[Biojava-dev] Clean-up Patch

[Marcus Malcom]

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