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Packages that use FastaSequence | |
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compbio.data.sequence | A data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project. |
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.sequence |
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Methods in compbio.data.sequence that return types with arguments of type FastaSequence | |
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java.util.List<FastaSequence> |
Alignment.getSequences()
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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 | |
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static boolean |
SequenceUtil.isNucleotideSequence(FastaSequence s)
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Method parameters in compbio.data.sequence with type arguments of type FastaSequence | |
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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 |
Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence | |
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Alignment(java.util.List<FastaSequence> sequences,
AlignmentMetadata metadata)
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Alignment(java.util.List<FastaSequence> sequences,
Program program,
char gapchar)
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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(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 limits the values defined by this Limit |
static LimitExceededException |
LimitExceededException.newLimitExceeded(Limit<?> limit,
java.util.List<FastaSequence> seqs)
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