[Biojava-l] Biojava tutorial revisisted

[Michael L. Heuer]

Hello Keith,

The jakarta apache projects use several different implementations of
xml/stylesheet-based formats and systems to generate web and paper
versions of documentation, but at this point it's probably best just to
stick with DocBook.  If we want to move to something else at a later
date, we could just transform them to the new format ...

see

> http://cvs.apache.org/viewcvs.cgi/xml-cocoon2/src/documentation/

for example.

   michael


On 9 May 2002, Keith James wrote:

> >>>>> "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
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