Package com.biomatters.geneious.publicapi.documents.sequence

Interface ExtendedNucleotideGraph

All Superinterfaces:

NucleotideGraph

All Known Implementing Classes:

CompactQualityOnlyGraph, DefaultNucleotideGraph, DefaultNucleotideGraphSequence

public interface ExtendedNucleotideGraph
extends NucleotideGraph

Provides an extended interface to a NucleotideGraph.

Ideally this interface would not be a separate interface from NucleotideGraph, but because NucleotideGraph is an interface, the functionality provided by ExtendedNucleotideGraph could not added to NucleotideGraph without breaking backwards compatibility of the API.

Nested Class Summary

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph

NucleotideGraph.ImmutableGraphProvider

Method Summary

Modifier and Type	Method	Description
int	getLeadingGapsLength()	Get the number of leading residues in the sequence this graph corresponds to that are all gaps.
int	getTrailingGapsLength()	Get the number of trailing residues in the sequence this graph corresponds to that are all gaps.

Methods inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph

getChromatogramLength, getChromatogramPositionForResidue, getChromatogramValue, getSequenceLength, getSequenceQuality, hasChromatogramPositionsForResidues, hasChromatogramValues, hasSequenceQualities

Method Detail

getLeadingGapsLength

int getLeadingGapsLength()

Get the number of leading residues in the sequence this graph corresponds to that are all gaps. NucleotideGraph.getSequenceQuality(int) and NucleotideGraph.getChromatogramPositionForResidue(int) will both return Integer.MIN_VALUE for residueIndices less than the number of leading gaps.

Note, an implementation may choose to return 0 from this method even if it has leading end gaps or any value less than or equal to the number of leading gaps it has.

Returns:

the number of leading residues in the sequence this graph corresponds to that are all gaps.

getTrailingGapsLength

int getTrailingGapsLength()

Get the number of trailing residues in the sequence this graph corresponds to that are all gaps. NucleotideGraph.getSequenceQuality(int) and NucleotideGraph.getChromatogramPositionForResidue(int) will both return Integer.MIN_VALUE for residueIndices within this much of NucleotideGraph.getSequenceLength().

Note, an implementation may choose to return 0 from this method even if it has trailing end gaps or any value less than or equal to the number of trailing gaps it has.

Returns:

the number of trailing residues in the sequence this graph corresponds to that are all gaps.