Package org.biojava.nbio.core.sequence.io

Class FastaWriterHelper

java.lang.Object
org.biojava.nbio.core.sequence.io.FastaWriterHelper
public class FastaWriterHelper extends Object
The class that should be used to write out fasta file of a sequence collection
Author:
Scooter Willis

  • Constructor Details

    • FastaWriterHelper

      public FastaWriterHelper()

  • Method Details

    • writeProteinSequence

      public static void writeProteinSequence(File file, Collection<ProteinSequence> proteinSequences) throws Exception
      Write collection of protein sequences to a file
      Parameters:
      file -
      proteinSequences -
      Throws:
      Exception

    • writeProteinSequence

      public static void writeProteinSequence(OutputStream outputStream, Collection<ProteinSequence> proteinSequences) throws Exception
      Write collection of protein sequences to a stream
      Parameters:
      outputStream -
      proteinSequences -
      Throws:
      Exception

    • writeGeneSequence

      public static void writeGeneSequence(File file, Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws Exception
      Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
      Parameters:
      file -
      geneSequences -
      Throws:
      Exception

    • writeGeneSequence

      public static void writeGeneSequence(OutputStream outputStream, Collection<GeneSequence> geneSequences, boolean showExonUppercase) throws Exception
      Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
      Parameters:
      outputStream -
      dnaSequences -
      Throws:
      Exception

    • writeNucleotideSequence

      public static void writeNucleotideSequence(File file, Collection<DNASequence> dnaSequences) throws Exception
      Write a collection of NucleotideSequences to a file
      Parameters:
      file -
      dnaSequences -
      Throws:
      Exception

    • writeNucleotideSequence

      public static void writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences) throws Exception
      Write a collection of NucleotideSequences to a file
      Parameters:
      outputStream -
      dnaSequences -
      Throws:
      Exception

    • writeSequence

      public static void writeSequence(File file, Sequence<?> sequence) throws Exception
      Write a sequence to a file
      Parameters:
      file -
      sequence -
      Throws:
      Exception

    • writeSequence

      public static void writeSequence(OutputStream outputStream, Sequence<?> sequence) throws Exception
      Write a sequence to OutputStream
      Parameters:
      outputStream -
      sequence -
      Throws:
      Exception

    • writeSequences

      public static void writeSequences(OutputStream outputStream, Collection<Sequence<?>> sequences) throws Exception
      Method which will write your given Sequences to the specified OutputStream. This is a very generic method which writes just the AccessionID of the Sequence as the FASTA header.
      Parameters:
      outputStream - Stream to write to; can be System.out
      sequences - The sequences to write out
      Throws:
      Exception - Thrown normally thanks to IO problems