[Biojava-l] Biojava tutorial revisisted

[Keith James]

>>>>> "Chun-Nuan" == Chun-Nuan Chen <chun@bioweircom.org> writes:

    Chun-Nuan> Hi, I revisisted the biojava tutorial and found a few
    Chun-Nuan> things that may need correction. I believe most of them
    Chun-Nuan> are just typos:

Good points. Comments below:

    Chun-Nuan> ||"java *eventbasedparsing.TutorialEx1*
    Chun-Nuan> files/ncbiblast/shortBlastn.out"| | 2.in Keith James'
    Chun-Nuan> "|Parsing Fasta search output": java
    Chun-Nuan> *search/FastaSearchParse* files/fp_queries.db
    Chun-Nuan> files/fp_demo.db files/fp_demo.m10

    Chun-Nuan> should be:

    Chun-Nuan> java *search.FastaSearchParse* files/fp_queries.db
    Chun-Nuan> files/fp_demo.db files/fp_demo.m10

As you point out, this has become obsolete, so I have now completely
removed the tutorial. I have recently begun working on a combined set
of documentation which contains material from some of the web
tutorials and will be expanded to cover new areas.

To replace the tutorial I removed I am working on an expanded version
which incorporates coverage of the newer Blast/Fasta system. My aim to
have a single document in CVS which will be maintained in sync with
the codebase.

The latest version of the combined docs is in biojava-live/docs

biojava-doc-main.xml Book framework
biojava-doc-ch01.xml Beginning BioJava - obtaining, installation
biojava-doc-ch02.xml Symbols and SymbolLists - from web tutorial
biojava-doc-ch03.xml Sequences and Features - from web tutorial
biojava-doc-ch04.xml Sequence I/O - from web tutorial
biojava-doc-ch05.xml Changeability, Mutability and Events - from web tutorial
biojava-doc-ch06.xml Representing Search Results - new (in progress)

Chapter 6 will contain a replacement for the material I removed.

    Chun-Nuan> 4. This is not an error or typo and is related to the
    Chun-Nuan> style of the code blocks in the tutorial. The css class
    Chun-Nuan> for the code block is nice for displaying on the screen
    Chun-Nuan> but is not printer-friendly. It consumes a lot of ink
    Chun-Nuan> but the code is barely readable.

The new combined documentation uses DocBook so there will be HTML,
DVI, PostScript and PDF versions. As the printable forms are created
using LaTeX this should address the readability problems.

If I can find a suitable pure-Java alternative to Jade/OpenJade then I
will add an Ant build task for the docs. Otherwise I will make a
separate tarball containing just the docs pre-built using Jade.

Of course, how fast all this progresses depends on my free time -
which isn't much at the moment ;) Thanks for the comments - feedback
is always welcome.

Keith

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, UK