RE: [Biojava-l] A Simple Genbank Parser Runs Out of Memory

Hi - Most JVMs give you only 32 or 64M of space to operate in for large genome sized GenBank files (or big chunks of chromosomes) this is not sufficient. Typing java -X at the prompt will give you all the extended options for your particular JVM. The JVM will complain if you try to give it more m

[Biojava-l] RevCompSequence - call for input

I am creating a new class: RevCompSequence to allow reverse complementing of Sequence with all of its Features. It uses a ProjectedFeatureHolder to project the features. I have included a createFeature(Feature.Template) method which gets the projected location and projected strand of a Feature.Tem

RE: [Biojava-l] ah hah. Now I know why: it's a bug, perhaps in MSFAlignment

I wrote that original code, and yes it is a bug, I had not thought about making a correction for gaps. The type keyword is often not there and I have seen it in a variety of formats. I think the following might be the best 1) regex the type and *try* to match it to some of the "Types" we have s

RE: [Biojava-l] A Simple Genbank Parser Runs Out of Memory

Larry I forget what the default memory allocation is for the jvm, but there is an argument -Xmx that will allow you to increase the heap size. Maybe that will fix the problem. Mike > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] > Sent: Friday, March 01, 2002 2

[Biojava-l] ah hah. Now I know why: it's a bug, perhaps in MSFAlignment

Relating to the previous email I posted, I believe this might be a bug. In MSFAlignmentFormat, between lines 137 and 155 is the test to see if the given report is a DNA, Protein, or RNA. Its method is to go through the entire report, find out how many a's, t's, g's, c's, and u's there are.

[Biojava-l] A Simple Genbank Parser Runs Out of Memory

I created a simple parser based on the Genbank demo, to test a proof of concept. I ran it on a large Genbank source file ( contains over 160,000 "sequences"). The program processed 34,170 sequences then crashed with the java.lang.OutOfMemoryError . I ran this on an NT with 768mb ram, using the

[Biojava-l] force it to be dna sequence and not protein

Hi, In the course of debugging this parser program I am doing for ClustalW report, I realized that all along it has been thinking that it is a peptide sequence alignment. This is the code fragment: AlignmentFormat format = new MSFAlignmentFormat(); Alignment alignment

[Biojava-l] Extended Deadline: March 11; Joint International Conferences in Computer Science; Las Vegas, June 24-27, 2002

EXTENDED DEADLINE FOR SUBMISSIONS - New Deadline: March 11, 2002 C A L L F O R P A P E R S = The 2002 International Multiconferences in Computer Science (14 Joint Int'l Conferences) Monte Carlo

[Biojava-l] java1.3.1 or older...

I have java 1.3.1 and all the biojava demo work fine. I am wondering if I would encounter problems when I tie the application as a web-interface, using netscape. Does netscape (even latest) have problems displaying the java 1.3.1 or upgrade problems? thanks for your input. -Geetha.

Re: [Biojava-l] exception with no stacktrace

After actually downloading the source code and debugged through the read method, I know why. For some reason, ClustalW output I got has a double o after the name of the sequence! Name: Plate_2-F3_contig__TC68100_ oo Len: 1675 Check: 298 Weight: 9.6 But that double o is not in the actual

RE: [Biojava-l] exception with no stacktrace

Sorry, I can't replicate your error. When I run your code, a class cast exception is generated where SymbolList list is assigned, but no null pointer exception. Anyone else want to take a swing? Greg > -Original Message- > From: Guoneng Zhong [mailto:[EMAIL PROTECTED]] > Sent: Friday,

Re: [Biojava-l] exception with no stacktrace

This is the function that has the code I included: private static void readFile() throws Exception{ String file = "[some path]"; AlignmentFormat format = new MSFAlignmentFormat(); BufferedReader reader = new BufferedReader(new FileReader(file)); if(false){

Re: [Biojava-l] GappedSymbol lists and Features

Hi Tim, This is an API bug in GappedSymbolList - it should be exposing the list it wraps via a getWrappedSequence type of method. You would then be able to cast this to Sequence and play with features. If you are already playing about with the BioJava source code, would you like to expose thi

[Biojava-l] GappedSymbol lists and Features

I've been doing some work on the multiple alignment stuff in biojava. I've found that the existing org.biojava.bio.seq.io.MSFAlignmentFormat class doesn't really seem to work, and have been re-engineering it to work and be more generic. I'll contribute this work when complete. My question relates

[Biojava-l] Call for Papers - NETTAB 2002

Dear biojava members, I'm glad to announce the launch of the Call for Contributions for the NETTAB 2002 Workshop on "Agents in Bioinformatics". I think this is a good chance to improve awareness, understanding and skills in software agents, also due to the vicinity to the AAMAS conference. I ho