## TODO: Move this into the Java GUI Makefile (in RNAstructure/java_interface)
## That way it can stay in sync better with changes to the GUI

# Move to the RNAstructure main directory.
cd ../../;

SRC_ROOT=java_interface/src
SRC_MAIN=$SRC_ROOT/ur_rna/RNAstructureUI
SRC_DRAWING=$SRC_MAIN/drawing
SRC_UI_UTILS=$SRC_MAIN/utilities

SRC_TESTER=$SRC_ROOT/ur_rna/GUITester
SRC_UTIL=$SRC_ROOT/ur_rna/Utilities

PKG_ROOT=ur_rna
PKG_MAIN=${PKG_ROOT}.RNAstructureUI
PKG_TESTER=${PKG_ROOT}.GUITester
PKG_UTIL=${PKG_ROOT}.Utilities

LIB=java_interface/lib
JAVA_CLASSPATH=${SRC_ROOT}:$LIB/abbot.jar:$LIB/gnu-regexp-*.jar:$LIB/jdom-*.jar

OS=$(uname -s 2>/dev/null)
# Perform some replacements to normalize the output of uname on various systems.
case "$OSTYPE" in 
	cygwin|msys) 	OS=Windows 	;;
	darwin*) 		OS=Mac 		;;
	linux*)			OS=Linux 	;;
	*)				OS=UNKNOWN	;;
esac
if [[ $OS == Windows ]]; then
  JAVA_CLASSPATH="${JAVA_CLASSPATH//:/\;}" #replace : with ; on Windows.
  if ! type -p javadoc &>/dev/null; then
	  if [[ ! -d $JAVA_HOME ]]; then
		JDKS=( /cygdrive/c/Program\ Files/Java/jdk*/bin )
		[[ ${#JDKS[@]} -eq 0 || ! -d ${JDKS[0]} ]] && JDKS=( /cygdrive/c/'Program Files (x86)'/Java/jdk*/bin )
		[[ ${#JDKS[@]} -eq 0 || ! -d ${JDKS[0]} ]] && echo >&2 "Cannot find JDK. Please set JAVA_HOME to point to a valid jdk folder."
		export JAVA_HOME=${JDKS[@]: -1}
	  fi
	  export PATH="$PATH:$JAVA_HOME/bin"
  fi
fi

echo "JAVA_CLASSPATH: ${JAVA_CLASSPATH}"


# Copy the HTML files that expand Javadoc comments to their proper places and names so the Javadoc tool will use them.
cp manual/javadoc/comments/Overview.html overview.html
cp manual/javadoc/comments/DrawingSource.html ${SRC_DRAWING}/package.html
cp manual/javadoc/comments/DrawingSourceDialogs.html ${SRC_DRAWING}/dialogs/package.html
cp manual/javadoc/comments/DrawingSourceMenus.html ${SRC_DRAWING}/menus/package.html
cp manual/javadoc/comments/DrawingSourceProxy.html ${SRC_DRAWING}/proxy/package.html
cp manual/javadoc/comments/DrawingSourceRunners.html ${SRC_DRAWING}/runners/package.html
cp manual/javadoc/comments/InterfaceSource.html ${SRC_MAIN}/package.html
cp manual/javadoc/comments/InterfaceSourceMenus.html ${SRC_MAIN}/menus/package.html
cp manual/javadoc/comments/InterfaceSourceStartup.html ${SRC_MAIN}/package.html
cp manual/javadoc/comments/InterfaceSourceWindows.html ${SRC_MAIN}/windows/package.html
cp manual/javadoc/comments/Utilities.html ${SRC_UI_UTILS}/package.html

# flags for javadoc
javadocFlags=( 
	-private -encoding UTF-8 -nodeprecated 
	-overview overview.html 
	-sourcepath ${SRC_ROOT} 
	-d manual/javadoc/html 
	-classpath "${JAVA_CLASSPATH}"
	#-link http://download.oracle.com/javase/6/docs/api/
)

#list all RNAstructure java packages to document
javadocPackages=(  
	${PKG_MAIN} 
	${PKG_MAIN}.menus 
	${PKG_MAIN}.windows 
	#${PKG_MAIN}.drawing
	${PKG_MAIN}.drawing.dialogs 
	${PKG_MAIN}.drawing.menus 
	${PKG_MAIN}.drawing.proxy 
	${PKG_MAIN}.drawing.runners 
	${PKG_MAIN}.utilities 
	${PKG_TESTER} 
	${PKG_TESTER}.ScriptParser 
	${PKG_TESTER}.GuiTools 
	${PKG_TESTER}.GuiTools.Matchers 
	${PKG_UTIL} 
	${PKG_UTIL}.annotation
)

#Move the old directory if it exists
rm -f manual/javadoc/javadoc_{warnings,errors,output}.txt
rm -rf manual/javadoc/html.older
[[ -d manual/javadoc/html.old ]] && mv manual/javadoc/html.old manual/javadoc/html.older
[[ -d manual/javadoc/html ]] && mv manual/javadoc/html manual/javadoc/html.old

echo javadoc "${javadocFlags[@]}" "${javadocPackages[@]}"
# Run the javadoc command 
{ { javadoc "${javadocFlags[@]}" "${javadocPackages[@]}"; } 2> >(tee manual/javadoc/javadoc_warnings.txt >&2); } \
                                   &> >(tee manual/javadoc/javadoc_output.txt)

grep 'error:' manual/javadoc/javadoc_warnings.txt > manual/javadoc/javadoc_errors.txt

# Delete any copied files.
rm -f overview.html
rm -f ${SRC_DRAWING}/package.html
rm -f ${SRC_DRAWING}/dialogs/package.html
rm -f ${SRC_DRAWING}/menus/package.html
rm -f ${SRC_DRAWING}/proxy/package.html
rm -f ${SRC_DRAWING}/runners/package.html
rm -f ${SRC_MAIN}/package.html
rm -f ${SRC_MAIN}/menus/package.html
rm -f ${SRC_MAIN}/startup/package.html
rm -f ${SRC_MAIN}/windows/package.html
rm -f ${SRC_UI_UTILS}/package.html