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

Class GenbankReaderHelper

java.lang.Object
org.biojava.nbio.core.sequence.io.GenbankReaderHelper
public class GenbankReaderHelper extends Object
Author:
Scooter Willis

  • Constructor Details

    • GenbankReaderHelper

      public GenbankReaderHelper()

  • Method Details

    • readGenbankDNASequence

      public static LinkedHashMap<String,DNASequence> readGenbankDNASequence(File file, boolean lazySequenceLoad) throws 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:
      Exception

    • readGenbankProteinSequence

      public static LinkedHashMap<String,ProteinSequence> readGenbankProteinSequence(File file, boolean lazySequenceLoad) throws 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:
      Exception

    • readGenbankProteinSequence

      public static LinkedHashMap<String,ProteinSequence> readGenbankProteinSequence(File file) throws Exception
      Read a Genbank file containing amino acids with setup that would handle most cases.
      Parameters:
      file -
      Returns:
      Throws:
      Exception

    • readGenbankProteinSequence

      public static LinkedHashMap<String,ProteinSequence> readGenbankProteinSequence(InputStream inStream) throws 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:
      Exception

    • readGenbankDNASequence

      public static LinkedHashMap<String,DNASequence> readGenbankDNASequence(InputStream inStream) throws Exception
      Read a Genbank DNA sequence
      Parameters:
      inStream -
      Returns:
      Throws:
      Exception

    • readGenbankDNASequence

      public static LinkedHashMap<String,DNASequence> readGenbankDNASequence(File file) throws Exception
      Parameters:
      file -
      Returns:
      Throws:
      Exception

    • main

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