From 29f2df23dee2d87df1d19db87fd3f79451462ba6 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 2 Jul 2019 23:30:52 +0100 Subject: [PATCH] JAL-3111 JAL-3150 revised Jalview archive documentation and noted instructions about converting Jalview project files pre Jalview 2.1. --- help/help/html/features/jalarchive.html | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/help/help/html/features/jalarchive.html b/help/help/html/features/jalarchive.html index 94180a6..ef6cb4f 100755 --- a/help/help/html/features/jalarchive.html +++ b/help/help/html/features/jalarchive.html @@ -28,18 +28,23 @@ Jalview Project Archives

-

These are java archives of an XML file containing alignments, - trees and Jalview display information. A data exchange standard is - currently being developed, so there is no stable schema yet, but - Jalview web services will soon make use of the same interchange - format.

+

These are Zip archives of an XML file containing alignments, + trees, Principal Component Analyses (since 2.11.0), 3D structures, + and display information for Jalview, VARNA, Jmol and UCSF Chimera. + XML documents conform to a schema, and changes to the format are + made to ensure future versions of Jalview will be able to read old + Jalview project files.

- For those who want to know...
Jalview uses java classes - automatically created using Castor. - Jalview 2.08 uses descriptor classes which significantly increase - the speed of marshalling / unmarshalling java objects into XML. - Files created prior to Jalview 2.08 can still be read in, but they - will be saved in the new format. + For those who want to know...
Jalview 2.11.0 + onwards employ the JAX-B java to XML binding framework to read and + write Jalview project files. Earlier versions of Jalview employed Castor. Jalview 2.08 used + descriptor classes which significantly increase the speed of + marshalling / unmarshalling java objects into XML.

+ Files created prior to Jalview 2.08 can no longer be read by Jalview + 2.11.0. If you need to import old project files, then please import + them to Jalview 2.10.5 (available from the Jalview version archive) + and save the project again to convert it to the new format.

-- 1.7.10.2