Uses of Class
compbio.data.sequence.FastaSequence

Packages that use FastaSequence

Package	Description
compbio.data.sequence	A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.
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

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

Modifier and Type	Field and Description
protected java.util.List<FastaSequence>	Alignment.sequences

Methods in compbio.data.sequence that return FastaSequence

Modifier and Type	Method and Description
FastaSequence	FastaReader.next() Reads the next FastaSequence from the input
private static FastaSequence	FastaReader.toFastaSequence(java.lang.String singleFastaEntry)

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

Modifier and Type	Method and Description
java.util.List<FastaSequence>	Alignment.getSequences()
static java.util.List<FastaSequence>	SequenceUtil.openInputStream(java.lang.String inFilePath) Reads and parses Fasta or Clustal formatted file into a list of FastaSequence objects
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

Modifier and Type	Method and Description
static boolean	SequenceUtil.isNucleotideSequence(FastaSequence s)

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

Modifier and Type	Method and Description
static void	SequenceUtil.writeClustal(java.io.OutputStream outStream, java.util.List<FastaSequence> sequences, char gapChar)
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
static void	SequenceUtil.writeFastaKeepTheStream(java.io.OutputStream outstream, java.util.List<FastaSequence> sequences, int width)

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

Constructor and Description
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

Modifier and Type	Method and Description
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 this limit.
static LimitExceededException	LimitExceededException.newLimitExceeded(Limit<?> limit, java.util.List<FastaSequence> seqs)