Package org.snpeff.util

Class GprSeq

  • public class GprSeq
extends java.lang.Object

    • Constructor Summary

      Constructors 
      Constructor Description
      GprSeq()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static byte aa2Code​(char aa)
      Convert from AA char to code
      static byte[] aa2Code​(java.lang.String aa)
      Convert from AA sequence to codes
      static int aaPairCode​(byte aaCode1, byte aaCode2)
      Code an AA-pair
      static int aaPairCode​(char aa1, char aa2)
      Code an AA-pair
      static java.lang.String changeQuality​(java.lang.String qualityStr, org.biojava.nbio.genome.io.fastq.FastqVariant fqSrc, org.biojava.nbio.genome.io.fastq.FastqVariant fqDst)
      Change a fastQ encoding in a quality sequence
      static char code2aa​(byte aacode)
      Convert from AA_code to AA letter
      static java.lang.String code2aa​(byte[] aacodes)
      Convert from AA_code to AA letter
      static java.lang.String code2aa​(int[] aacodes)
      Convert from AA_code to AA letter
      static java.lang.String code2aaPair​(int code)  
      static char code2dna​(byte dnacode)
      Convert from DNA_code to DNA letter
      static byte dna2Code​(char base)
      Convert from DNA letter to code
      static java.lang.String fastaSimpleRead​(java.lang.String fastaFile)
      Read a fasta file containing one (and only one) sequence
      static java.lang.String fastqId​(org.biojava.nbio.genome.io.fastq.Fastq fastq)
      Get an ID from a fastq
      static boolean isAmbiguous​(java.lang.String sequence)
      Are there any ambiguous bases in this sequence?
      static java.lang.String padN​(java.lang.String seq, int size)  
      static char randBase​(java.util.Random random)
      Random base
      static java.lang.String randSequence​(java.util.Random random, int len)
      Random sequence
      static java.lang.String readId​(java.lang.String line)
      Create an ID: Remove everything after the first space char.
      static java.lang.String removeExt​(java.lang.String fileName)  
      static java.lang.String reverse​(java.lang.String seq)
      Reverse of a string (sequence)
      static java.lang.String reverseWc​(java.lang.String seq)
      Reverse Watson-Cricks complement
      static java.lang.String showMismatch​(java.lang.String seq1, java.lang.String seq2, java.lang.String prefix)
      Show differences between two sequences
      static java.lang.String string2fasta​(java.lang.String name, java.lang.String sequence)
      Transform into a FASTA formatted string
      static char wc​(char base)
      Watson-Cricks complement
      static java.lang.String wc​(java.lang.String seq)
      Watson-Cricks complement

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • BASES

        public static final char[] BASES

      • AMINO_ACIDS

        public static final char[] AMINO_ACIDS

      • KNOWN_FILE_EXTENSIONS

        public static final java.lang.String[] KNOWN_FILE_EXTENSIONS

      • AA_TO_CODE

        public static byte[] AA_TO_CODE

      • CODE_TO_AA

        public static char[] CODE_TO_AA

      • DNA_TO_CODE

        public static byte[] DNA_TO_CODE

      • CODE_TO_DNA

        public static char[] CODE_TO_DNA

    • Constructor Detail

      • GprSeq

        public GprSeq()

    • Method Detail

      • aa2Code

        public static byte aa2Code​(char aa)
        Convert from AA char to code

      • aa2Code

        public static byte[] aa2Code​(java.lang.String aa)
        Convert from AA sequence to codes

      • aaPairCode

        public static int aaPairCode​(byte aaCode1,
                             byte aaCode2)
        Code an AA-pair

      • aaPairCode

        public static int aaPairCode​(char aa1,
                             char aa2)
        Code an AA-pair

      • changeQuality

        public static java.lang.String changeQuality​(java.lang.String qualityStr,
                                             org.biojava.nbio.genome.io.fastq.FastqVariant fqSrc,
                                             org.biojava.nbio.genome.io.fastq.FastqVariant fqDst)
        Change a fastQ encoding in a quality sequence

      • code2aa

        public static char code2aa​(byte aacode)
        Convert from AA_code to AA letter

      • code2aa

        public static java.lang.String code2aa​(byte[] aacodes)
        Convert from AA_code to AA letter

      • code2aa

        public static java.lang.String code2aa​(int[] aacodes)
        Convert from AA_code to AA letter

      • code2aaPair

        public static java.lang.String code2aaPair​(int code)

      • code2dna

        public static char code2dna​(byte dnacode)
        Convert from DNA_code to DNA letter

      • dna2Code

        public static byte dna2Code​(char base)
        Convert from DNA letter to code

      • fastaSimpleRead

        public static java.lang.String fastaSimpleRead​(java.lang.String fastaFile)
        Read a fasta file containing one (and only one) sequence

      • fastqId

        public static java.lang.String fastqId​(org.biojava.nbio.genome.io.fastq.Fastq fastq)
        Get an ID from a fastq
        Parameters:
        fastq -
        Returns:
        Fastq's id

      • isAmbiguous

        public static boolean isAmbiguous​(java.lang.String sequence)
        Are there any ambiguous bases in this sequence?

      • padN

        public static java.lang.String padN​(java.lang.String seq,
                                    int size)

      • randBase

        public static char randBase​(java.util.Random random)
        Random base

      • randSequence

        public static java.lang.String randSequence​(java.util.Random random,
                                            int len)
        Random sequence

      • readId

        public static java.lang.String readId​(java.lang.String line)
        Create an ID: Remove everything after the first space char. Remove trailing '/1' or '/2' (if any)

      • removeExt

        public static java.lang.String removeExt​(java.lang.String fileName)

      • reverse

        public static java.lang.String reverse​(java.lang.String seq)
        Reverse of a string (sequence)

      • reverseWc

        public static java.lang.String reverseWc​(java.lang.String seq)
        Reverse Watson-Cricks complement

      • showMismatch

        public static java.lang.String showMismatch​(java.lang.String seq1,
                                            java.lang.String seq2,
                                            java.lang.String prefix)
        Show differences between two sequences

      • string2fasta

        public static java.lang.String string2fasta​(java.lang.String name,
                                            java.lang.String sequence)
        Transform into a FASTA formatted string

      • wc

        public static char wc​(char base)
        Watson-Cricks complement

      • wc

        public static java.lang.String wc​(java.lang.String seq)
        Watson-Cricks complement