- Containment - Class in org.dishevelled.bio.assembly.gfa1
-
Containment GFA 1.0 record.
- Containment(Reference, Reference, int, String, Map<String, Tag>) - Constructor for class org.dishevelled.bio.assembly.gfa1.Containment
-
Create a new containment GFA 1.0 record.
- containment(Containment) - Method in class org.dishevelled.bio.assembly.gfa1.Gfa1Adapter
-
Notify this abstract GFA 1.0 listener of a GFA 1.0 containment.
- containsFc() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key FC.
- containsFc() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key FC.
- containsFc() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key FC.
- containsFc() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key FC.
- containsFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key FC, for fragment count.
- containsFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key FC, for fragment count.
- containsFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key FC, for fragment count.
- containsFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key FC, for fragment count.
- containsId() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return true if the tags for this segment contain
the reserved key ID.
- containsId() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this segment contain
the reserved key ID.
- containsKc() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key KC.
- containsKc() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key KC.
- containsKc() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key KC.
- containsKc() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key KC.
- containsKmerCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key KC, for k-mer count.
- containsKmerCount() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key KC, for k-mer count.
- containsKmerCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key KC, for k-mer count.
- containsKmerCount() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key KC, for k-mer count.
- containsLength() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key LN, for length.
- containsLn() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key LN.
- containsMappingQuality() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key MQ, for mapping quality.
- containsMappingQuality() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key MQ, for mapping quality.
- containsMismatchCount() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return true if the tags for this containment contain
the reserved key NM, for mismatch count.
- containsMismatchCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key NM, for mismatch count.
- containsMismatchCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key NM, for mismatch count.
- containsMq() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key MQ.
- containsMq() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key MQ.
- containsNm() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return true if the tags for this containment contain
the reserved key NM.
- containsNm() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key NM.
- containsNm() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key NM.
- containsRc() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return true if the tags for this containment contain
the reserved key RC.
- containsRc() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key RC.
- containsRc() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key RC.
- containsRc() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key RC.
- containsRc() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key RC.
- containsReadCount() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return true if the tags for this containment contain
the reserved key RC, for read count.
- containsReadCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return true if the tags for this link contain
the reserved key RC, for read count.
- containsReadCount() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key RC, for read count.
- containsReadCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key RC, for read count.
- containsReadCount() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key RC, for read count.
- containsSequenceChecksum() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key SH, for SHA-256 checksum of the
sequence.
- containsSequenceChecksum() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key SH, for SHA-256 checksum of the
sequence.
- containsSequenceUri() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key UR.
- containsSequenceUri() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key UR.
- containsSh() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key SH.
- containsSh() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key SH.
- containsTagKey(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return true if this GFA record contains the specified tag key.
- containsTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key TS, for trace spacing.
- containsTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return true if the tags for this fragment contain
the reserved key TS, for trace spacing.
- containsTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return true if the tags for this gap contain
the reserved key TS, for trace spacing.
- containsTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return true if the tags for this header contain
the reserved key TS, for trace spacing.
- containsTs() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return true if the tags for this edge contain
the reserved key TS.
- containsTs() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return true if the tags for this fragment contain
the reserved key TS.
- containsTs() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return true if the tags for this gap contain
the reserved key TS.
- containsTs() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return true if the tags for this header contain
the reserved key TS.
- containsUr() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key UR.
- containsUr() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key UR.
- containsVersionNumber() - Method in class org.dishevelled.bio.assembly.gfa1.Header
-
Return true if the tags for this header contain
the reserved key VN, for version number.
- containsVersionNumber() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return true if the tags for this header contain
the reserved key VN, for version number.
- containsVn() - Method in class org.dishevelled.bio.assembly.gfa1.Header
-
Return true if the tags for this header contain
the reserved key VN.
- containsVn() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return true if the tags for this header contain
the reserved key VN.
- Gap - Class in org.dishevelled.bio.assembly.gfa2
-
Gap GFA 2.0 record.
- Gap(String, Reference, Reference, int, Integer, Map<String, Tag>) - Constructor for class org.dishevelled.bio.assembly.gfa2.Gap
-
Create a new gap GFA 2.0 record.
- gap(Gap) - Method in class org.dishevelled.bio.assembly.gfa2.Gfa2Adapter
-
Notify this abstract GFA 2.0 listener of a GFA 2.0 gap.
- getAlignment() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the alignment for this edge, if any.
- getAlignment() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the alignment for this fragment, if any.
- getAlignmentOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the alignment for this edge.
- getAlignmentOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return an optional wrapping the alignment for this fragment.
- getCigar() - Method in class org.dishevelled.bio.assembly.gfa2.Alignment
-
Return the cigar for this alignment, if any.
- getCigarOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Alignment
-
Return an optional wrapping the cigar for this alignment.
- getContained() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the contained reference for this containment.
- getContainer() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the container reference for this containment.
- getDistance() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return the distance for this gap.
- getExternal() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the external reference for this fragment.
- getFc() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the Type=i value for the reserved key FC
as an integer.
- getFc() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the Type=i value for the reserved key FC
as an integer.
- getFc() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the Type=i value for the reserved key FC
as an integer.
- getFc() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the Type=i value for the reserved key FC
as an integer.
- getFcOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional Type=i value for the reserved key FC
as an integer.
- getFcOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional Type=i value for the reserved key FC
as an integer.
- getFcOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional Type=i value for the reserved key FC
as an integer.
- getFcOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional Type=i value for the reserved key FC
as an integer.
- getFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the fragment count for this link (Type=i value for
the reserved key FC as an integer).
- getFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return true if the tags for this segment contain
the reserved key FC, for fragment count.
- getFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the fragment count for this edge (Type=i value for
the reserved key FC as an integer).
- getFragmentCount() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return true if the tags for this segment contain
the reserved key FC, for fragment count.
- getFragmentCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional wrapping the fragment count for this link
(Type=i value for the reserved key FC as an integer).
- getFragmentCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional wrapping the fragment count for this segment
(Type=i value for the reserved key FC as an integer).
- getFragmentCountOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the fragment count for this edge
(Type=i value for the reserved key FC as an integer).
- getFragmentCountOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional wrapping the fragment count for this segment
(Type=i value for the reserved key FC as an integer).
- getFragmentEnd() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the fragment end position for this fragment.
- getFragmentStart() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the fragment start position for this fragment.
- getId() - Method in class org.dishevelled.bio.assembly.gfa.Reference
-
Return the identifier for this reference.
- getId() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the Type=Z value for the reserved key ID
as a string.
- getId() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the Type=Z value for the reserved key ID
as a string.
- getId() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the identifier for this segment.
- getId() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the identifier for this edge, if any.
- getId() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return the identifier for this gap, if any.
- getId() - Method in class org.dishevelled.bio.assembly.gfa2.Path
-
Return the identifier for this path, if any.
- getId() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the identifier for this segment.
- getId() - Method in class org.dishevelled.bio.assembly.gfa2.Set
-
Return the identifier for this set, if any.
- getIdOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return an optional Type=Z value for the reserved key ID
as a string.
- getIdOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional Type=Z value for the reserved key ID
as a string.
- getIdOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the identifier for this edge.
- getIdOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return an optional wrapping the identifier for this gap.
- getIdOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Path
-
Return an optional wrapping the identifier for this path.
- getIdOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
- getIdOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Set
-
Return an optional wrapping the identifier for this set.
- getIds() - Method in class org.dishevelled.bio.assembly.gfa2.Set
-
Return an immutable unordered set of identifiers for this set.
- getKc() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the Type=i value for the reserved key KC
as an integer.
- getKc() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the Type=i value for the reserved key KC
as an integer.
- getKc() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the Type=i value for the reserved key KC
as an integer.
- getKc() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the Type=i value for the reserved key KC
as an integer.
- getKcOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional Type=i value for the reserved key KC
as an integer.
- getKcOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional Type=i value for the reserved key KC
as an integer.
- getKcOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional Type=i value for the reserved key KC
as an integer.
- getKcOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional Type=i value for the reserved key KC
as an integer.
- getKmerCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the k-mer count for this link (Type=i value for
the reserved key KC as an integer).
- getKmerCount() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the k-mer count for this segment (Type=i value for
the reserved key KC as an integer).
- getKmerCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the k-mer count for this edge (Type=i value for
the reserved key KC as an integer).
- getKmerCount() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the k-mer count for this segment (Type=i value for
the reserved key KC as an integer).
- getKmerCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional wrapping the k-mer count for this link
(Type=i value for the reserved key KC as an integer).
- getKmerCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional wrapping the k-mer count for this segment
(Type=i value for the reserved key KC as an integer).
- getKmerCountOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the k-mer count for this edge
(Type=i value for the reserved key KC as an integer).
- getKmerCountOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional wrapping the k-mer count for this segment
(Type=i value for the reserved key KC as an integer).
- getLength() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the length of this segment (Type=i value for
the reserved key LN as an integer).
- getLength() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the length for this segment.
- getLengthOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional wrapping the length of this segment
(Type=i value for the reserved key LN as an integer).
- getLn() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the Type=i value for the reserved key LN
as an integer.
- getLnOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional Type=i value for the reserved key LN
as an integer.
- getMappingQuality() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the mapping quality for this link (Type=i value for
the reserved key MQ as an integer).
- getMappingQuality() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the mapping quality for this edge (Type=i value for
the reserved key MQ as an integer).
- getMappingQualityOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional wrapping the mapping quality for this link
(Type=i value for the reserved key MQ as an integer).
- getMappingQualityOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the mapping quality for this edge
(Type=i value for the reserved key MQ as an integer).
- getMismatchCount() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the mismatch count for this containment (Type=i value
for the reserved key NM as an integer).
- getMismatchCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the mismatch count for this link (Type=i value for
the reserved key NM as an integer).
- getMismatchCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the mismatch count for this edge (Type=i value for
the reserved key NM as an integer).
- getMismatchCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return an optional wrapping the mismatch count for this containment
(Type=i value for the reserved key NM as an integer).
- getMismatchCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional wrapping the mismatch count for this link
(Type=i value for the reserved key NM as an integer).
- getMismatchCountOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the mismatch count for this edge
(Type=i value for the reserved key NM as an integer).
- getMq() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the Type=i value for the reserved key MQ
as an integer.
- getMq() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the Type=i value for the reserved key MQ
as an integer.
- getMqOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional Type=i value for the reserved key MQ
as an integer.
- getMqOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional Type=i value for the reserved key MQ
as an integer.
- getName() - Method in class org.dishevelled.bio.assembly.gfa.Tag
-
Return the name of this tag.
- getName() - Method in class org.dishevelled.bio.assembly.gfa1.Path
-
Return the name for this path.
- getNm() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the Type=i value for the reserved key NM
as an integer.
- getNm() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the Type=i value for the reserved key NM
as an integer.
- getNm() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the Type=i value for the reserved key NM
as an integer.
- getNmOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return an optional Type=i value for the reserved key NM
as an integer.
- getNmOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional Type=i value for the reserved key NM
as an integer.
- getNmOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional Type=i value for the reserved key NM
as an integer.
- getOrdinal() - Method in class org.dishevelled.bio.assembly.gfa1.Traversal
-
Return the ordinal for this traversal.
- getOrientation() - Method in class org.dishevelled.bio.assembly.gfa.Reference
-
Return the orientation for this reference.
- getOverlap() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the overlap in cigar format for this containment, if any.
- getOverlap() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the overlap in cigar format for this link, if any.
- getOverlap() - Method in class org.dishevelled.bio.assembly.gfa1.Traversal
-
Return the overlap in cigar format for this traversal, if any.
- getOverlapOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return an optional wrapping the overlap in cigar format for this containment.
- getOverlapOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional wrapping the overlap in cigar format for this link.
- getOverlapOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Traversal
-
Return an optional wrapping the overlap for this traversal.
- getOverlaps() - Method in class org.dishevelled.bio.assembly.gfa1.Path
-
Return an immutable list of overlaps in cigar format for this path,
or null if none exist.
- getOverlapsOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Path
-
Return an optional wrapping the list of overlaps in cigar format for this path.
- getPathName() - Method in class org.dishevelled.bio.assembly.gfa1.Traversal
-
Return the path name for this traversal.
- getPosition() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the position for this containment (0-based coordinate system).
- getPosition() - Method in class org.dishevelled.bio.assembly.gfa2.Position
-
Return the position for this position.
- getRc() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the Type=i value for the reserved key RC
as an integer.
- getRc() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the Type=i value for the reserved key RC
as an integer.
- getRc() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the Type=i value for the reserved key RC
as an integer.
- getRc() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the Type=i value for the reserved key RC
as an integer.
- getRc() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the Type=i value for the reserved key RC
as an integer.
- getRcOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return an optional Type=i value for the reserved key RC
as an integer.
- getRcOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional Type=i value for the reserved key RC
as an integer.
- getRcOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional Type=i value for the reserved key RC
as an integer.
- getRcOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional Type=i value for the reserved key RC
as an integer.
- getRcOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional Type=i value for the reserved key RC
as an integer.
- getReadCount() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return the read count for this containment (Type=i value for the
reserved key RC as an integer).
- getReadCount() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the read count for this link (Type=i value for
the reserved key RC as an integer).
- getReadCount() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the read count for this segment (Type=i value for
the reserved key RC as an integer).
- getReadCount() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the read count for this edge (Type=i value for
the reserved key RC as an integer).
- getReadCount() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the read count for this segment (Type=i value for
the reserved key RC as an integer).
- getReadCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Containment
-
Return an optional wrapping the read count for this containment
(Type=i value for the reserved key RC as an integer).
- getReadCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return an optional wrapping the read count for this link
(Type=i value for the reserved key RC as an integer).
- getReadCountOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional wrapping the read count for this segment
(Type=i value for the reserved key RC as an integer).
- getReadCountOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the read count for this edge
(Type=i value for the reserved key RC as an integer).
- getReadCountOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional wrapping the read count for this segment
(Type=i value for the reserved key RC as an integer).
- getReferences() - Method in class org.dishevelled.bio.assembly.gfa2.Path
-
Return an immutable list of references for this path.
- getSegmentEnd() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the segment end position for this fragment.
- getSegmentId() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the segment identifier for this fragment.
- getSegments() - Method in class org.dishevelled.bio.assembly.gfa1.Path
-
Return an immutable list of segment references for this path.
- getSegmentStart() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the segment start position for this fragment.
- getSequence() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the sequence for this segment, if any.
- getSequence() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the sequence for this segment, if any.
- getSequenceChecksum() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the SHA-256 checksum of the sequence for this segment
(Type=H value for the reserved key SH as a byte array).
- getSequenceChecksum() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the SHA-256 checksum of the sequence for this segment
(Type=H value for the reserved key SH as a byte array).
- getSequenceChecksumOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional wrapping the SHA-256 checksum of the sequence
for this segment (Type=H value for the reserved key SH
as a byte array).
- getSequenceChecksumOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional wrapping the SHA-256 checksum of the sequence
for this segment (Type=H value for the reserved key SH
as a byte array).
- getSequenceOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional wrapping the sequence for this segment.
- getSequenceOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional wrapping the sequence for this segment.
- getSequenceUri() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the URI or local file-system path of the sequence for
this segment (Type=Z value for the reserved key UR
as a string).
- getSequenceUri() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the URI or local file-system path of the sequence for
this segment (Type=Z value for the reserved key UR
as a string).
- getSequenceUriOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional wrapping the URI or local file-system path of
the sequence for this segment (Type=Z value for the reserved key
UR as a string).
- getSequenceUriOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional wrapping the URI or local file-system path of
the sequence for this segment (Type=Z value for the reserved key
UR as a string).
- getSh() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the Type=H value for the reserved key SH
as a byte array.
- getSh() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the Type=H value for the reserved key SH
as a byte array.
- getShOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional Type=H value for the reserved key SH
as a byte array.
- getShOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional Type=H value for the reserved key SH
as a byte array.
- getSource() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the source reference for this link.
- getSource() - Method in class org.dishevelled.bio.assembly.gfa1.Traversal
-
Return the source reference for this traversal.
- getSource() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the source reference for this edge.
- getSource() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return the source reference for this gap.
- getSourceEnd() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the source end position for this edge.
- getSourceStart() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the source start position for this edge.
- getTagByteArray(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=H field value for the specified key parsed into a byte array.
- getTagByteArrayOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=H field value for the specified key parsed into a byte array.
- getTagBytes(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=H field value for the specified key parsed into an immutable list of bytes.
- getTagBytesOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=H field value for the specified key parsed into an immutable list of bytes.
- getTagCharacter(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=A field value for the specified key parsed into a character.
- getTagCharacterOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=A field value for the specified key parsed into a character.
- getTagFloat(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=f field value for the specified key parsed into a float.
- getTagFloatOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=f field value for the specified key parsed into a float.
- getTagFloats(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=B first letter f field value for the specified key parsed
into an immutable list of floats.
- getTagFloatsOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=B first letter f field value for the specified key parsed
into an immutable list of floats.
- getTagInteger(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=i field value for the specified key parsed into an integer.
- getTagIntegerOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=i field value for the specified key parsed into an integer.
- getTagIntegers(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=B first letter [cCsSiI] field value for the specified key parsed
into an immutable list of integers.
- getTagIntegersOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=B first letter [cCsSiI] field value for the specified key parsed
into an immutable list of integers.
- getTags() - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an immutable map of tags keyed by tag name
for this GFA record.
- getTagString(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return the Type=Z field value for the specified key parsed into a string.
- getTagStringOpt(String) - Method in class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Return an optional wrapping the Type=Z field value for the specified key parsed into a string.
- getTarget() - Method in class org.dishevelled.bio.assembly.gfa1.Link
-
Return the target reference for this link.
- getTarget() - Method in class org.dishevelled.bio.assembly.gfa1.Traversal
-
Return the target reference for this traversal.
- getTarget() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the target reference for this edge.
- getTarget() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return the target reference for this gap.
- getTargetEnd() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the target end position for this edge.
- getTargetStart() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the target start position for this edge.
- getTrace() - Method in class org.dishevelled.bio.assembly.gfa2.Alignment
-
Return the trace as an immutable list of Integers, or null if
this alignment does not have a trace.
- getTraceOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Alignment
-
Return an optional wrapping the trace for this alignment.
- getTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the trace spacing for this edge (Type=i value for
the reserved key TS as an integer).
- getTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the trace spacing for this fragment (Type=i value for
the reserved key TS as an integer).
- getTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return the trace spacing for this gap (Type=i value for
the reserved key TS as an integer).
- getTraceSpacing() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return the trace spacing for this header (Type=i value for
the reserved key TS as an integer).
- getTraceSpacingOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional wrapping the trace spacing for this edge
(Type=i value for the reserved key TS as an integer).
- getTraceSpacingOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return an optional wrapping the trace spacing for this fragment
(Type=i value for the reserved key TS as an integer).
- getTraceSpacingOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return an optional wrapping the trace spacing for this gap
(Type=i value for the reserved key TS as an integer).
- getTraceSpacingOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return an optional wrapping the trace spacing for this header
(Type=i value for the reserved key TS as an integer).
- getTs() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return the Type=i value for the reserved key TS
as an integer.
- getTs() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return the Type=i value for the reserved key TS
as an integer.
- getTs() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return the Type=i value for the reserved key TS
as an integer.
- getTs() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return the Type=i value for the reserved key TS
as an integer.
- getTsOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Edge
-
Return an optional Type=i value for the reserved key TS
as an integer.
- getTsOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Fragment
-
Return an optional Type=i value for the reserved key TS
as an integer.
- getTsOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return an optional Type=i value for the reserved key TS
as an integer.
- getTsOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return an optional Type=i value for the reserved key TS
as an integer.
- getType() - Method in class org.dishevelled.bio.assembly.gfa.Tag
-
Return the type for this tag.
- getUr() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return the Type=Z value for the reserved key UR
as a string.
- getUr() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return the Type=Z value for the reserved key UR
as a string.
- getUrOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Segment
-
Return an optional Type=Z value for the reserved key UR
as a string.
- getUrOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Segment
-
Return an optional Type=Z value for the reserved key UR
as a string.
- getValue() - Method in class org.dishevelled.bio.assembly.gfa.Tag
-
Return the value for this tag.
- getVariance() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return the variance for this gap, if any.
- getVarianceOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Gap
-
Return an optional wrapping the variance for this gap.
- getVersionNumber() - Method in class org.dishevelled.bio.assembly.gfa1.Header
-
Return the version number for this header (Type=Z value for the
reserved key VN as a string).
- getVersionNumber() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return the version number for this header (Type=Z value for the
reserved key VN as a string).
- getVersionNumberOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Header
-
Return an optional wrapping the version number for this header
(Type Z value for the reserved key VN as a string).
- getVersionNumberOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return an optional wrapping the version number for this header
(Type Z value for the reserved key VN as a string).
- getVn() - Method in class org.dishevelled.bio.assembly.gfa1.Header
-
Return the Type=Z value for the reserved key VN
as a string.
- getVn() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return the Type=Z value for the reserved key VN
as a string.
- getVnOpt() - Method in class org.dishevelled.bio.assembly.gfa1.Header
-
Return an optional Type=Z value for the reserved key VN
as a string.
- getVnOpt() - Method in class org.dishevelled.bio.assembly.gfa2.Header
-
Return an optional Type=Z value for the reserved key VN
as a string.
- Gfa1Adapter - Class in org.dishevelled.bio.assembly.gfa1
-
Abstract implementation of a Graphical Fragment Assembly (GFA) 1.0 listener.
- Gfa1Adapter() - Constructor for class org.dishevelled.bio.assembly.gfa1.Gfa1Adapter
-
- Gfa1Listener - Interface in org.dishevelled.bio.assembly.gfa1
-
Graphical Fragment Assembly (GFA) 1.0 listener.
- Gfa1Reader - Class in org.dishevelled.bio.assembly.gfa1
-
Graphical Fragment Assembly (GFA) 1.0 reader.
- Gfa1Record - Class in org.dishevelled.bio.assembly.gfa1
-
Graphical Fragment Assembly (GFA) 1.0 record.
- Gfa1Record(Map<String, Tag>) - Constructor for class org.dishevelled.bio.assembly.gfa1.Gfa1Record
-
Create a new GFA 1.0 record with the specified tags.
- Gfa1Writer - Class in org.dishevelled.bio.assembly.gfa1
-
Graphical Fragment Assembly (GFA) 1.0 writer.
- Gfa2Adapter - Class in org.dishevelled.bio.assembly.gfa2
-
Abstract implementation of a Graphical Fragment Assembly (GFA) 2.0 listener.
- Gfa2Adapter() - Constructor for class org.dishevelled.bio.assembly.gfa2.Gfa2Adapter
-
- Gfa2Listener - Interface in org.dishevelled.bio.assembly.gfa2
-
Graphical Fragment Assembly (GFA) 2.0 listener.
- Gfa2Reader - Class in org.dishevelled.bio.assembly.gfa2
-
Graphical Fragment Assembly (GFA) 2.0 reader.
- Gfa2Record - Class in org.dishevelled.bio.assembly.gfa2
-
Graphical Fragment Assembly (GFA) 2.0 record.
- Gfa2Record(Map<String, Tag>) - Constructor for class org.dishevelled.bio.assembly.gfa2.Gfa2Record
-
Create a new GFA 2.0 record with the specified tags.
- Gfa2Writer - Class in org.dishevelled.bio.assembly.gfa2
-
Graphical Fragment Assembly (GFA) 2.0 writer.
- GfaRecord - Class in org.dishevelled.bio.assembly.gfa
-
Graphical Fragment Assembly (GFA) record.
- GfaRecord(Map<String, Tag>) - Constructor for class org.dishevelled.bio.assembly.gfa.GfaRecord
-
Create a new GFA record with the specified tags.