Protein Family Alignment Annotation Tool svncode

added missing file

added files

Fixes for:

[ 1041476 ] File->save / save as progress bar
[ 1041537 ] edit->set-> start index..

Redid how the -j option works.

Now -j just means look for the given files as a resource
following -j is align.name and then optionally tree.name

adding missing file

Added command line changes marked with:

// phdana cmd line

Argument usage is like tihs

if there are 2 or more parmas and the 2nd param is -analysis
then 1st param is an alignment file and cmd-line driven pfaat is executed (legacy code)
else if first parameter is -j
then 2nd param is a jar, 3rd is an alignment file IN that jar and 4th is optionally a nhx tree file in that jar
else
first parameter is treated like an alignment file, and an optional 2nd parameter is treated as an nhx tree file

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adding missing file

[ 1011750 ] label atoms

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