Package org.biojava.nbio.data.sequence

Class FastaSequence

java.lang.Object
org.biojava.nbio.data.sequence.FastaSequence
All Implemented Interfaces:
Comparable<FastaSequence>
public final class FastaSequence extends Object implements 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 Details

    • FastaSequence

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

  • Method Details

    • getId

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

    • getSequence

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

    • countMatchesInSequence

      public static int countMatchesInSequence(String theString, String theRegExp)

    • getFormattedFasta

      public String getFormattedFasta()

    • getOnelineFasta

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

    • getFormatedSequence

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

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • compareTo

      public int compareTo(FastaSequence o)
      Specified by:
      compareTo in interface Comparable<FastaSequence>