Field Detail

• FASTA_DESC_LINE

  public static final java.util.regex.Pattern FASTA_DESC_LINE

Constructor Detail

• FastaParser

  public FastaParser()

Method Detail

• main

  public static void main(java.lang.String[] args)

• isLikelyFasta

  public static boolean isLikelyFasta(java.io.File f)
                               throws java.io.IOException

  Throws:

  java.io.IOException

• isLikelyFasta

  public static boolean isLikelyFasta(java.io.InputStream is)
                               throws java.io.IOException

  Throws:

  java.io.IOException

• parseMsa

  public static Msa parseMsa(java.io.File f)
                      throws java.io.IOException

  Throws:

  java.io.IOException

• parseMsa

  public static Msa parseMsa(java.io.InputStream is)
                      throws java.io.IOException

  Throws:

  java.io.IOException

• parseMsa

  public static Msa parseMsa(java.lang.String s)
                      throws java.io.IOException

  Throws:

  java.io.IOException

• parseMsa

  public static Msa parseMsa(byte[] bytes)
                      throws java.io.IOException

  Throws:

  java.io.IOException

• parse

  public static java.util.List<MolecularSequence> parse(java.io.File f)
                                                 throws java.io.IOException

  Throws:

  java.io.IOException

• parse

  public static java.util.List<MolecularSequence> parse(java.io.InputStream is)
                                                 throws java.io.IOException

  Throws:

  java.io.IOException