+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=2ec79c02d827012990a6e689a877e2377ddf0a6e;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;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 new file mode 100644 index 0000000..2ec79c0 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -0,0 +1,985 @@ + + + + + + +Uses of Class compbio.data.sequence.FastaSequence + + + + + + + + + + + + +

+ + + + + + + + + + + + + + + +

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+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) + +
+
+ +