Uses of Class
compbio.data.sequence.FastaSequence

Packages that use FastaSequence

compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
compbio.data.msa.jaxws
compbio.data.sequence	A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.
compbio.engine
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.
compbio.pipeline._jpred
compbio.runner	Utilities commonly used by all runners.
compbio.ws.server

Uses of FastaSequence in compbio.data.msa

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

String	MsaWS.align(List<FastaSequence> sequences) Align a list of sequences with default settings.
String	SequenceAnnotation.analize(List<FastaSequence> sequences) Analyse the sequences.
String	MsaWS.customAlign(List<FastaSequence> sequences, List<Option<T>> options) Align a list of sequences with options.
String	SequenceAnnotation.customAnalize(List<FastaSequence> sequences, List<Option<T>> options) Analyse the sequences according to custom settings defined in options list.
String	MsaWS.presetAlign(List<FastaSequence> sequences, Preset<T> preset) Align a list of sequences with preset.
String	SequenceAnnotation.presetAnalize(List<FastaSequence> sequences, Preset<T> preset) Analyse the sequences according to the preset settings.

Uses of FastaSequence in compbio.data.msa.jaxws

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

List<FastaSequence>	PresetAnalize.getFastaSequences()
List<FastaSequence>	PresetAlign.getFastaSequences()
List<FastaSequence>	CustomAnalize.getFastaSequences()
List<FastaSequence>	CustomAlign.getFastaSequences()
List<FastaSequence>	Analize.getFastaSequences()
List<FastaSequence>	Align.getFastaSequences()

Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence

void	PresetAnalize.setFastaSequences(List<FastaSequence> fastaSequences)
void	PresetAlign.setFastaSequences(List<FastaSequence> fastaSequences)
void	CustomAnalize.setFastaSequences(List<FastaSequence> fastaSequences)
void	CustomAlign.setFastaSequences(List<FastaSequence> fastaSequences)
void	Analize.setFastaSequences(List<FastaSequence> fastaSequences)
void	Align.setFastaSequences(List<FastaSequence> fastaSequences)

Uses of FastaSequence in compbio.data.sequence

Methods in compbio.data.sequence that return FastaSequence

FastaSequence

FastaReader.next() Reads the next FastaSequence from the input

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

List<FastaSequence>	Alignment.getSequences()
static List<FastaSequence>	SequenceUtil.openInputStream(String inFilePath) Reads and parses Fasta or Clustal formatted file into a list of FastaSequence objects
static List<FastaSequence>	SequenceUtil.readFasta(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(OutputStream os, List<FastaSequence> sequences) Writes FastaSequence in the file, each sequence will take one line only
static void	SequenceUtil.writeFasta(OutputStream outstream, 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(OutputStream outstream, List<FastaSequence> sequences, int width)

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

Alignment(List<FastaSequence> sequences, AlignmentMetadata metadata)

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

Uses of FastaSequence in compbio.engine

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

static <T> ConfiguredExecutable<T>	Configurator.configureExecutable(Executable<T> executable, List<FastaSequence> dataSet)
static <T,V> Executable.ExecProvider	LoadBalancer.getEngine(Executable<V> executable, List<FastaSequence> dataSet)

Uses of FastaSequence in compbio.metadata

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

static int	Limit.getAvgSequenceLength(List<FastaSequence> data) Calculates an average sequence length of the dataset
boolean	Limit.isExceeded(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, List<FastaSequence> seqs)

Uses of FastaSequence in compbio.pipeline._jpred

Constructor parameters in compbio.pipeline._jpred with type arguments of type FastaSequence

Pairwise(List<FastaSequence> sequences)

Uses of FastaSequence in compbio.runner

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

static void

Util.writeInput(List<FastaSequence> sequences, ConfiguredExecutable<?> exec)

Uses of FastaSequence in compbio.ws.server

Method parameters in compbio.ws.server with type arguments of type FastaSequence

String	ClustalWS.align(List<FastaSequence> sequences)
String	_MsaService.align(List<FastaSequence> sequences)
String	MuscleWS.align(List<FastaSequence> sequences)
String	MafftWS.align(List<FastaSequence> sequences)
String	TcoffeeWS.align(List<FastaSequence> sequences)
String	ProbconsWS.align(List<FastaSequence> sequences)
String	ClustalOWS.align(List<FastaSequence> sequences)
static <T> String	WSUtil.align(List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger, String callingMethod, Limit<T> limit)
String	AAConWS.analize(List<FastaSequence> sequences)
String	SequenceAnnotationService.analize(List<FastaSequence> sequences)
static <T> String	WSUtil.analize(List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, String method, Limit<T> limit)
String	ClustalOWS.customAlign(List<FastaSequence> sequences, List<Option<ClustalO>> options)
String	ClustalWS.customAlign(List<FastaSequence> sequences, List<Option<ClustalW>> options)
String	MafftWS.customAlign(List<FastaSequence> sequences, List<Option<Mafft>> options)
String	MuscleWS.customAlign(List<FastaSequence> sequences, List<Option<Muscle>> options)
String	ProbconsWS.customAlign(List<FastaSequence> sequences, List<Option<Probcons>> options)
String	_MsaService.customAlign(List<FastaSequence> sequences, List<Option<T>> options)
String	TcoffeeWS.customAlign(List<FastaSequence> sequences, List<Option<Tcoffee>> options)
String	DisemblWS.customAnalize(List<FastaSequence> sequences, List<Option<Disembl>> options)
String	GlobPlotWS.customAnalize(List<FastaSequence> sequences, List<Option<GlobPlot>> options)
String	SequenceAnnotationService.customAnalize(List<FastaSequence> sequences, List<Option<T>> options)
String	ClustalOWS.presetAlign(List<FastaSequence> sequences, Preset<ClustalO> preset)
String	ClustalWS.presetAlign(List<FastaSequence> sequences, Preset<ClustalW> preset)
String	MafftWS.presetAlign(List<FastaSequence> sequences, Preset<Mafft> preset)
String	MuscleWS.presetAlign(List<FastaSequence> sequences, Preset<Muscle> preset)
String	ProbconsWS.presetAlign(List<FastaSequence> sequences, Preset<Probcons> preset)
String	_MsaService.presetAlign(List<FastaSequence> sequences, Preset<T> preset)
String	TcoffeeWS.presetAlign(List<FastaSequence> sequences, Preset<Tcoffee> preset)
String	DisemblWS.presetAnalize(List<FastaSequence> sequences, Preset<Disembl> preset)
String	GlobPlotWS.presetAnalize(List<FastaSequence> sequences, Preset<GlobPlot> preset)
String	IUPredWS.presetAnalize(List<FastaSequence> sequences, Preset<IUPred> preset)
String	SequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, Preset<T> preset)
static void	WSUtil.validateAAConInput(List<FastaSequence> sequences)
static void	WSUtil.validateFastaInput(List<FastaSequence> sequences)