-Uses of Class compbio.data.sequence.FastaSequence -

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FFastaSequence.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FFastaSequence.html;h=0000000000000000000000000000000000000000;hb=0bbebf27d045b1345bc042bdf24ef2e6808df251;hp=af4c05de9a23c45ee78213575ed4ec033bd96b4f;hpb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;p=jabaws.git diff --git a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html deleted file mode 100644 index af4c05d..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html +++ /dev/null @@ -1,985 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.FastaSequence - - - - - - - - - - - - -

- - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

- -

- PREV - NEXT

- FRAMES - NO FRAMES - - - - -

- - - -

- -

-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.
- -

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() - -
-
- -

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) - -
-
- -

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 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 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) - -
-
- -

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) - -
-
- -

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) - -
-
- -

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) - -
-
- -

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) - -
-
- -

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) - -
-
- -

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) - -
-
- -