From 6d69275a18e2773d73d84b9fe4291e7313abfda4 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 2 Dec 2014 13:21:49 +0000 Subject: [PATCH] JAL-1517 documentation for 2.8.2 release --- help/help.jhm | 2 + help/helpTOC.xml | 295 +++++++++++----------- help/html/colourSchemes/annotationColouring.html | 6 + help/html/releases.html | 102 ++++---- help/html/whatsNew.html | 76 +++++- 5 files changed, 278 insertions(+), 203 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index b6b0063..6a7a112 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -57,6 +57,7 @@ + @@ -122,6 +123,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 1d45e7a..57dbe4b 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -1,153 +1,154 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html index 75d9f55..5100c6b 100755 --- a/help/html/colourSchemes/annotationColouring.html +++ b/help/html/colourSchemes/annotationColouring.html @@ -58,6 +58,12 @@ symbols and graphs, this may be black by default, so your alignment will be coloured black. +
  • Secondary structure annotation colouring
    By + default, Jalview will employ the helix or sheet colours to shade + sequences and columns by available secondary structure annotation + tracks. In the case of RNA, each structure is processed to identify + distinct RNA helices and rendered in the same way as the RNA Helices shading scheme. Structure based sequence shading was added in Jalview 2.8.2
  • The colour scheme can display a colour gradient from a colour representing the minimum value in the selected annotation to a colour representing the maximum value in the selected annotation. Use the diff --git a/help/html/releases.html b/help/html/releases.html index 1f5ca08..38a92ad 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -44,10 +44,11 @@
    - 2.8.2
    18/11/2014     + 2.8.2
    2/12/2014
    General
      +
    • Updated Java code signing certificate donated by Certum.PL.
    • Features and annotation preserved when performing pairwise alignment
    • RNA pseudoknot annotation can be @@ -126,20 +127,28 @@ user preset
    • MSA web services warns user if they were launched with invalid input
      • -
    • Jalview cannot contact dasregisty (Java 8)
      • +
    • Jalview cannot contact DAS Registy when running on Java 8
      • +
    • + + 'Superpose with' submenu not shown when new view created +
      • -
    Applet + Deployment and Documentation
    • 2G and 1G options in launchApp have no effect on memory allocation
    • launchApp service doesn't automatically open www.jalview.org/examples/exampleFile.jar if no file is given
      • -
    - Application Known issues +
  • + + InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is + available +
    • + Application Known issues
    • @@ -147,10 +156,6 @@ to right
    • - - 'Superpose with' submenu not shown when new view created -
      • -
    • retrieval fails but progress bar continues for DAS retrieval with large number of ID @@ -165,51 +170,44 @@ structure tracks are rearranged
    • - - InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is - available + + invalid rna structure positional highlighting does not highlight + position of invalid base pairs
    • - - invalid rna structure positional highlighting isn't useful + + out of memory errors are not raised when saving jalview project + from alignment window file menu +
      • +
    • + + Switching to RNA Helices colouring doesn't propagate to + structures +
      • +
    • + + colour by RNA Helices not enabled when user created annotation + added to alignment +
      • +
    • + + Jalview icon not shown on dock in Mountain Lion/Webstart +
      • +
    Applet Known Issues +
      +
    • + + JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies +
      • +
    • + + Jalview and Jmol example not compatible with IE9
      • -
    -
      -
    • - - out of memory errors are not raised when saving jalview project - from alignment window file menu -
      • -
    • - - Switching to RNA Helices colouring doesn't propagate to - structures -
      • -
    • - - colour by RNA Helices not enabled when user created annotation - added to alignment -
      • TOFIX -
    • - - Jalview icon not shown on dock in Mountain Lion/Webstart -
      • -
    - Applet Known Issues -
      -
    • - - JalviewLite needs JmolApplet and JmolData jar dependencies -
      • -
    • - - Jalview and Jmol example not compatible with IE9 -
      • -
    • Sort by annotation score doesn't reverse order when - selected
      • -
    - +
  • Sort by annotation score doesn't reverse order when + selected
    • + +
    diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 4ca6e93..a5d5d4a 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -31,10 +31,78 @@ development team.
    It incorporates many minor improvements and bug-fixes, and new features for working with 3D structure data, shading alignments by secondary structure and generation of alignment - figures as Scalable Vector Graphics. -
    As ever, the highlights are detailed below, and the full list is - given in the - Jalview 2.8.2 Release Notes. + figures as Scalable Vector Graphics.
    The majority of + improvements in this version of Jalview concern the desktop + application. As ever, the highlights are detailed below, + and the full list is given in the Jalview 2.8.2 Release Notes.

    +

    + Annotation visualisation
    The alignment window + includes a new Annotations menu which provides controls for + the layout and display of sequence, group and alignment associated + annotation rows. It also now includes the Autocalculated + Annotation submenu (formerly located in the View menu), which + includes settings for the calculation and display of sequence + consensus, logos, and amino acid conservation for the alignment and + subgroups. +

    +

    + Sequence associated annotation
    New controls + have also been added to the Sequence ID popup menu for the propagation + and display of sequence associated annotation such as secondary + structure assignments and disorder predictions. Annotation associated + with one or a group of sequence already shown on the alignment may be + shown or hidden, and any available annotation from 3D structure or + calculations performed in other Jalview windows can be copied to the + alignment + via the Add Reference Annotation option.
    + The Colour by annotation function has also been + improved, allowing secondary structure annotation to be used to shade + sequences and alignment columns. Protein sequences can be coloured + according to the presence of a helix or sheet at each position, and + RNA sequences can be shaded according to each structure's stem/helix + pattern - which enables different RNA folding topologies to be quickly + identified. +

    +

    + 3D Structural data analysis and display
    + Jalview now employs Jmol's PDB data API to retrieve secondary + structure assignments made by the DSSP algorithm. It can also employ + web services to obtain secondary structure assignments from RNA + structures. These assignments are shown as sequence associated + annotation for sequences which have cross-references to the PDB, or + have had PDB files associated with them via the Structures + submenu of the sequence ID popup menu. The extraction and display of + secondary structure and B-factor column annotation is controlled via + a new Structure tab in the Jalview Desktop's + Preferences dialog box. +

    +

    + Interoperation with UCSF Chimera
    The desktop + application can now be configured to employ UCSF Chimera for the + display of 3D structure data. UCSF Chimera is a python-based + high-performance molecular graphics and animation system developed by + the Resource for Biocomputing, Visualisation, and Informatics at the + University of California.
    Jalview employs the 'StructureViz' + communication mechanism developed for Cytoscape by Morris et al. + (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism + allows Jalview to send commands to Chimera, enabling structures to be + superimposed and shaded according to associated multiple aligmment + views.
    Support for Chimera in Jalview 2.8.2 is experimental, and we + would appreciate feedback ! Please send your comments to + jalview-discuss@jalview.org, and keep up to date with this feature's + development via http://issues.jalview.org/browse/JAL-1333. +

    +

    + Export of alignment figures as Scalable Vector + Graphics
    Scalable Vector Graphics (SVG) files are now widely + supported by web browsers and graphics design programs, and allow + high-quality graphics for interactive exploration and publication. + Jalview now supports the generation of SVGs interactively (via the + Export) menu, and from the command line for server-side figure + generation. +

    + -- 1.7.10.2