#!/bin/csh
# Unix script file to run JalView
# -------------------------------
# Author: Michele Clamp 1998
# -------------------------------

#Change this line to reflect where your JDK classes are and where jalview.jar is
setenv CLASSPATH .:/usr/local/java/lib/classes.zip:$BIRCH/java/jalview-1.7.5b/jalview-1.7.5b.jar

#Change this line to reflect where you java binary is
setenv JAVA_EXE java


#This actually runs the program
# $1 is the alignment file
# $2 is the alignment format MSF|FASTA|CLUSTAL|PIR

#$JAVA_EXE jalview.AlignFrame $1 File $2
java -classpath /usr/local/java/lib/classes.zip:$BIRCH/java/jalview/jalview-1.7.5b.jar\
       jalview.AlignFrame $1 File $2\
#       jalview.AlignFrame $1 $2\
#        jalview.AlignFrame \
       -srsServer srs.ebi.ac.uk/srs5bin/cgi-bin/ -database swissprot 

# add extra command line options to the previous command as follows:

#   -mail <mailserver>
#   -srsServer <srsServer>  - see the README file for details
#   -database <database>    - srs database name

# example :  %JAVA_EXE% jalview.AlignFrame %1 File %2 -mail circinus.ebi.ac.uk -srsServer srs.ebi.ac.uk/srs5bin/cgi-bin/ -database swissprot 
~

