Class GenbankReaderHelper


  • public class GenbankReaderHelper
    extends java.lang.Object
    Author:
    Scooter Willis
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void main​(java.lang.String[] args)  
      static java.util.LinkedHashMap<java.lang.String,​DNASequence> readGenbankDNASequence​(java.io.File file)  
      static java.util.LinkedHashMap<java.lang.String,​DNASequence> readGenbankDNASequence​(java.io.File file, boolean lazySequenceLoad)
      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.
      static java.util.LinkedHashMap<java.lang.String,​DNASequence> readGenbankDNASequence​(java.io.InputStream inStream)
      Read a Genbank DNA sequence
      static java.util.LinkedHashMap<java.lang.String,​ProteinSequence> readGenbankProteinSequence​(java.io.File file)
      Read a Genbank file containing amino acids with setup that would handle most cases.
      static java.util.LinkedHashMap<java.lang.String,​ProteinSequence> readGenbankProteinSequence​(java.io.File file, boolean lazySequenceLoad)
      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.
      static java.util.LinkedHashMap<java.lang.String,​ProteinSequence> readGenbankProteinSequence​(java.io.InputStream inStream)
      Read a Genbank file containing amino acids with setup that would handle most cases.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • 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