From f60e6568f57c64d60a5a06f6920878d6e5063010 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 4 May 2018 15:05:41 +0100 Subject: [PATCH] =?utf8?q?JAL-2906=20removed=20mention=20of=20experimental=20?= =?utf8?q?features,=20updated=20what=E2=80=99s=20new=20for=202.10.4=20releas?= =?utf8?q?e,=20and=20help=20TOC.?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/help.jhm | 1 + help/helpTOC.xml | 2 ++ help/html/features/chimera.html | 59 ++++++++++++++++---------------------- help/html/menus/desktopMenu.html | 2 +- help/html/releases.html | 21 ++++++++++---- help/html/whatsNew.html | 31 +++++++++----------- 6 files changed, 59 insertions(+), 57 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index f129193..d9a201a 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -54,6 +54,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 20dd8db..b218b88 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -24,6 +24,8 @@ + + diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 68ac465..e1227de 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -211,41 +211,32 @@ structure in the alignment. The regions used to calculate the superposition will be highlighted using the 'Cartoon' rendering style, and the remaining data shown as a chain - trace.

+ trace.
+
-
  • EXPERIMENTAL FEATURES
    - - These are only available if the Tools→Enable - Experimental Features option is enabled. (Since Jalview 2.10.2) -
      -
    • Write Jalview features
      Selecting - this option will create new residue attributes for any - features currently visible in the associated alignment - views, allowing those positions to be selected and - analysed with via Chimera's 'Render by Attribute' tool - (found in the Tools submenu called Structure Analysis).
      -
      If you use this option, please remember to select - the Refresh Menus option in Chimera's Render by - Attribute dialog box in order to see the attributes - derived from Jalview sequence features. -
      - View - this function's issue in Jalview's bug tracker
      • -
    • Fetch Chimera Attributes
      This - submenu lists available Chimera residue attributes that - can be imported as Jalview features on associated - sequences.
      This is particularly useful for - transferring quantitative positional annotation. For - example, structure similarity for an alignment can be - visualised by transferring the local RMSD attributes - generated by Chimera's Match->Align tool onto aligned - sequences and displayed with a Graduated feature colour - scheme. -       View - this function's issue in Jalview's bug tracker
      • -
    • -
  • Help
    +
  • Write Jalview + features
    Selecting this option will create + new residue attributes for any features currently visible in + the associated alignment views, allowing those positions to + be selected and analysed with via Chimera's 'Render by + Attribute' tool (found in the Tools submenu called Structure + Analysis).

    If you use this option, please + remember to select the Refresh Menus option in + Chimera's Render by Attribute dialog box in order to see the + attributes derived from Jalview sequence features. +
    • +
  • Fetch Chimera Attributes
    This + submenu lists available Chimera residue attributes that can + be imported as Jalview features on associated sequences.
    This + is particularly useful for transferring quantitative + positional annotation. For example, structure similarity for + an alignment can be visualised by transferring the local + RMSD attributes generated by Chimera's Match->Align tool + onto aligned sequences and displayed with a Graduated feature colour + scheme.
    • + +
  • Help
    • Chimera Help
      diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index a93ce4b..d716e33 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -86,7 +86,7 @@ the Groovy Console for interactive scripting.
      • -
    • Enable Experimental Features Enable or disable features still under development in Jalview's user interface. This setting is remembered in your preferences. +
  • Vamsas For more details, read the diff --git a/help/html/releases.html b/help/html/releases.html index 8ea4eb0..9c8b5e3 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -77,9 +77,9 @@ li:before {
    • - Structure Chooser controls to - control superposition of multiple structures and open - structures in existing views + New Structure Chooser control + for disabling automatic superposition of multiple + structures and open structures in existing views
    • Mouse cursor changes to indicate Sequence @@ -96,7 +96,7 @@ li:before {
    • Improved performance when rendering lots - of features + of features (particularly when transparency is disabled)
    @@ -116,6 +116,12 @@ li:before { sequence as gaps
  • + Cross-reference handling improved: CDS not handled correctly if transcript has no UTR +
    • +
  • + +
    • +
  • Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
    • @@ -178,7 +184,12 @@ li:before { Copy consensus sequence option in applet should copy the group consensus when popup is opened on it - + + Batch Mode +
      +
    • + Fixed ID width preference is not respected +
    New Known Defects
      diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d3972f5..b98f4bc 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -27,27 +27,24 @@ What's new in Jalview 2.10.4 ?

      - This is the February 2018 release of Jalview, with several minor bug fixes and enhanvements. - The full list bugs fixed in this release can be found in the 2.10.4 - Release Notes. In addition, Jalview 2.10.4 provides: + This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:

        -
      • +
      • Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
        • +
      • Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
        • +
      • Critical patches for running Jalview on OSX with Java 10
        • +
      • Easier adjustment of the Alignment ID panel and annotation panel
        • +
      • Improved support for mapping between 3D Structures and Uniprot Protein Sequences
        • +
      • Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
        • +
      • New buttons on the Structure Chooser for adding structures + to an existing view, and disabling automatic superposition + according to linked alignments.
        • +
      • Annotation transfer between Chimera and Jalview (formerly only + available in 'Experimental' mode)

      - Experimental Features -

      -

      - Remember, please enable the Experimental Features option in - the Jalview Desktop's Tools menu, and then restart Jalview - if you want to try out features below: + The full list bugs fixed in this release can be found in the 2.10.4 + Release Notes.

      - - -- 1.7.10.2