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