public class FastaReaderTools extends java.lang.Object
FastaReaderHelper
does not offer.Constructor and Description |
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FastaReaderTools() |
Modifier and Type | Method and Description |
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static java.util.Map<java.lang.String,org.biojava3.core.sequence.DNASequence> |
readDNAAlignment(java.io.File file)
Reads an alignment contained in a FASTA file.
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static java.util.Map<java.lang.String,org.biojava3.core.sequence.DNASequence> |
readDNAAlignment(java.io.InputStream stream)
Reads an alignment contained in a FASTA file.
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public FastaReaderTools()
public static java.util.Map<java.lang.String,org.biojava3.core.sequence.DNASequence> readDNAAlignment(java.io.File file) throws java.io.IOException
FastaReaderHelper.readFastaDNASequence(InputStream)
the AlignmentAmbiguityNucleotideCompoundSet
is used here, so that alignments containing gaps and ambiguity codes can also be processed.file
- the file to read the data fromjava.io.IOException
public static java.util.Map<java.lang.String,org.biojava3.core.sequence.DNASequence> readDNAAlignment(java.io.InputStream stream) throws java.io.IOException
FastaReaderHelper.readFastaDNASequence(InputStream)
the AlignmentAmbiguityNucleotideCompoundSet
is used here, so that alignments containing gaps and ambiguity codes can also be processed.stream
- the stream to read the data fromjava.io.IOException