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Packages that use FastaSequence | |
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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 |
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Method parameters in compbio.data.msa with type arguments of type FastaSequence | |
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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 |
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Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence | |
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List<FastaSequence> |
PresetAnalize.getFastaSequences()
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List<FastaSequence> |
PresetAlign.getFastaSequences()
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List<FastaSequence> |
CustomAnalize.getFastaSequences()
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List<FastaSequence> |
CustomAlign.getFastaSequences()
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List<FastaSequence> |
Analize.getFastaSequences()
|
List<FastaSequence> |
Align.getFastaSequences()
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Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence | |
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void |
PresetAnalize.setFastaSequences(List<FastaSequence> fastaSequences)
|
void |
PresetAlign.setFastaSequences(List<FastaSequence> fastaSequences)
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void |
CustomAnalize.setFastaSequences(List<FastaSequence> fastaSequences)
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void |
CustomAlign.setFastaSequences(List<FastaSequence> fastaSequences)
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void |
Analize.setFastaSequences(List<FastaSequence> fastaSequences)
|
void |
Align.setFastaSequences(List<FastaSequence> fastaSequences)
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Uses of FastaSequence in compbio.data.sequence |
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Methods in compbio.data.sequence that return FastaSequence | |
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FastaSequence |
FastaReader.next()
Reads the next FastaSequence from the input |
Methods in compbio.data.sequence that return types with arguments of type FastaSequence | |
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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 | |
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static boolean |
SequenceUtil.isNucleotideSequence(FastaSequence s)
|
Method parameters in compbio.data.sequence with type arguments of type FastaSequence | |
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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 | |
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Alignment(List<FastaSequence> sequences,
AlignmentMetadata metadata)
|
|
Alignment(List<FastaSequence> sequences,
Program program,
char gapchar)
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Uses of FastaSequence in compbio.engine |
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Method parameters in compbio.engine with type arguments of type FastaSequence | ||
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static
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Configurator.configureExecutable(Executable<T> executable,
List<FastaSequence> dataSet)
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static
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LoadBalancer.getEngine(Executable<V> executable,
List<FastaSequence> dataSet)
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Uses of FastaSequence in compbio.metadata |
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Method parameters in compbio.metadata with type arguments of type FastaSequence | |
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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 |
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Constructor parameters in compbio.pipeline._jpred with type arguments of type FastaSequence | |
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Pairwise(List<FastaSequence> sequences)
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Uses of FastaSequence in compbio.runner |
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Method parameters in compbio.runner with type arguments of type FastaSequence | |
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static void |
Util.writeInput(List<FastaSequence> sequences,
ConfiguredExecutable<?> exec)
|
Uses of FastaSequence in compbio.ws.server |
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