#!/bin/sh

# Get BioLegato environment variables.
if [ -f $BIRCH/admin/setblenv.profile.$BIRCH_PLATFORM.source ]
   then
      . $BIRCH/admin/setblenv.profile.$BIRCH_PLATFORM.source
fi 

BIOLEGATO_HOME=$BIRCH/java/bioLegato
export BIOLEGATO_HOME


# The location of anciliary data files used by bioLegato.
BL_DATA_DIR=$BIRCH/dat/bltree
export BL_DATA_DIR


BL_PROPERTIES=$BL_DATA_DIR/bltree.properties
export BL_PROPERTIES

# The -dir switch is mainly for launching bioLegato from the birch launcher. By 
# prompting the user for a working folder, we help enforce good file organization
# habits.
if [ $# -gt 0 ]
then
   if [ ${1} = "-dir" ]
   then

      # Get rid of the -dir switch, and send the remaining command line arguments to bioLegato
      shift

      #Prompt the user to choose a working directory
      #CHANGEDIR=`java -cp "$BIRCH/script" DirChooser "Where do you want to work? Choose a folder."`
      CHANGEDIR=`java -jar $BIRCH/script/DirChooser2.jar "Where do you want to work? Choose a folder."`

      if [ -d "$CHANGEDIR" ]; then
	  cd "$CHANGEDIR"
      fi
   fi
fi

################################################################
#             User Preferences that override defaults          #
################################################################

BIRCHSettingsFile=$HOME/.config/BIRCH/BIRCHsettings.source
if [ -f $BIRCHSettingsFile ]
   then
      . $BIRCHSettingsFile
fi

BLHelperFile=$HOME/.config/BIRCH/BLHelper.source
if [ -f $BLHelperFile ]
   then
      . $BLHelperFile
fi

java -jar $BIOLEGATO_HOME/sequence.jar $*


# ------------------------ LOGGING ------------------------------
# For future use when we have a secure logging method.

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