Uses of Class
compbio.metadata.Preset

Packages that use Preset

Package	Description
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
compbio.data.msa.jaxws
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.ws.client	A command line client and web services testing client for JAva Bioinformatics Analysis Web Services.
compbio.ws.server

Uses of Preset in compbio.data.msa

Methods in compbio.data.msa with parameters of type Preset

Modifier and Type	Method and Description
java.lang.String	MsaWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<T> preset) Align a list of sequences with preset.
java.lang.String	SequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences, Preset<T> preset) Analyse the sequences according to the preset settings.

Uses of Preset in compbio.data.msa.jaxws

Fields in compbio.data.msa.jaxws declared as Preset

Modifier and Type	Field and Description
private Preset	PresetFold.preset
private Preset	PresetAnalize.preset
private Preset	PresetAlign.preset

Methods in compbio.data.msa.jaxws that return Preset

Modifier and Type	Method and Description
Preset	PresetFold.getPreset()
Preset	PresetAnalize.getPreset()
Preset	PresetAlign.getPreset()

Methods in compbio.data.msa.jaxws with parameters of type Preset

Modifier and Type	Method and Description
void	PresetFold.setPreset(Preset preset)
void	PresetAnalize.setPreset(Preset preset)
void	PresetAlign.setPreset(Preset preset)

Uses of Preset in compbio.metadata

Fields in compbio.metadata with type parameters of type Preset

Modifier and Type	Field and Description
(package private) java.util.List<Preset<T>>	PresetManager.preset

Methods in compbio.metadata that return Preset

Modifier and Type	Method and Description
Preset<T>	PresetManager.getPresetByName(java.lang.String presetName)

Methods in compbio.metadata that return types with arguments of type Preset

Modifier and Type	Method and Description
java.util.List<Preset<T>>	PresetManager.getPresets()

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

Modifier and Type	Method and Description
void	PresetManager.setPresets(java.util.List<Preset<T>> presets)

Uses of Preset in compbio.ws.client

Methods in compbio.ws.client that return Preset

Modifier and Type	Method and Description
(package private) static <T> Preset<T>	MetadataHelper.getPreset(Metadata<T> msaws, java.lang.String presetName) Returns Preset by its name

Methods in compbio.ws.client with parameters of type Preset

Modifier and Type	Method and Description
(package private) static <T> Alignment	Jws2Client.align(java.io.File file, MsaWS<T> msaws, Preset<T> preset, java.util.List<Option<T>> customOptions) Align sequences from the file using MsaWS
(package private) static ScoreManager	AAConClient.analize(java.io.File file, SequenceAnnotation<AAConWS> wsproxy, Preset<AAConWS> preset, java.util.List<Option<AAConWS>> customOptions) Calculate conservation for sequences loaded from the file
(package private) static <T> ScoreManager	Jws2Client.analize(java.io.File file, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions) Calculate conservation for sequences loaded from the file
(package private) static <T> ScoreManager	Jws2Client.analize(java.util.List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions) Calculate conservation for sequences loaded from a FASTA record list structure
private <T> boolean	WSTester.testDefaultAnalyse(java.util.List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions)

Method parameters in compbio.ws.client with type arguments of type Preset

Modifier and Type	Method and Description
private <T> boolean	WSTester.presetAlign(MsaWS<T> msaws, java.util.List<Preset<T>> presets) Calls alignment with preset

Uses of Preset in compbio.ws.server

Methods in compbio.ws.server with parameters of type Preset

Modifier and Type	Method and Description
java.lang.String	ClustalOWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<ClustalO> preset)
java.lang.String	ClustalWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<ClustalW> preset)
java.lang.String	GLprobsWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<GLprobs> preset)
java.lang.String	MafftWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Mafft> preset)
java.lang.String	MSAprobsWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<MSAprobs> preset)
java.lang.String	MuscleWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Muscle> preset)
java.lang.String	ProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Probcons> preset)
java.lang.String	TcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Tcoffee> preset)
java.lang.String	AAConWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<AACon> preset)
java.lang.String	DisemblWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<Disembl> preset)
java.lang.String	GlobPlotWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<GlobPlot> preset)
java.lang.String	IUPredWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<IUPred> preset)
java.lang.String	RNAalifoldWS.presetAnalize(java.util.List<FastaSequence> sequences, Preset<RNAalifold> preset)
java.lang.String	SequenceAnnotationService.presetAnalize(java.util.List<FastaSequence> sequences, Preset<T> preset)