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

Class FastaWriterHelper

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

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void writeGeneSequence​(java.io.File file, java.util.Collection<GeneSequence> geneSequences, boolean showExonUppercase)
      Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
      static void writeGeneSequence​(java.io.OutputStream outputStream, java.util.Collection<GeneSequence> geneSequences, boolean showExonUppercase)
      Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
      static void writeNucleotideSequence​(java.io.File file, java.util.Collection<DNASequence> dnaSequences)
      Write a collection of NucleotideSequences to a file
      static void writeNucleotideSequence​(java.io.OutputStream outputStream, java.util.Collection<DNASequence> dnaSequences)
      Write a collection of NucleotideSequences to a file
      static void writeProteinSequence​(java.io.File file, java.util.Collection<ProteinSequence> proteinSequences)
      Write collection of protein sequences to a file
      static void writeProteinSequence​(java.io.OutputStream outputStream, java.util.Collection<ProteinSequence> proteinSequences)
      Write collection of protein sequences to a stream
      static void writeSequence​(java.io.File file, Sequence<?> sequence)
      Write a sequence to a file
      static void writeSequence​(java.io.OutputStream outputStream, Sequence<?> sequence)
      Write a sequence to OutputStream
      static void writeSequences​(java.io.OutputStream outputStream, java.util.Collection<Sequence<?>> sequences)
      Method which will write your given Sequences to the specified OutputStream.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • FastaWriterHelper

        public FastaWriterHelper()

    • Method Detail

      • writeProteinSequence

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

      • writeProteinSequence

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

      • writeGeneSequence

        public static void writeGeneSequence​(java.io.File file,
                                     java.util.Collection<GeneSequence> geneSequences,
                                     boolean showExonUppercase)
                              throws java.lang.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:
        java.lang.Exception

      • writeGeneSequence

        public static void writeGeneSequence​(java.io.OutputStream outputStream,
                                     java.util.Collection<GeneSequence> geneSequences,
                                     boolean showExonUppercase)
                              throws java.lang.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:
        java.lang.Exception

      • writeNucleotideSequence

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

      • writeNucleotideSequence

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

      • writeSequence

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

      • writeSequence

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

      • writeSequences

        public static void writeSequences​(java.io.OutputStream outputStream,
                                  java.util.Collection<Sequence<?>> sequences)
                           throws java.lang.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:
        java.lang.Exception - Thrown normally thanks to IO problems