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java.lang.Objectorg.biojava3.core.sequence.io.FastaWriter<S,C>
public class FastaWriter<S extends Sequence<?>,C extends Compound>
The FastaWriter writes a collection of sequences to an outputStream. FastaWriterHelper should be used to write out sequences. Each sequence loaded from a fasta file retains the original Fasta header and that is used when writing to the stream. This behavior can be overwritten by implementing a custom FastaHeaderFormatInterface.
Constructor Summary | |
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FastaWriter(OutputStream os,
Collection<S> sequences,
FastaHeaderFormatInterface<S,C> headerFormat)
Use default line length of 60 |
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FastaWriter(OutputStream os,
Collection<S> sequences,
FastaHeaderFormatInterface<S,C> headerFormat,
int lineLength)
Set custom lineLength |
Method Summary | |
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int |
getLineLength()
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static void |
main(String[] args)
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void |
process()
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void |
setLineLength(int lineLength)
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void |
setLineSeparator(String lineSeparator)
Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat)
os
- sequences
- headerFormat
- public FastaWriter(OutputStream os, Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat, int lineLength)
os
- sequences
- headerFormat
- lineLength
- Method Detail |
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public void setLineSeparator(String lineSeparator)
lineSeparator
- public void process() throws Exception
Exception
public static void main(String[] args)
public int getLineLength()
public void setLineLength(int lineLength)
lineLength
- the lineLength to set
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