1. pdflatex TheJalviewTutorial.tex will (after three passes) generate a properly formatted pdf file TheJalviewTutorial.pdf
Caveats: ensure your pdftools cope with version 1.5 pdf files (latest pdf tools and cygwin tex packages work here).
-2. use acrobat professional to optimise the TheJalviewTutorial.pdf
- - reduces size from 27M to about 5M.
+1.5 run the generated PDF through ps2pdf (ps2pdf TheJalviewTutorial.pdf latest/TheJalviewTutorial.pdf) - reduces size from 47MB to 10MB
+2. use acrobat professional to optimise latest/TheJalviewTutorial.pdf
+ - reduces size from ~11M to about 5M.
- No command line script is available to do this.
-3. Save the optimised PDF as latest/TheJalviewTutorial.pdf and check it in when checking in the final tex file used to create it.
+3. Save the optimised PDF as latest/TheJalviewTutorial_screen.pdf and check it in when checking in the final tex file used to create it.
+Things to check
+* images should be high-resolution in the latest/TheJalviewTutorial.pdf, lower resolution in the screen optimised file.
+* all special symbols (submenu arrows, etc) should be visible in both versions of the PDF (see 'conventions used in this manual' and 'reordering the alignment' sections for good examples).