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| -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.metadata | -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. | -
| -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)
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-- 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()
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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()
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-- |
-
- List<FastaSequence> |
-Align.getFastaSequences()
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-- |
-
- -
| 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)
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-- |
-
| -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 | -|
|---|---|
- List<FastaSequence> |
-Alignment.getSequences()
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-- |
-
-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)
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-- |
-
- -
| 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)
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-- |
-
- -
| 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.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)
-
-- |
-
-
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