From 3718374f2f04d51deff53707e4e6cbd52d144bf1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 3 Jul 2019 18:05:14 +0100 Subject: [PATCH] JAL-3111 more whats new --- help/help/html/menus/alwcalculate.html | 2 +- help/help/html/whatsNew.html | 70 ++++++++++++++++++++++++-------- 2 files changed, 54 insertions(+), 18 deletions(-) diff --git a/help/help/html/menus/alwcalculate.html b/help/help/html/menus/alwcalculate.html index d08f713..8862955 100755 --- a/help/help/html/menus/alwcalculate.html +++ b/help/help/html/menus/alwcalculate.html @@ -73,7 +73,7 @@ parsed into sequence associated annotation which can then be used to sort the alignment via the Sort by→Score menu.
-

Translate as cDNA
This +

Translate as cDNA
This option is visible for nucleotide alignments. Selecting this option shows the DNA's calculated protein product in a new split frame window. Note diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index aaef948..c5f4f75 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,34 +24,52 @@
- Jalview 2.11 - major and minor new features + Jalview 2.11 - new installer and new capabilities

Jalview 2.11 introduces support for loading VCF files, and new filters and shading models for sequence features. Under the hood, we've addressed many bugs, and also made some important changes in the way the Jalview desktop is installed and launched.

-
VCF Support. Proteins and genomic contigs with - chromosomal location annotation (such as protein coding genes - retrieved from Ensembl) can be annotated with variants imported from a local VCF file.

The Jalview Launcher and Update System
Jalview's new installation model means you'll only need to download and install Jalview once. After installation, Jalview will automatically keep itself up to date. The launcher also sets Jalview's memory automatically, so you'll never again have to manually configure Java's memory settings.
We are grateful - to Install4J who provided us with a free license for their - installation system, and Jalview's over the air update system is - based on Three Rings' Getdown system.
+ to ej Technologies for providing a free open source project + license for install4j, + and also to Three + Rings Design for Jalview's new over the air update system: Getdown. +
VCF Support. Proteins and genomic contigs with + chromosomal location annotation (such as protein coding genes + retrieved from Ensembl) can be annotated with variants imported from a local VCF file.
+
Feature filters and attribute colourschemes. A new + Feature Display + Settings dialog allows filters and feature attribute based + colourschemes to be constructed, and a new filters column + added to the Feature + Settings dialog. Jalview's sequence feature datamodel has also + been further optimised, and is now maintained as a separate + library IntervalStoreJ
+
Alternative tables for CDS translation. The Translate as CDNA option now + offers alternative amino acid coding schemes.
+
PCA plots stored in Jalview Projects
The PCA viewer user interface has + also been improved.

Backup files
Jalview will automatically create backups when overwriting existing files, and - unlike with earlier versions, should Jalview crash during a save, the original - file will be unaffected.
-
PCA plots stored in Jalview Projects
The PCA - viewer has also been enhanced and the user interface revised.
-
-
+ file will be unaffected. The Backups tab in + Jalview's preferences dialog allows the number and format of + backup filenames to be configured.

The full list of bugs fixed in this release can be found in the Jalview and Java 11, 13, and onwards

The Jalview application comes bundled with its own independent - Java installation which will be updated automatically from - www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 - runtime, but installations will be migrated to the latest Java - release once remaining issues have been addressed.
+ Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 + runtime which will be kept up to date. A Java 11 based installation + is available from the Jalview development pages.
+
+ Saying goodbye...
Long time Jalview users will notice + that this release no longer features the + Vamsas desktop menu, or a Distributed + Annotation System (DAS) tab on the feature settings dialog. + DAS is no longer supported by major bioinformatics databases, and we + decided that it was no longer feasible to maintain either JDAS or + the VAMSAS client library which rely on out-dated Java XML binding + technologies. +
+
+ Next up...
Keep an eye on the Jalview web site for + news about JalviewJS - the web based JavaScript implementation of + Jalview. Whilst Jalview 2.11 has been in development, we have also + been working with Prof. Bob Hanson (Jmol and JSmol) to enable + Jalview to run as both a Java application and a JavaScript app in a + web page. To find out more, see the JalviewJS web page. +
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