Package org.biojava.nbio.data.sequence

Class FastaSequence

  • All Implemented Interfaces:
    java.lang.Comparable<FastaSequence>
    public final class FastaSequence
extends java.lang.Object
implements java.lang.Comparable<FastaSequence>
    A FASTA formatted sequence. Please note that this class does not make any assumptions as to what sequence it store e.g. it could be nucleotide, protein or even gapped alignment sequence! The only guarantee it makes is that the sequence does not contain white space characters e.g. spaces, new lines etc
    Since:
    3.0.2
    Version:
    1.0
    Author:
    pvtroshin

    • Constructor Detail

      • FastaSequence

        public FastaSequence​(java.lang.String id,
                     java.lang.String sequence)
        Upon construction the any whitespace characters are removed from the sequence
        Parameters:
        id -
        sequence -

    • Method Detail

      • getId

        public java.lang.String getId()
        Gets the value of id
        Returns:
        the value of id

      • getSequence

        public java.lang.String getSequence()
        Gets the value of sequence
        Returns:
        the value of sequence

      • countMatchesInSequence

        public static int countMatchesInSequence​(java.lang.String theString,
                                         java.lang.String theRegExp)

      • getFormattedFasta

        public java.lang.String getFormattedFasta()

      • getOnelineFasta

        public java.lang.String getOnelineFasta()
        Returns:
        one line name, next line sequence, no matter what the sequence length is

      • getFormatedSequence

        public java.lang.String getFormatedSequence​(int width)
        Format sequence per width letter in one string. Without spaces.
        Returns:
        multiple line formated sequence, one line width letters length

      • getLength

        public int getLength()
        Returns:
        sequence length

      • toString

        public java.lang.String toString()
        Same as oneLineFasta
        Overrides:
        toString in class java.lang.Object

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • equals

        public boolean equals​(java.lang.Object obj)
        Overrides:
        equals in class java.lang.Object

      • compareTo

        public int compareTo​(FastaSequence o)
        Specified by:
        compareTo in interface java.lang.Comparable<FastaSequence>