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

[Josh Burdick]

On Fri, 2007-04-20 at 10:44 +0800, mark.schreiber at novartis.com wrote:
> 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.
> 
  I'm not currently compiling all of BioJava, and didn't know how to add
the file as a resource.  So I'm afraid I haven't set the pathname to
something sensible.

  But I created a small test file which is a fragment of chromosome 18.

  The relevant files are:

http://keyfitz.org/jburdick/read_nib_file_java/NibFile.java
http://keyfitz.org/jburdick/read_nib_file_java/NibFileTest.java
http://keyfitz.org/jburdick/read_nib_file_java/chr18_chunk.nib
http://keyfitz.org/jburdick/read_nib_file_java/readme.txt

  Josh

> 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
> 

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