[Biojava-l] I'm available for Java/Unix/Tool development

I'm located in the SF bay area and if anyone needs any Java or Tcl tools built just let me know... My resume is located here: http://www.diablosoft.net/KasianFranks-profile.html Thanks, K.F. __ Do You Yahoo!? Get email at your own domain with Yaho

RE: [Biojava-l] Distributions and collections

> -Original Message- > From: Matthew Pocock [mailto:[EMAIL PROTECTED]] > Sent: Thursday, March 08, 2001 12:59 AM > To: Schreiber, Mark > Cc: '[EMAIL PROTECTED]' > Subject: Re: [Biojava-l] Distributions and collections > > > Hi Mark, > > I think that Distribution is closest in apperanc

RE: [Biojava-l] RE: Bug in HashedAlphabetIndex??

> -Original Message- > From: Matthew Pocock [mailto:[EMAIL PROTECTED]] > Sent: Thursday, March 08, 2001 5:00 AM > To: Schreiber, Mark > Cc: '[EMAIL PROTECTED]' > Subject: Re: [Biojava-l] RE: Bug in HashedAlphabetIndex?? > > > Hi Mark, > > I've fixed this on the main trunk. Thomas, coul

FW: [Biojava-l] Boot Camp

Gotta remember to send to the *list*... Sorry Matthew! From: Wiepert, Mathieu Sent: Wednesday, March 07, 2001 10:43 AM To: 'Matthew Pocock' Subject:RE: [Biojava-l] Boot Camp I just wanted to find out if there was more information regarding this. A colleague of mine is quite

Re: [Biojava-l] RE: Bug in HashedAlphabetIndex??

Hi Mark, I've fixed this on the main trunk. Thomas, could you port this to the 1.1 branch? The two issues this brings up are a) I think that the SymbolList FiniteAlphabet.symbols() is unnecisary. If you want to iterate over an alphabet or find its size, you can just use the methods in Finite

Re: [Biojava-l] RE: Bug in HashedAlphabetIndex??

Hi Mark, This looks like something I should sort out. If you build an alphabet that represents the cross-product of other aphabets, its size is obviously the product of the sizes of each alphabet you combine. This can get very large, esp for alignments (protein^10 = 20^10 = 1.024e13 symbols).

[Biojava-l] The hierarchical ChangeTypes are on the trunk

As promised last week, I've committed a patch which makes ChangeType object hierarchical. You can now build a tree of ChangeTypes, rooted at ChangeType.UNKNOWN. Listening for any specific ChangeType will also catch any subtypes. The code I've checked in is more-or-less exactly as initially prop

Re: [Biojava-l] Basis and Atomic Symbols

Hi Mark, Just by way of observation, we have found that instanceof is vastly more time-efficient in a range of VMs than catching ClassCastException. This is because the memory churn/introspection cost associated with building the stack-trace data structures is huge compared to taking the class

Re: [Biojava-l] Distributions and collections

Hi Mark, I think that Distribution is closest in apperance to Map. Because it represents a probability distribution, it places certain restrictions on both the keys (symbols) and the values (doubles). Every Distribution has an associated Alphabet, which has size and iterator methods. An Alphab

Re: [Biojava-l] Compiling with Jikes

On Sun, Mar 04, 2001 at 12:11:41AM -0800, Bradley A. Smith wrote: > Has anyone successfully compiled BioJava 1.10 with the IBM Jikes compiler? I receive >many errors. I believe some of the errors are allowed by the Sun compiler although >they are valid errors. Is anyone interested in fixing the

[Biojava-l] writeSequence

Hi, I've committed a few files related to writing various file formats (list below). The code is still incomplete, although everything builds and writeSequence(sequence, "embl", stream) called on an EmblLikeFormat instance will dump most of a Sequence to STDOUT as EMBL format. What's missing?