[Biojava-dev] Clean-up Patch

[Thomas Down]

Hi Marcus.

I've applied most of this (it's just checking into CVS at the moment,
might take some time...).  The bulk of it worked fine with
"patch -p0 <../clean-up-patch.txt".  The two things I've left outi
for now:

    - Two added files called .classpath and .project.  These look
      like they're configuration files for Eclipse (which I've never
      tried myself).  I don't object to these going into biojava,
      but it would be good if you could post a brief explanation
      of what's going on (what is the "natures" element, for instance).
      Can you (or some other Eclipse user) make sure they stay
      up to date?

    - Some of the hunks relating to the Agave package, which
      were failing because of all the blank lines in these source
      files.  I think we should fix these files properly -- I'll
      write a script to do at some point.

Thanks for the cleanups.  If you think you'll be doing some
regular biojava hacking, drop me a note and I'll get an
account created on the CVS server.

Thanks,

     Thomas.

Once upon a time, Marcus Malcom wrote:
> I am very interested in the BioJava project. I have created a CVS patch
> file that includes various "clean-up" items for the biojava-live module
> (I assume this is the one that most development is done in). Here's the
> URL from which the patch can be downloaded from:
> 
> 	http://students.washington.edu/malcom/BioJava/
> 
> The patched items fall into 3 categories:
> 
> 1) Correcting static field/method accessing in a non-static fashion.
> 2) Assignment to variable having no effect.
> 3) Organizing the imports (no longer used import statements).
> 
> Here are examples of #1 & #2:
> 
> 1) Correcting static field/method accessing in a non-static fashion. For
> example: in the Constructor of org.biojava.bio.program.Meme
> 
> 	Meme(InputStream is, SymbolTokenization symParser)
> 
>     while( true ) {
> 	int nt = st.nextToken();
> 	if (nt == st.TT_EOF) {
> 	  return;
> 	} else if (nt == st.TT_WORD) {
> 
> Here's the code that does this:
> 	st.TT_EOF
> 	st.TT_WORD
> 
> 2) Assignment to variable having no effect:
> 
> 	org.biojava.utils.xml.ResourceEntityResolver
> 
> 	public ResourceEntityResolver(String[] path, ClassLoader classLoader) {
> 		this.lineWidth = lineWidth;
> 	}
> 
> I would be happy to commit this myself, if that is preferable. I would
> also love to put some of my free time into BioJava. Please let me know
> if I can be of use.
> 
> Oh and about the patch. I have been having trouble getting my CVS
> patches to "patch". So if this doesn't work I wouldn't be surprised.
> Please let me know if that is the case.
> 
> Thank you,
> 
> Marcus Malcom
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