#!/bin/sh

# Special code for text editors used by bioLegato and scripts called by bioLegato
# Nedit crashes in some Linux systems due to libraries set in BIRCHLIBS.
# nedit_wrapper unsets LD_LIBRARY_PATH before calling nedit.
# gedit opens all files in a single window. gedit_wrapper.sh forces
# gedit to open each file in different window.
# choose_edit_wrapper.sh returns the name of the wrapper to use
# for each editor, or just returns GDE_TEXTEDIT if there is no
# wrapper.
GDE_TEXTEDIT=`choose_edit_wrapper.sh`
export GDE_TEXTEDIT   

BIOLEGATO_HOME=$BIRCH/java/bioLegato

# There is an error in ImportFileAction.java that tries to read
# BIOLEGATIO_COLOURMASK_DIR, rather than BIOLEGATO_COLOURMASK_DIR.
# When the bug is fixed, this section can be simplified.
#BIOLEGATO_COLOURMASK_DIR=$birch/dat/bldna/seqcolors
#export BIOLEGATO_COLOURMASK_DIR
#BIOLEGATIO_COLOURMASK_DIR=$BIOLEGATO_COLOURMASK_DIR
#export BIOLEGATIO_COLOURMASK_DIR


#GDE_MAKEMENUS_DIR=$BLDNA_HELP_DIR
#export GDE_MAKEMENUS_DIR

GDE_HELP_DIR=$BLDNA_HELP_DIR
export GDE_HELP_DIR


#New environment variables for bioLegato 0.7.2. These
# will replace the old variables
echo 'BLDNA_HELP_DIR: '$BLDNA_HELP_DIR
BL_HOME=$BIRCH/java/bioLegato
export BL_HOME
GDE_MAKEMENUS_DIR=$BLDNA_HELP_DIR
export GDE_MAKEMENUS_DIR
BL_MASKS=$BLDNA_HELP_DIR/seqcolors
export BL_MASKS


#java -Xms6M -Xmx64M -jar $BIOLEGATO_HOME/biolegato.jar $*
#java -Xms6M -Xmx96M -jar $BIOLEGATO_HOME/biolegato.jar $*
#java -Xms6M -Xmx128M -jar $BIOLEGATO_HOME/biolegato.jar $*
#java -Xms6M -Xmx256M -jar $BIOLEGATO_HOME/biolegato.jar $*
#java -Xms6M -Xmx384M -jar $BIOLEGATO_HOME/biolegato.jar $*
java -jar $BIOLEGATO_HOME/biolegato.jar $*


# ------------------------ LOGGING ------------------------------
# Check to see if we can log when GDE is launched.
# If BIRCH is mounted read only, we don't crash the script

if [ "$BIRCH_LOGGING" -eq "1" ] 
    then
    echo `whoami` `date` >> $BIRCH/local/admin/biolegato.log
fi
