java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp ./tools/closure-compiler-v20230802.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level ADVANCED --warning_level QUIET --charset UTF-8 --js='./build/jalviewjs/site/swingjs/**.js' --js='!**/DatabaseReaction.js' --js='!**/FileTime.js' --js='!**/ChoiceFormat.js' --js='!**/TableView.js' --js='!**/JSVApplet.js' --js='!**/NativeMDLReactionReader.js' --js='!**/AsyncCallback.js' --js='!**/_ES6/jsutil.js' --js='!**/org/jmol/inchi/InChIJS.js' --js='!**/j2s/swingjs/JSUtil2.js' --js='!**/j2s/core/*.js' --js='!**/js/core/*' --js_output_file ./coreall-advanced.z.js > errors.txt

grep JSC_UNDEFINED_VARIABLE errors.txt  | perl -n -e 'm/.* variable (\S+) is undeclared/ && print "var $1;\n";'  > externs.txt

java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp ./tools/closure-compiler-v20230802.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level ADVANCED --warning_level QUIET --charset UTF-8 --js='./build/jalviewjs/site/swingjs/**.js' --js='!**/DatabaseReaction.js' --js='!**/FileTime.js' --js='!**/ChoiceFormat.js' --js='!**/TableView.js' --js='!**/JSVApplet.js' --js='!**/NativeMDLReactionReader.js' --js='!**/AsyncCallback.js' --js='!**/_ES6/jsutil.js' --js='!**/org/jmol/inchi/InChIJS.js' --js='!**/j2s/swingjs/JSUtil2.js' --js='!**/j2s/core/*.js' --js='!**/js/core/*' --js_output_file ./coreall-advanced.z.js --externs=./externs.txt

java -Xmx2g -Dfile.encoding=UTF-8 -Duser.country=GB -Duser.language=en -Duser.variant -cp ./tools/closure-compiler-v20230802.jar com.google.javascript.jscomp.CommandLineRunner --compilation_level SIMPLE --warning_level QUIET --charset UTF-8 --js='./build/jalviewjs/site/swingjs/**.js' --js='!**/DatabaseReaction.js' --js='!**/FileTime.js' --js='!**/ChoiceFormat.js' --js='!**/TableView.js' --js='!**/JSVApplet.js' --js='!**/NativeMDLReactionReader.js' --js='!**/AsyncCallback.js' --js='!**/_ES6/jsutil.js' --js='!**/org/jmol/inchi/InChIJS.js' --js='!**/j2s/swingjs/JSUtil2.js' --js='!**/j2s/core/*.js' --js='!**/js/core/*' --js_output_file ./coreall-simple.z.js --externs=./externs.txt

cat ./build/jalviewjs/site/swingjs/j2s/com/actelion/research/chem/io/NativeMDLReactionReader.js ./build/jalviewjs/site/swingjs/j2s/com/actelion/research/chem/reaction/DatabaseReaction.js ./build/jalviewjs/site/swingjs/j2s/java/nio/file/attribute/FileTime.js ./build/jalviewjs/site/swingjs/j2s/java/text/ChoiceFormat.js ./build/jalviewjs/site/swingjs/j2s/javax/swing/text/html/TableView.js ./build/jalviewjs/site/swingjs/j2s/jme/js/AsyncCallback.js ./build/jalviewjs/site/swingjs/j2s/jspecview/appletjs/JSVApplet.js > problems1.js

cat ./build/jalviewjs/site/swingjs/j2s/resources/_ES6/jsutil.js ./build/jalviewjs/site/swingjs/j2s/_ES6/jsutil.js ./build/jalviewjs/site/swingjs/j2s/org/jmol/inchi/InChIJS.js ./build/jalviewjs/site/swingjs/j2s/swingjs/JSUtil2.js > problems2.js

cat ./build/jalviewjs/site/swingjs/js/core/coretop2.js ./coreall-simple.z.js ./problems1.js ./problems2.js ./build/jalviewjs/site/swingjs/js/core/corebottom2.js > ./build/jalviewjs/site/swingjs/j2s/core/coreall.z.js


--


perl -p -i -e 's/colorPtToFFRGB\$javajs_util_T3d/colorPtToFFRGB\$javajs_util_T3/' $(grep -rl 'colorPtToFFRGB$javajs_util_T3d' ./build/jalviewjs/site/swingjs/j2s/)