C
- Compound a Sequence holdsAccessioned
, java.lang.Iterable<C>
AlignedSequence<S,C>
, MutableAlignedSequence<S,C>
, ProxySequenceReader<C>
, SequenceReader<C>
, SequenceView<C>
AbstractSequence
, ArrayListProxySequenceReader
, ArrayListSequenceReader
, BasicSequence
, BitSequenceReader
, CDSSequence
, ChromosomeSequence
, ComplementSequenceView
, DNASequence
, ExonSequence
, FourBitSequenceReader
, GenbankProxySequenceReader
, GeneSequence
, IntronSequence
, JoiningSequenceReader
, ProteinSequence
, ReversedSequenceView
, RNASequence
, RnaSequenceView
, SequenceFileProxyLoader
, SequenceProxyView
, SimpleAlignedSequence
, SingleCompoundSequenceReader
, StartCodonSequence
, StopCodonSequence
, StringProxySequenceReader
, TranscriptSequence
, TwoBitSequenceReader
, UniprotProxySequenceReader
public interface Sequence<C extends Compound> extends java.lang.Iterable<C>, Accessioned
Modifier and Type | Method | Description |
---|---|---|
int |
countCompounds(C... compounds) |
Returns the number of times we found a compound in the Sequence
|
java.util.List<C> |
getAsList() |
Returns the Sequence as a List of compounds
|
C |
getCompoundAt(int position) |
Returns the Compound at the given biological index
|
CompoundSet<C> |
getCompoundSet() |
Gets the compound set used to back this Sequence
|
int |
getIndexOf(C compound) |
Scans through the Sequence looking for the first occurrence of the given
compound
|
SequenceView<C> |
getInverse() |
Does the right thing to get the inverse of the current
Sequence.
|
int |
getLastIndexOf(C compound) |
Scans through the Sequence looking for the last occurrence of the given
compound
|
int |
getLength() |
Returns the length of the Sequence
|
java.lang.String |
getSequenceAsString() |
Returns the String representation of the Sequence
|
SequenceView<C> |
getSubSequence(java.lang.Integer start,
java.lang.Integer end) |
Returns a portion of the sequence from the different positions.
|
getAccession
int getLength()
C getCompoundAt(int position)
position
- Biological index (1 to n)int getIndexOf(C compound)
compound
- Compounds to look forint getLastIndexOf(C compound)
compound
- Compounds to look forjava.lang.String getSequenceAsString()
java.util.List<C> getAsList()
SequenceView<C> getSubSequence(java.lang.Integer start, java.lang.Integer end)
start
- Biological index start; must be greater than 0end
- Biological end; must be less than length + 1CompoundSet<C> getCompoundSet()
int countCompounds(C... compounds)
compounds
- Vargs of the compounds to countSequenceView<C> getInverse()