I am using the method below to load an EMBL file
BufferedReader br = new BufferedReader(new FileReader(emblFile));
stream = SeqIOTools.readEmbl(br);
while (stream.hasNext()){
seq = stream.nextSequence();
}
The problem is that this takes about 10 seconds
I often use the same EMBL files and o
Hi All,
We should look at easy ways to make finite sub-sets of the common
infinite alphabets play well e.g. give me the alphabet Integer[1..100],
ensuring that it implements FiniteAlphabet and therefore behaves in
cross-products efficiently.
I think for integers, it would be a fairly trivial addi
Hi Simon,
10 sec? That's bad. Do you have any -Xprof numbers to indicate where the
time is being wasted? The worst-case scenario is that 9.5 sec of this is
VM and BioJava initialization, but the profile should tell us what is
going on.
Matthew
pootle monster wrote:
>
> I am using the method
There are no unit tests for these. We're probably going to use the
isoelectric point class here so I've started writing some for both.
Question: Can anyone give me a reference for the avg/mono weights used
in the SymbolProperties table?
I was comparing with EMBOSS pepstats (which appears to be
I got the Mass Values from a Micromass cheat sheet that I have had with
me for years.
I found a URL that seems to match it at. It looks like they scanned the
card.
http://www.micromass.co.uk/resources/reference_tables/refp1s1.asp
Which is under the reference section of there site.
http://w
Hi,
I have done some work on the Serialization issue and I'm pretty
confident that you can safely serialize a sequence by sending it to an
object output stream which creates a binary stream which you can write
to a file. Not exactly a flat file but it retains the object structure.
- mark
> ---
Hi -
I have added a new GUI component to org.biojava.bio.gui called feature
tree. It uses and inner class as its tree model and displays a database
of sequences together with their features and annotations as a nested
tree. The critical method for the tree is the setSequenceDB() method.
Here is
Hi -
I have implemented this and checked it in. Currently the subalphabet implementation
extends SimpleAlphabet which constructs the whole alphabet and could get a bit heavy
weight for more than 100 or so symbols. When the Alphabet is constructed via the
IntegerAlphabet.getSubAlphabet(int min,
