org.strbio.mol.lib
Class BlastConstants

java.lang.Object
  extended by 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.