org.strbio.mol.lib
Class BlastConstants

java.lang.Object
  org.strbio.mol.lib.BlastConstants

public class BlastConstants
extends java.lang.Object

Some constants used in BLAST 2.0.6.

  Version 1.0, 1/26/99 - original version
  

Version:

1.0, 1/26/99

Author:

JMC

Field Summary

static java.lang.String

oneLetterBLAST one letter code used by BLAST.

Constructor Summary

BlastConstants()

Method Summary

static IMatrix	blosum62() The Blosum62 matrix, without the BZX* columns.
static char	num2ResBLAST(int x) Convert a number to amino acid one letter code (0-25), in the order shown in oneLetterBlast
static int	res2NumBLAST(char x) Convert an amino acid one letter code to a number (0-25), in the order shown in Residue.oneLetterBLAST.
static DVector	standardProb() What BLAST thinks are the standard probabilities of each residue occurring.

Methods inherited from class java.lang.Object

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

Field Detail

oneLetterBLAST

public static final java.lang.String oneLetterBLAST

one letter code used by BLAST. Note that not all of these are actual residues. Internally, matrix seems to be seqlength x 26, but only 20 saved in file (in same order as Residue.num2Res)

See Also:

Constant Field Values

Constructor Detail

BlastConstants

public BlastConstants()

Method Detail

num2ResBLAST

public static final char num2ResBLAST(int x)
                               throws java.lang.IllegalArgumentException

Convert a number to amino acid one letter code (0-25), in the order shown in oneLetterBlast

Throws:

java.lang.IllegalArgumentException - if your number is not 0-25.

res2NumBLAST

public static final int res2NumBLAST(char x)
                              throws java.lang.IllegalArgumentException

Convert an amino acid one letter code to a number (0-25), in the order shown in Residue.oneLetterBLAST.

Throws:

java.lang.IllegalArgumentException - if your code isn't an AA.

See Also:

Residue.oneLetterDefay, Residue.isRes(char)

standardProb

public static final DVector standardProb()

What BLAST thinks are the standard probabilities of each residue occurring. These have already been converted from BLAST order to standard order of AA (but starting with 0=A, not 0=dash).

blosum62

public static final IMatrix blosum62()

The Blosum62 matrix, without the BZX* columns. Note 0=ALA, not 0=dash.