Class FastaReaderHelper

Method Details

• readFastaDNASequence

  public static LinkedHashMap<String,DNASequence> readFastaDNASequence(File file, boolean lazySequenceLoad) throws IOException

  Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk. This allows the loading of large fasta files where you are only interested in one sequence based on accession id.

  Parameters:

  file -

  lazySequenceLoad -

  Returns:

  Throws:

  IOException

• readFastaProteinSequence

  public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(File file) throws IOException

  Read a fasta file containing amino acids with setup that would handle most cases.

  Parameters:

  file -

  Returns:

  Throws:

  IOException

• readFastaProteinSequence

  public static LinkedHashMap<String,ProteinSequence> readFastaProteinSequence(InputStream inStream) throws IOException

  Read a fasta file containing amino acids with setup that would handle most cases. User is responsible for closing InputStream because you opened it

  Parameters:

  inStream -

  Returns:

  Throws:

  IOException

• readFastaDNASequence

  public static LinkedHashMap<String,DNASequence> readFastaDNASequence(InputStream inStream) throws IOException

  Read a fasta DNA sequence

  Parameters:

  inStream -

  Returns:

  Throws:

  IOException

• readFastaDNASequence

  public static LinkedHashMap<String,DNASequence> readFastaDNASequence(File file) throws IOException

  Parameters:

  file -

  Returns:

  Throws:

  IOException

• main

  public static void main(String[] args) throws Exception

  Throws:

  Exception