(from Michael Jahr, jahr@clsp.jhu.edu)

Cairo: Alignment Inspection Tool

Cairo is now in relatively stable incarnations and ready for
use by the general public. Or by you guys, anyways. :) To invoke it:

	/export/mt/ws99/tools/bin/cairo 

You may want to add /export/mt/ws99/tools/bin/ to the end of your $PATH.

As you all know, cairo is the java-based alignment visualization tool that
Noah and I wrote. it requires java 1.2 to run, which in turn requires
Solaris 5.7 to run, so unfortunately it won't run on all of our machines.
We can talk to Jacob about upgrading the system software; until then we 
will only be able to run it on the newer systems.

The most important thing to know about cairo is how it looks for alignment
files...in order to appear in the file menu, they must be copied into the
directory 

	/export/mt/ws99/tools/visual/cairo/alignments

or one of its subdirectories. Moreover, because it is written as an 
applet, cairo has no way of listing directory contents and must rely 
on a file called "index" to tell it what's there. This file is generated 
by the script index.pl in the alignments directory, which is called 
automatically whenever you call tools/bin/cairo. Why does this matter? 
Because if you add new alignments to the directory when cairo is running, 
they will not appear in the menu until index.pl is called and you 
choose "update index" from the file menu.