
WEB DOCUMENTATION
-----------------
Documentation can be found on the SARSE web page: http://sarse.kvl.dk/

INSTALLATION REQUIREMENTS
-------------------------
- java version 1.5
- tcsh (/bin/tcsh -f)
- awk (e.g. /bin/gawk -f)
- bash (e.g. /usr/bin/env bash)
- perl (e.g. /usr/bin/perl -w)
- optional: GD.pm (a perl module used by alistem_plot)

See doc/install.txt for installation instructions.

QUICK START
-----------
To run the program execute bin/SARSE
There are 2 possible commandline parameters
--file=filename 
Opens the create project dialog, upon startup, with the given file as alignment
--project=projectname
Opens the named project upon startup

If both the above parameters are given a new project is created using the file and projectname specified.
Using the current working directory as project directory.

Projects are pr. default made in the directory from wich you have launched Sarse

See doc/howto.txt for a short description of som basic actions.
See the http://sarse.kvl.dk for a tutorial

References
----------
If you use this editor please reference:
Andersen, S.A., Lind-Thomsen, A.,Kristensen, S.E., Knudsen, B., Havgaard, J.H.,
 Larsen, N., Sestoft, P.,Kjems, J. and Gorodkin, J.(2006), Semi-automated detection and editing of structural groups in multiple alignments. (Submitted)

RELEASE NOTES
-------------
This is a new program and may contain some bugs and strange behavior. 
You are therefore encouraged to write to us with any bugs and inconsistencies
that you observe. You are also encouraged to make suggestions about new features,
 so Sarse can evolve into a complete and preferred Alignment Editor.

The program creates a directory structure that looks like this:

SARSE
|-bin
|-projects
|-tmp
|-lib
|-log
|-properties

bin: here is the binaries and shellscripts placed.
tmp: holds temporary files used by the editor.
lib: This is where the code-libraries is placed
log: log files goes here
properties: different default setup files

Installing from source
----------------------
If you download the source version of Sarse you can build most of the tools from 
source. Some of thge tools are scripts, and some are Java that dosn't need
to be recompiled. The packages that need compiling is done like this:
'cd' into <sarse director>/programs/rnadbtools/src
run 'make'
'cd' into <sarse director>/programs/pcluster/src
run 'make'
'cd' into <sarse director>/programs/pfold/src
run 'make'
Then you shoul have functional executables for all scripts.

Change history
--------------

Changed in 1.35
-----------------
- src distribution available
- small bug fix

Changed in 1.28
---------------
- SARSE_TMP removed
- default project dir is now cmd + modified filename
- programs are run from within project dir
- projects are removed from file menu
- table grid removed
- +1 bug i align_bp with no pairingmask fixed
- new directory structure for programs

Changed in 1.26
---------------
- File selection is now starting in current working directory
- A temporary directory is created in the startup-script, and 
   deleted when the program is ended.
- An environment variable SARSE_TMP is created that points to
	the temporary director. The variable is accesible for all 
	programs running under Sarse

Changed in 1.25
---------------
- Default project directory is now the directory from wich Sarse is startet 
- Java 1.5 required
- Commandline parameters --project and --file

Changed in 1.24
---------------
- minor bugfixes

Changed in 1.23
---------------
- Only 1 history window, always showing the currently active project
- Only 1 overview window, always showing the currently active project
- default project directory is the original directory of the file
- Default project name is the name of the file without the last postfix
	e.g. the file: example.col gives a default projectname of 'example'
- new installation documentation	 

Changed in 1.22
---------------
1: scfg.rate updated for pcluster and pfold

Changed in 1.21
---------------
1: Names have been deleted from the table header, because only 'nar' was seen anyway
2: Fixed some instability in Pcluster_pipe and Pfold_pipe regarding commandline parameters


