Uses of Class
compbio.data.sequence.FastaSequence

Packages that use FastaSequence

compbio.data.sequence	A data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project.
compbio.metadata	A meta-data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project.

Uses of FastaSequence in compbio.data.sequence

Methods in compbio.data.sequence that return types with arguments of type FastaSequence

java.util.List<FastaSequence>	Alignment.getSequences()
static java.util.List<FastaSequence>	SequenceUtil.readFasta(java.io.InputStream inStream) Reads fasta sequences from inStream into the list of FastaSequence objects

Methods in compbio.data.sequence with parameters of type FastaSequence

static boolean

SequenceUtil.isNucleotideSequence(FastaSequence s)

Method parameters in compbio.data.sequence with type arguments of type FastaSequence

static void	SequenceUtil.writeFasta(java.io.OutputStream os, java.util.List<FastaSequence> sequences) Writes FastaSequence in the file, each sequence will take one line only
static void	SequenceUtil.writeFasta(java.io.OutputStream outstream, java.util.List<FastaSequence> sequences, int width) Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence

Alignment(java.util.List<FastaSequence> sequences, AlignmentMetadata metadata)

Alignment(java.util.List<FastaSequence> sequences, Program program, char gapchar)

Uses of FastaSequence in compbio.metadata

Method parameters in compbio.metadata with type arguments of type FastaSequence

static int	Limit.getAvgSequenceLength(java.util.List<FastaSequence> data) Calculates an average sequence length of the dataset
boolean	Limit.isExceeded(java.util.List<FastaSequence> data) Checks if the number of sequences or their average length in the dataset exceeds limits the values defined by this Limit
static LimitExceededException	LimitExceededException.newLimitExceeded(Limit<?> limit, java.util.List<FastaSequence> seqs)