From 0bce27989320cd0b44a13151269749614d5cd312 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 9 Nov 2012 13:04:39 +0000 Subject: [PATCH] tweaking welcome message and what's new --- help/html/index.html | 29 +++--- help/html/whatsNew.html | 227 +++++++++++++++++------------------------------ 2 files changed, 97 insertions(+), 159 deletions(-) diff --git a/help/html/index.html b/help/html/index.html index dd757aa..695d9de 100755 --- a/help/html/index.html +++ b/help/html/index.html @@ -19,18 +19,25 @@ Jalview Documentation - -

-Jalview Documentation -

-Jalview (2009) is a fast Java multiple alignment editor and analysis tool. It -features many of the functions of AMAS, -for the analysis of sub-families and the prediction of functional sites, but is -fully interactive. (View the Jalview homepage at www.jalview.org). -

-

If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics:

+ +

Welcome to Jalview's built in documentation.

+

If you don't know what Jalview is, then in addition to the pages here, we also suggest you take a look at www.jalview.org.

+

Here are some good places to start:

+

If you are using the Jalview Desktop application and are looking + for something specific, then this help system also includes a search + box. If you're already viewing this in your web browser, then google + the online version of these pages. If you don't find what you are + looking for, or want to report a bug or make a feature request, then + get in contact over at http://www.jalview.org/community

+ +

Citing Jalview
If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics:

Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009),
"Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"
- Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033 + Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 39ef82f..5d00e19 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -21,179 +21,110 @@

- What's new ? -

-

Jalview 2.8 includes a brand new logo, which you'll see in file - browsers, splash screens, and also on the new look Jalview site.

-

- In addition to our new look, Jalview 2.8 includes a number of new - features.. some of which have been in development since July 2010. The - highlights are below, and - as usual, for a comprehensive list, take a - look at the Jalview 2.8 Release - Notes. -

-

- Highlights in Jalview Version 2.8 + What's new ?
+ Jalview 2.8 includes a number of enhancements and new features that + have been in development since July 2010. It is also the first Jalview + release to incorporate RNA visualization features developed by Lauren + Lui and Jan Engelhart during their Google Summer of Code projects + (http://code.google.com/soc/). As usual, you can find some highlights + below, but to see the comprehensive list, take a look at the look at + the Jalview 2.8 Release Notes.

+ Highlights in Jalview Version 2.8 +
  • RNA
    • -
  • Parse and display T-COFFEE alignment quality scores (thanks to Paolo Tomassi of the Notredame Group)
    • -
  • Per sequence alignment annotation shading
    • -
  • Enhanced PCA viewer: more export options, and switch between - different PCA modes and residue score models
    • -
  • New Jalview Desktop database fetcher GUI
    • -
  • Support for DAS 1.6 and DAS 2.0 sources (thanks to new JDAS Distributed Annotation client library)
    • -
  • Export sequence database annotation as HTML report
    • -
  • Normalised Sequence Logo Display
    • +
  • Parse and display T-COFFEE + alignment quality scores (thanks to Paolo Tomasso of the Notredame + Group) +
    • +
  • Per + sequence alignment annotation shading
    • +
  • Enhanced PCA viewer: more + export options, and switch between different PCA modes and residue + score models +
    • +
  • New Jalview Desktop database + fetcher GUI +
    • +
  • Support for DAS 1.6 and DAS 2.0 sources (thanks to the new + JDAS Distributed Annotation client library (see + http://code.google.com/p/jdas))
    • +
  • Export sequence database annotation as an HTML report
    • +
  • Normalised Sequence + Logo Display

    • - Issues Resolved (a select list - see the release history for full details) - + Issues resolved in the Jalview Desktop

    -

    - Issues in the Jalview Desktop

    - - Issues specific to the JalviewLite Applet +

    + Issues specific to the JalviewLite Applet +

    - Issues affecting both applet and application +

    + Issues affecting both applet and application +

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