[Bioclusters] Java Vs C++(Qt) for Bioinformatics

Angulo, David dangulo at cti.depaul.edu
Thu May 24 17:58:49 EDT 2007

Java really is going to be slower.  For professional software, I'd still
go with C++.  But, Java has many advantages, as you clearly enumerate.

I think your time doesn't need to be spent on analyzing C++ vs. Java,
but rather better ways to manage your data and better ways to access
your data from your application.  >1Gb data size will really benefit
from thorough analysis, but you won't have any problems with 6Mb (in
either C++ or Java).

David Sigfredo Angulo
DePaul University

-----Original Message-----
From: bioclusters-bounces+dangulo=cti.depaul.edu at bioinformatics.org
[mailto:bioclusters-bounces+dangulo=cti.depaul.edu at bioinformatics.org]
On Behalf Of Mr. Syed Aijaz
Sent: Wednesday, May 23, 2007 5:51 PM
To: bioclusters at bioinformatics.org
Subject: [Bioclusters] Java Vs C++(Qt) for Bioinformatics

Hello All,

Just wondering what bioinformatics community thinks of is best to use:
1. Java Swings (1.6+)
2. C++ Qt (4.0)

My visualziation tool requires accessing data which is in the order of
few hundred MBs we are expecting this to hit GBs soon. I am planning
not to hold up all the data. However, I will have to hold up some data
(a few hunderds of thousands (O(100,000)) of data entities, each costing
around ~60 bytes). As the tool is supposed to be a interactive, what
be good alternative between Java Vs C++? I am leaning towards Java,
reason being:
1. Comprehensive GUI
2. Java not that Slow, as they say!
3. Huge API, DBMS, XML, DRMAA, . . . . .
4. No deployment pain, although a little application
   specific deployment may be required example: preference files etc
5. Automated Garbage collection, less trouble in maintaining memory.
   Although it has a little overhead, it can be reduced by efficient
handling of data???
6. efficient multi threading, not system level fork, etc??????
7. Java has growing number of Bioinformatics applications

Kindly share your opinion regarding the aforementioned debate. Thank you
time and participation!!

Kind Regards,
Bioclusters maillist  -  Bioclusters at bioinformatics.org

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