Class FastaReaderHelper


  • public class FastaReaderHelper
    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> readFastaDNASequence​(java.io.File file)  
      static java.util.LinkedHashMap<java.lang.String,​DNASequence> readFastaDNASequence​(java.io.File file, boolean lazySequenceLoad)
      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.
      static java.util.LinkedHashMap<java.lang.String,​DNASequence> readFastaDNASequence​(java.io.InputStream inStream)
      Read a fasta DNA sequence
      static java.util.LinkedHashMap<java.lang.String,​ProteinSequence> readFastaProteinSequence​(java.io.File file)
      Read a fasta file containing amino acids with setup that would handle most cases.
      static java.util.LinkedHashMap<java.lang.String,​ProteinSequence> readFastaProteinSequence​(java.io.InputStream inStream)
      Read a fasta 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

      • FastaReaderHelper

        public FastaReaderHelper()
    • Method Detail

      • readFastaDNASequence

        public static java.util.LinkedHashMap<java.lang.String,​DNASequence> readFastaDNASequence​(java.io.File file,
                                                                                                       boolean lazySequenceLoad)
                                                                                                throws java.io.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:
        java.io.IOException
      • readFastaProteinSequence

        public static java.util.LinkedHashMap<java.lang.String,​ProteinSequence> readFastaProteinSequence​(java.io.File file)
                                                                                                        throws java.io.IOException
        Read a fasta file containing amino acids with setup that would handle most cases.
        Parameters:
        file -
        Returns:
        Throws:
        java.io.IOException
      • readFastaProteinSequence

        public static java.util.LinkedHashMap<java.lang.String,​ProteinSequence> readFastaProteinSequence​(java.io.InputStream inStream)
                                                                                                        throws java.io.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:
        java.io.IOException
      • readFastaDNASequence

        public static java.util.LinkedHashMap<java.lang.String,​DNASequence> readFastaDNASequence​(java.io.InputStream inStream)
                                                                                                throws java.io.IOException
        Read a fasta DNA sequence
        Parameters:
        inStream -
        Returns:
        Throws:
        java.io.IOException
      • readFastaDNASequence

        public static java.util.LinkedHashMap<java.lang.String,​DNASequence> readFastaDNASequence​(java.io.File file)
                                                                                                throws java.io.IOException
        Parameters:
        file -
        Returns:
        Throws:
        java.io.IOException
      • main

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