Re: [Biojava-l] getting involved

2006-01-12 Thread Simon Rouane
Thanks for everyones comments. I'll do a bit more reading and then get back to you... Is your testing done using JUNIT? Simon. From: [EMAIL PROTECTED] To: "Simon Rouane" <[EMAIL PROTECTED]> CC: [email protected], [EMAIL PROTECTED] Subject: Re: [Biojava-l] getting involved Date: Thu, 12 Ja

[Biojava-l] Re: strange pdb

2006-01-12 Thread Tamas Horvath
(wow... stupid linewrap...)It seems to me, that we need a variance tag for the Group or Atom object...As a beginning... The altloc is supposedly means variation of the atomsposition, but it seems to me, it makes more sense to treat the alternates asalternative groups, as in the cases I've so far

Re: [Biojava-l] Generalized HMM in biojava?

2006-01-12 Thread Matthew Pocock
On Wednesday 11 January 2006 16:03, wendy wong wrote: > Thanks! > Now I have two questions about the SimpleEmissionState class: > > 1. advance: I am not entirely sure what it does. So if my state emits > 4 symbols at a time do I set it to {4}? If you are emitting 4 symbols at a time, then you shou

Re: [Biojava-l] Re: strange pdb

2006-01-12 Thread Andreas Prlic
Hi Tamas, the Atoms have an altLoc field. - only the pdb parser did not capture that information... I committed a fix to cvs. Cheers, Andreas On 12 Jan 2006, at 12:52, Tamas Horvath wrote: (wow... stupid linewrap...)It seems to me, that we need a variance tag for the Group or Atom object

[Biojava-l] strange pdb

2006-01-12 Thread Tamas Horvath
Hi!I've just stubled upon a strange pdb parsing fenomenon. Look at thefollowing pdb file:ATOM 1 N GLU 326 14.783 14.947 -11.793 1.00 46.17NATOM 2 CA GLU 326 15.471 16.220 -11.447 1.00 39.29CATOM 3 C GLU 326 14.978 16.646 -10.075 1.00 37.04CATOM