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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.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
 java.lang.String MsaWS.align(java.util.List<FastaSequence> sequences)
          Align a list of sequences with default settings.
 java.lang.String SequenceAnnotation.analize(java.util.List<FastaSequence> sequences)
          Analyse the sequences.
 java.lang.String MsaWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options)
          Align a list of sequences with options.
 java.lang.String SequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options)
          Analyse the sequences according to custom settings defined in options list.
 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 FastaSequence in compbio.data.msa.jaxws
 

Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence
 java.util.List<FastaSequence> PresetAnalize.getFastaSequences()
           
 java.util.List<FastaSequence> PresetAlign.getFastaSequences()
           
 java.util.List<FastaSequence> CustomAnalize.getFastaSequences()
           
 java.util.List<FastaSequence> CustomAlign.getFastaSequences()
           
 java.util.List<FastaSequence> Analize.getFastaSequences()
           
 java.util.List<FastaSequence> Align.getFastaSequences()
           
 

Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
 void PresetAnalize.setFastaSequences(java.util.List<FastaSequence> fastaSequences)
           
 void PresetAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences)
           
 void CustomAnalize.setFastaSequences(java.util.List<FastaSequence> fastaSequences)
           
 void CustomAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences)
           
 void Analize.setFastaSequences(java.util.List<FastaSequence> fastaSequences)
           
 void Align.setFastaSequences(java.util.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
 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
static boolean SequenceUtil.isNucleotideSequence(FastaSequence s)
           
 

Method parameters in compbio.data.sequence with type arguments of type FastaSequence
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
Alignment(java.util.List<FastaSequence> sequences, AlignmentMetadata metadata)
           
Alignment(java.util.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, java.util.List<FastaSequence> dataSet)
           
static
<T,V> Executable.ExecProvider
LoadBalancer.getEngine(Executable<V> executable, java.util.List<FastaSequence> dataSet)
           
 

Uses of FastaSequence in compbio.metadata
 

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

Uses of FastaSequence in compbio.runner
 

Method parameters in compbio.runner with type arguments of type FastaSequence
static void Util.writeInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec)
           
 

Uses of FastaSequence in compbio.ws.server
 

Method parameters in compbio.ws.server with type arguments of type FastaSequence
 java.lang.String MafftWS.align(java.util.List<FastaSequence> sequences)
           
 java.lang.String ClustalOWS.align(java.util.List<FastaSequence> sequences)
           
 java.lang.String ProbconsWS.align(java.util.List<FastaSequence> sequences)
           
 java.lang.String TcoffeeWS.align(java.util.List<FastaSequence> sequences)
           
 java.lang.String ClustalWS.align(java.util.List<FastaSequence> sequences)
           
 java.lang.String MuscleWS.align(java.util.List<FastaSequence> sequences)
           
static
<T> java.lang.String
WSUtil.align(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger, java.lang.String callingMethod, Limit<T> limit)
           
 java.lang.String AAConWS.analize(java.util.List<FastaSequence> sequences)
           
 java.lang.String SequenceAnnotationService.analize(java.util.List<FastaSequence> sequences)
           
static
<T> java.lang.String
WSUtil.analize(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, java.lang.String method, Limit<T> limit)
           
 java.lang.String ClustalOWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalO>> options)
           
 java.lang.String ClustalWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalW>> options)
           
 java.lang.String MafftWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Mafft>> options)
           
 java.lang.String MuscleWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Muscle>> options)
           
 java.lang.String ProbconsWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Probcons>> options)
           
 java.lang.String TcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Tcoffee>> options)
           
 java.lang.String DisemblWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<Disembl>> options)
           
 java.lang.String GlobPlotWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<GlobPlot>> options)
           
 java.lang.String SequenceAnnotationService.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options)
           
 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 MafftWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Mafft> 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 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 SequenceAnnotationService.presetAnalize(java.util.List<FastaSequence> sequences, Preset<T> preset)
           
static void WSUtil.validateAAConInput(java.util.List<FastaSequence> sequences)
           
static void WSUtil.validateFastaInput(java.util.List<FastaSequence> sequences)
           
 

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