org.strbio.app
Class Align

java.lang.Object
  extended by org.strbio.app.Align

public class Align
extends java.lang.Object

Shows alignment of a given sequence with a fold. Run with no options to see valid command line options.

  Version 1.5, 1/30/1 - would sometimes incorrectly report ASns as ASpc
  Version 1.47, 1/8/1 - added -showmodeller
  Version 1.46, 9/7/00 - added -renum hacks
  Version 1.45, 8/28/00 - added -op support for casp format
  Version 1.44, 1/7/00 - added Sippl90 potential
  Version 1.43, 11/11/99 - added apsiblast, rpsiblast, arpsiblast
  Version 1.42, 10/28/99 - precalculates dihedrals where needed
  Version 1.41, 7/8/99 - added -saveparam option, -resume option
  Version 1.4, 6/4/99 - added -allmatches option
  Version 1.39, 5/18/99 - added -jdb option
  Version 1.38, 3/11/99 - added -using option
  Version 1.37, 2/26/99 - adapted to new GapModel API.
  Version 1.36, 2/25/99 - ident is no longer scaled.
  Version 1.35, 2/24/99 - added optimization for ASns
  Version 1.34, 2/1/99 - added Blast scoring options
  Version 1.33, 11/9/98 - can save predicted alignment
  Version 1.32, 9/2/98 - added table option to defay matrix
  Version 1.31, 8/3/98 - changed possible JMCPotential reference states
  Version 1.3, 7/9/98 - added separate, sigma to JMCPotential
  Version 1.2, 4/7/98 - can use substitution matrices, also fixed docs.
  Version 1.1, 4/3/98 - new scoring function scheme.
  Version 1.0, 3/25/98 - adapted from align 1.592
  

Version:
1.5, 1/30/1
Author:
JMC
See Also:
ThreadSet

Constructor Summary
Align()
           
 
Method Summary
static void main(java.lang.String[] argv)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Align

public Align()
Method Detail

main

public static final void main(java.lang.String[] argv)