Uses of Class
jgromacs.data.Sequence

Packages that use Sequence

jgromacs.data	jgromacs.data is a collection of classes representing multiple levels of structural data
jgromacs.io	jgromacs.io provides parsers for reading and methods for writing GROMACS files

Uses of Sequence in jgromacs.data

Methods in jgromacs.data that return Sequence

Sequence	Sequence.concat(Sequence other) Returns the given sequence concatenated to this sequence
Sequence	Alignment.getConsensusSequence() Returns the (majority) consensus sequence of the alignment
Sequence	Sequence.getReverse() Returns the reverse sequence
Sequence	Structure.getSequence() Returns the amino acid sequence of the structure
Sequence	Alignment.getSequence(int i) Returns sequence #i of the alignment
Sequence	Sequence.getSubSequence(int begin, int end) Returns subsequence beginning at sequence position #begin and ending at sequence position #end
Sequence	Sequence.getSubSequenceFrom(int begin) Returns subsequence beginning at sequence position #begin
Sequence	Sequence.getSubSequenceTo(int end) Returns subsequence ending at sequence position #end

Methods in jgromacs.data that return types with arguments of type Sequence

java.util.ArrayList<Sequence>

Alignment.getSequencesAsArrayList() Returns sequences of the alignment as an ArrayList object

Methods in jgromacs.data with parameters of type Sequence

void	Alignment.addSequence(Sequence seq) Adds a new sequence to the alignment
Sequence	Sequence.concat(Sequence other) Returns the given sequence concatenated to this sequence
boolean	Sequence.containsSubSequence(Sequence subsequence) Returns true if the given subsequence is contained in this sequence
void	Alignment.removeSequence(Sequence seq) Removes the given sequence from the alignment
void	Alignment.setSequence(int i, Sequence seq) Replaces sequence #i of the alignment with a new sequence

Uses of Sequence in jgromacs.io

Methods in jgromacs.io that return Sequence

static Sequence

IOData.readSequenceFromFASTA(java.lang.String filename) Reads a sequence from the given FASTA file

Methods in jgromacs.io with parameters of type Sequence

static void

IOData.writeSequenceToFASTA(java.lang.String filename, Sequence sequence) Writes a sequence to the given FASTA file