jalviewTutorial: README ======================= 14th August 2008: J.B. Procter. This is a refactored version of the Jalview Tutorial for Jalview Version 2.2 which was created by David Martin in 2006. TheJalviewTutorial.tex is the main tex file. images/ contain the images included in the tutorial. They are PDFs created to PDF 1.5 standard (which is higher than the PDF tools available on Kinshar at time of writing). data/ contains the data used to create the tutorial images and useful data artefacs that might be provided to user. Jalview Tutorial.doc is the original word document created by the Jalview 2 team giving the basic outline used to create the tutorial. Building the document ===================== The raw output of the tex->PDF conversion should not be checked in, only the final optimised PDF. 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). 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_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).