From: jprocter Date: Wed, 7 Nov 2012 15:42:19 +0000 (+0000) Subject: Jalview 2.8 release notes and whats new! text X-Git-Tag: Release_2_8~2^2~22 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=32254db18cc678b675db8d0cd72a525a6034bf01;p=jalview.git Jalview 2.8 release notes and whats new! text --- diff --git a/help/html/releases.html b/help/html/releases.html index b8ad47c..a7963df 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -33,369 +33,536 @@
Issues Resolved
- -
2.8
08/11/2012
-Application -
  • Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega) - -
  • -
  • JABAWS server status indicator in Web Services preferences -
  • -
  • VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window -
  • -
  • Updated jalview build and deploy framework for OSX mountain lion, windows 7, and 8 -
  • -
  • Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes -
  • + +
    + 2.8
    08/11/2012 +
    + Application +
  • Support for JABAWS 2.0 Services (AACon alignment + conservation, protein disorder and Clustal Omega) + + +
  • +
  • + JABAWS + server status indicator in Web Services preferences +
  • +
  • + VARNA + (http://varna.lri.fr) viewer for RNA structures in Jalview + alignment window +
  • +
  • + Updated + jalview build and deploy framework for OSX mountain lion, windows + 7, and 8 +
  • +
  • Nucleotide substitution matrix for PCA that supports RNA + and ambiguity codes +
  • -
  • Improved sequence database retrieval GUI
  • Support fetching and database reference look up against multiple DAS sources -
  • -
  • Jalview project improvements -Applet - -General - -Documentation and Development - - -Application - - - -Applet - -General - - - - - -
    - 2.7 -
    27/09/2011 -
    - Application - Applet - General - Documentation and Development - - Application - Applet - General - Documentation and Development - - - + +
  • +
  • + horizontal + scrolling gesture support +
  • +
  • Visual progress indicator when PCA calculation is running +
  • +
  • Simpler JABA web services menus +
  • +
  • + visual + indication that web service results are still being retrieved from + server +
  • +
  • + Serialise + the dialogs that are shown when jalview starts up for first time +
  • +
  • + Jalview + user agent string for interacting with HTTP services +
  • +
  • + DAS + 1.6 and DAS 2.0 source support using new JDAS client library +
  • + Applet + General + Documentation and Development + + Application + Applet + General + + + + +
    + 2.7
    27/09/2011 +
    + + Application + Applet + General + Documentation and Development + + Application + Applet + General + Documentation and Development + + +
    2.6.1 diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index c260b5a..d9b6360 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -20,43 +20,184 @@ What's new ? -

    - 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 Desktop Version 2.8 -

    -
      +

      + 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 +

      +
        +
      • Improved JABA client and new JABAWS 2.0 Services +
          +
        • AACon alignment conservation
        • +
        • Protein disorder - DisEMBL, RONN, GlobPlot and IUPred
        • +
        • Clustal Omega - huge protein alignments
        • +
        +
      • +
      • Support for RNA +
          +
        • Import sequence and alignment associated WUSS or VIENNA + secondary structure notation from stockholm and clustalW files or + as jalview annotation.
        • +
        • Interactive editing of RNA secondary structure annotation
        • +
        • Colour scheme for purine/pyrimidine and to highlight RNA + helices
        • +
        • RNA canonical base pair consensus score and sequence logo
        • +
        • Embedded VARNA RNA + secondary structure viewer in the Desktop +
        • +
        See Nucleic Acid Support for full + details.
      • +
      • Parse and display T-COFFEE alignment quality scores
      • +
      • Shade individual sequence positions according to alignment + annotation scores
      • +
      • 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
      • +
      • Export sequence database annotation as HTML report
      • +
      • Normalised Sequence Logo Display
      • +
      +

      + Issues Resolved (a select list - see the release history for full details) + +

      +

      + Issues in the Jalview Desktop +

        +
      • PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch + REST service +
      • +
      • + + Stop + windows being moved outside desktop on OSX +
      • +
      • + Filetype + associations not installed for webstart launch +
      • +
      • + Jalview + does not always retrieve progress of a JABAWS job execution in full + once it is complete +
      • +
      • + View + all structures superposed fails with exception +
      • +
      • + Jnet + job queues forever if a very short sequence is submitted for + prediction +
      • +
      • + Structure + view highlighting doesn't work on windows 7 +
      • +
      • + Jalview + desktop fails to launch with exception when using proxy +
      • +
      • + Tree + calculation reports 'you must have 2 or more sequences + selected' when selection is empty +
      • +
      • + DAS + Sequence retrieval with range qualification results in sequence xref + which includes range qualification +
      • +
      • + Cannot + close news reader when JABAWS server warning dialog is shown +
      • +
      • + Edited + sequence not submitted to web service +
      • +
      • + Jalview + 2.7 Webstart and InstallAnywhere installer doesn't unpack and run + on OSX Mountain Lion +
          +
        • The workaround for webstart is to go into the Security + panel (gatekeeper symbol) under System settings, and select the + 'allow any code to run' setting.
        • +
        +
      • +
      • + Annotation + panel not given a scroll bar when sequences with alignment annotation + are pasted into the alignment +
      • +
      • + Sequence + associated annotation rows not associated when loaded from jalview + project +
      • +
      • + Exceptions + when copy/paste sequences with grouped annotation rows to new window +
      • +
      • + Browser + launch fails with NPE on java 1.7 +
      • -
      • New Purine/Pyrimidine colour scheme
      • -
      • Colouring of RNA secondary structure by helices. See Nucleic Acid Support
      • -
      • Embedded VARNA RNA secondary structure viewer. -
      +
    -

    - Issues Resolved (a select list - see the release history for full details) - -

    -

    - Issues in the Jalview Desktop -

      -
    - Issues specific to the JalviewLite Applet -
      -
    - Issues affecting both applet and application -
      -
    + Issues specific to the JalviewLite Applet +
      +
    • + Sequence + features are momentarily displayed before they are hidden using + hidefeaturegroups applet parameter +
    • +
    • + loading + features via javascript API automatically enables feature display +
    • +
    • + scrollToColumnIn + javascript API method doesn't work +
    • +
    + Issues affecting both applet and application + General +
      +
    • + Redundancy + removal fails for rna alignment +
    • +
    • + PCA + window shows grey box when first opened on OSX +
    • +
    • + Letters + coloured pink in sequence logo when alignment coloured with clustalx +
    • +
    • + Choosing + fonts without letter symbols defined causes exceptions and redraw + errors +
    • +
    • + Initial + PCA plot view is not same as manually reconfigured view +
    • +