with the specified tags.
Header(Map<String,Tag> tags) Create a new header GFA 1.0 record.
Link(Reference source, Reference target, String overlap, Map<String,Tag> tags) Create a new link GFA 1.0 record.
Path(String name, List<Reference> segments, List<String> overlaps, Map<String,Tag> tags) Create a new path GFA 1.0 record.
Segment(String id, String sequence, Map<String,Tag> tags) Create a new segment 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.

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

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

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.
Gfa2Record(Map<String,Tag> tags) Create a new GFA 2.0 record with the specified tags.
Header(Map<String,Tag> tags) Create a new header GFA 2.0 record.
Path(String id, List<Reference> references, Map<String,Tag> tags) Create a new path GFA 2.0 record.
Segment(String id, int length, String sequence, Map<String,Tag> tags) Create a new segment GFA 2.0 record.
Set(String id, Set<String> ids, Map<String,Tag> tags) Create a new set GFA 2.0 record.