included instructions to use ps2pdf to reduce the size of file generated by pdflatex...

diff --git a/README b/README
index a52e510..eaf6613 100644 (file)
--- a/README
+++ b/README
@@ -26,9 +26,13 @@ The raw output of the tex->PDF conversion should not be checked in, only the fin
 
 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).
 

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index db1e65f..1bcef5a 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -3,7 +3,8 @@
 \usepackage[format=hang,margin=10pt]{caption}
 \usepackage{footnote}
 \usepackage{graphicx}
-\usepackage{amssymb}
+\usepackage{fouriernc}
+%\usepackage{amssymb}
 \usepackage{epstopdf}
 \usepackage{hyperref}
 \usepackage{subfigure}
@@ -149,8 +150,8 @@ colouring.} and includes a javascript API to allow customisable display of align
 
 
 Jalview 2.8 was released in November 2012. The Jalview Desktop in this version
-provides access to protein and nucleic acid sequence, alignment and structure databases, and
-includes the Jmol\footnote{ Provided under the LGPL licence at
+provides access to protein and nucleic acid sequence, alignment and structure
+databases, and includes the Jmol\footnote{ Provided under the LGPL licence at
 \url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of RNA secondary structure. A
 Distributed Annotation System (DAS) client\footnote{jDAS - released under Apache license (v2.0) at \url{http://code.google.com/p/jdas}} which facilitates the retrieval and display of third party sequence
 annotation in association with sequences and any associated structure. It also

diff --git a/latest/README b/latest/README
index 38ded5e..153eeca 100644 (file)
--- a/latest/README
+++ b/latest/README
@@ -1,6 +1,12 @@
 Generating the TheJalviewTutorial_Screen.pdf\r
 --------------------------------------------\r
 \r
+Note: before any pdf optimization can be performed, you need to preprocess the raw pdf generated by pdflatex by:\r
+ps2pdf TheJalviewTutorial.pdf TheJalviewTutorial_pdfopt.pdf\r
+\r
+The above command should complete with no errors. The resulting file can be safely operated on with the Adobe PDF optimizer to downsample images without losing any of the special characters (e.g. the double right arrows for menu/submenu paths or the arrow key symbols).\r
+\r
+\r
 The PDF Optimizer setting of Adobe Acrobat 7 was used with the following settings:\r
 Compatibility: Acrobat 4.0 and later\r
 Images: Bicubic (always).   \r

diff --git a/latest/TheJalviewTutorial.pdf b/latest/TheJalviewTutorial.pdf
index 455f252..6c152ad 100644 (file)
Binary files a/latest/TheJalviewTutorial.pdf and b/latest/TheJalviewTutorial.pdf differ

diff --git a/latest/TheJalviewTutorial_screen.pdf b/latest/TheJalviewTutorial_screen.pdf
index 20d40b6..cc1ecb2 100644 (file)
Binary files a/latest/TheJalviewTutorial_screen.pdf and b/latest/TheJalviewTutorial_screen.pdf differ