[Biojava-dev] reading a subsequence from a .nib file

[mark.schreiber at novartis.com]

Hi Josh -

Looks good.  Just one thing, your JUnit test contains a hardcoded file 
path to the test file which means it is not portable. Could you modify 
that so that it loads the file from the classpath as a resource (see some 
of the IO unit tests for examples). Can you also provide the test file.

Best regards,

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





Josh Burdick <jburdick at keyfitz.org>
04/20/2007 02:26 AM

 
        To:     mark.schreiber at novartis.com
        cc:     biojava-dev at lists.open-bio.org
        Subject:        Re: [Biojava-dev] reading a subsequence from a .nib file


On Tue, 2007-04-03 at 09:03 +0800, mark.schreiber at novartis.com wrote:
> Hi -
> 
> Too my knowledge nothing like this exists in BioJava. Could someone take 

> it the last mile and make it produce SymbolLists?
> 
  I went ahead and added a method getSymbolListByLocation() which takes
the string and converts it to a SymbolList using DNATools.  There are
bound to be more efficient ways to do this, but I think this a
reasonable start.

  The files are in the same locations:

http://www.keyfitz.org/jburdick/read_nib_file_java/NibFile.java
http://www.keyfitz.org/jburdick/read_nib_file_java/NibFileTest.java

  Hopefully someone will find this code useful.

  Josh

> - Mark
> 
> Mark Schreiber
> Research Investigator (Bioinformatics)
> 
> Novartis Institute for Tropical Diseases (NITD)
> 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
> 
> phone +65 6722 2973
> fax  +65 6722 2910
> 

[...]