Constructor Detail

• GenbankReaderHelper

  public GenbankReaderHelper​()

Method Detail

• readGenbankDNASequence

  public static java.util.LinkedHashMap<java.lang.String,DNASequence> readGenbankDNASequence​(java.io.File file,
                                                                                             boolean lazySequenceLoad)
                                                                                      throws java.lang.Exception

  Selecting lazySequenceLoad=true will parse the Genbank 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 Genbank files where you are only interested in one sequence based on accession id.

  Parameters:

  file -

  lazySequenceLoad -

  Returns:

  Throws:

  java.lang.Exception

• readGenbankProteinSequence

  public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readGenbankProteinSequence​(java.io.File file,
                                                                                                     boolean lazySequenceLoad)
                                                                                              throws java.lang.Exception

  Selecting lazySequenceLoad=true will parse the Genbank 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 Genbank files where you are only interested in one sequence based on accession id.

  Parameters:

  file -

  lazySequenceLoad -

  Returns:

  Throws:

  java.lang.Exception

• readGenbankProteinSequence

  public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readGenbankProteinSequence​(java.io.File file)
                                                                                              throws java.lang.Exception

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

  Parameters:

  file -

  Returns:

  Throws:

  java.lang.Exception

• readGenbankProteinSequence

  public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> readGenbankProteinSequence​(java.io.InputStream inStream)
                                                                                              throws java.lang.Exception

  Read a Genbank 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:

  java.lang.Exception

• readGenbankDNASequence

  public static java.util.LinkedHashMap<java.lang.String,DNASequence> readGenbankDNASequence​(java.io.InputStream inStream)
                                                                                      throws java.lang.Exception

  Read a Genbank DNA sequence

  Parameters:

  inStream -

  Returns:

  Throws:

  java.lang.Exception

• readGenbankDNASequence

  public static java.util.LinkedHashMap<java.lang.String,DNASequence> readGenbankDNASequence​(java.io.File file)
                                                                                      throws java.lang.Exception

  Parameters:

  file -

  Returns:

  Throws:

  java.lang.Exception

• main

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

  Throws:

  java.lang.Exception