
Near Optimal Alignment Display  
Version:  rel-2-1
2004/06/14 19:11:17   
===============================

Prerequisites: 
--------------

To run the software you will need to have a version of Java greater than 1.3.

You can obtain Java from http://java.sun.com.

You can test the version of Java you have by typing the following:

	% java -version

If you get an error message indicating that java cannot be found, then you
need to be sure that the java executable is in your PATH.  Generally, 
installation of java simply involves unpacking a directory.  Within that
directory is a directory named bin, which must be added to your path.  
For example:

	(for bash/ksh/sh)
	% export PATH=$PATH:/someplace/java_distribution/bin

	(for csh/tcsh)

	% setenv PATH $PATH:/someplace/java_distribution/bin

Once your path is set correctly you should be able to run the command above
to verify you have the correct version.

Note that the $JAVA_HOME variable must also be set.  This is simply set to 
the directory where the java was unpacked.  Continuing with the example 
above, you would simply do the following:
	
	(for bash/ksh/sh)
	% export JAVA_HOME=/someplace/java_distribution

	(for csh/tcsh)
	% setenv JAVA_HOME /someplace/java_distribution


All necessary jars have been included with this distribution.

Mac OS X Note:  Because of a bug in the GlyphVector rendering class your
version of java needs to by >= version 1.4.1 which, I believe, implies the
need for OS X 10.2 (Jaguar) or greater.

Windows Note:  I have not tried compiling or running this software on
Windows and am not likely to.  Your mileage may vary.


noptdisplay Binary Distribution  (running the software)
--------------------------------------------------------

To use the binary distribution, simply unpack the distribution:

    % tar -xvzf noptdisplay_bin-X.X.tar.gz

Installation is simply a matter of copying the jar files found in the 
nopdisplay_bin-X.X/lib directory to your favored location.  Alternatively,
the jars may be left where they are and you can run the software from
the noptdisplay_bin-X.X directory.

See the "Running" section for details on running the software.


noptdisplay Source Distribution (building the software)
--------------------------------------------------------

Compilation of the noptdisplay software should be relatively straightforward
as all necessary libraries are included with the distribution.  Simply
unpack the distribution:

    % tar -xvzf noptdisplay_src-X.X.tar.gz

Then execute the build script to build everything:

	% build.sh all

The build script simply sets the java CLASSPATH to include the correct
libraries and then invokes ant (included).  The jars will be placed in the 
lib directory.

NOTE: that the source distribution does not include a keystore with which to
sign the jars.  You should only be concerned with signing the jars if you
intend to run application via webstart or as an applet.  You do NOT need to
sign the jars for normal invocation.

I don't provide my keystore because you are not me and _I_ don't want to be
signing _your_ code.  See:

	http://java.sun.com/docs/books/tutorial/security1.2/toolsign/index.html

for details on how to do this.


Running
-------

To run the application without any input: 

	% java -jar lib/noptdisplay.jar 

To run the application with an alignment file input: 

	% java -jar lib/noptdisplay.jar -a examples/sample_alignments 

To run the application with both alignment input and feature input:

	% java -jar lib/noptdisplay.jar -a examples/sample_alignments -f examples/sample_features.gff

To run the application with URL's instead: 

	% java -jar lib/noptdisplay.jar -A http://your.url/file -F http://your.url/features.gff


File Input Formats
------------------

Currently the alignment file must be in the format output by the noptalign
program. This is a somewhat cumbersome format, so you can expect it to change.

The feature file must be in the GFF format.  
See http://www.sanger.ac.uk/Software/formats/GFF/ for details.


Authors
-------

Michael E. Smoot <mes5k@cs.virginia.edu>


Feel free to contact <mes5k@cs.virginia.edu> with any questions or comments.
