From: jprocter Date: Mon, 26 Sep 2011 14:37:31 +0000 (+0100) Subject: updated documentation table of contents, menus and whats new for 2.7 X-Git-Tag: Release_2_7~13 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c78133920a45e1b5b0b1bea5807f3ae880425914;p=jalview.git updated documentation table of contents, menus and whats new for 2.7 --- diff --git a/help/help.jhm b/help/help.jhm index 6ed0d7b..261d6d0 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -17,6 +17,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index a1cf057..6da4490 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -20,10 +20,12 @@ - - + + + + diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index e108ded..03502f5 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -68,6 +68,8 @@
  • Java Console
    Toggles the display of a the Jalview Java Console window. This setting will be remembered in your user preferences.
  • +
  • Jalview News
    + Opens the Jalview News dialog box.
  • Groovy Console... (only available if groovy is on the classpath)
    Open's the Groovy Console for interactive scripting.
  • diff --git a/help/html/releases.html b/help/html/releases.html index 19ff3e7..b67b69b 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -37,163 +37,166 @@
    2.7 -
    20/09/2011 +
    27/09/2011
    Application
      -
    • tweaked default layout of web services menu
    • -
    • view/alignment association menu to enable user to easily +
    • Jalview Desktop News Reader
    • +
    • Tweaked default layout of web services menu
    • +
    • View/alignment association menu to enable user to easily specify which alignment a multi-structure view takes its colours/correspondences from
    • -
    • allow properties file location to be specified as URL
    • -
    • extend jalview project to preserve associations between +
    • Allow properties file location to be specified as URL
    • +
    • Extend jalview project to preserve associations between many alignment views and a single Jmol display
    • Store annotation row height in jalview project file
    • -
    • annotation row column label formatting attributes stored +
    • Annotation row column label formatting attributes stored in project file
    • -
    • annotation row order for auto-calculated annotation rows +
    • Annotation row order for auto-calculated annotation rows preserved in jalview project file
    • -
    • visual progress indication when Jalview state is saved +
    • Visual progress indication when Jalview state is saved using Desktop window menu
    • -
    • visual indication that command line arguments are still +
    • Visual indication that command line arguments are still being processed
    • -
    • groovy script execution from URL
    • -
    • colour by annotation default min and max colours in +
    • Groovy script execution from URL
    • +
    • Colour by annotation default min and max colours in preferences
    • -
    • automatically associate PDB files dragged onto an +
    • Automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs
    • -
    • update JGoogleAnalytics to latest release (0.3)
    • +
    • Update JGoogleAnalytics to latest release (0.3)
    • 'view structures' option to open many structures in same window
    • Sort associated views menu option for tree panel
    • -
    • group all JABA and non-JABA services for a particular +
    • Group all JABA and non-JABA services for a particular analysis function in its own submenu
    Applet
      -
    • userdefined and autogenerated annotation rows for groups
    • -
    • adjustment of alignment annotation pane height
    • -
    • annotation scrollbar for annotation panel
    • -
    • drag to reorder annotation rows in annotation panel
    • +
    • Userdefined and autogenerated annotation rows for groups
    • +
    • Adjustment of alignment annotation pane height
    • +
    • Annotation scrollbar for annotation panel
    • +
    • Drag to reorder annotation rows in annotation panel
    • 'automaticScrolling' parameter
    • -
    • allow sequences with partial ID string matches to be +
    • Allow sequences with partial ID string matches to be annotated from GFF/jalview features files
    • -
    • sequence logo annotation row in applet
    • +
    • Sequence logo annotation row in applet
    • Absolute paths relative to host server in applet parameters are treated as such
    • New in the JalviewLite javascript API:
        -
      • jalviewLite.js javascript library
      • +
      • JalviewLite.js javascript library
      • Javascript callbacks for
          -
        • applet initialisation
        • -
        • sequence/alignment mouse-overs and selections
        • +
        • Applet initialisation
        • +
        • Sequence/alignment mouse-overs and selections
      • scrollTo row and column alignment scrolling functions
      • -
      • select sequence/alignment regions from javascript
      • +
      • Select sequence/alignment regions from javascript
      • javascript structure viewer harness to pass messages between Jmol and Jalview when running as distinct applets
      • sortBy method
      • -
      • set of applet and application examples shipped with +
      • Set of applet and application examples shipped with documentation
      • -
      • new example to demonstrate jalviewLite and Jmol +
      • New example to demonstrate jalviewLite and Jmol javascript message exchange
    General
      -
    • enable Jmol displays to be associated with multiple +
    • Enable Jmol displays to be associated with multiple multiple alignments
    • Option to automatically sort alignment with new tree
    • -
    • user configurable link to enable redirects to a +
    • User configurable link to enable redirects to a www.jalview.org mirror
    • Jmol colours option for Jmol displays
    • -
    • configurable newline string when writing alignment and +
    • Configurable newline string when writing alignment and other flat files
    • Allow alignment annotation description lines to contain html tags
    Documentation and Development
      -
    • add groovy test harness for bulk load testing to examples +
    • Add groovy test harness for bulk load testing to examples
    • -
    • groovy script to load and align a set of sequences using a +
    • Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop
    • -
    • restructured javascript and applet api documentation
    • -
    • ant target to publish example html files with applet archive
    • -
    • netbeans project for building jalview from source
    • +
    • Restructured javascript and applet api documentation
    • +
    • Ant target to publish example html files with applet archive
    • +
    • Netbeans project for building jalview from source
    • ant task to create online javadoc for jalview source
    Application
      -
    • user defined colourscheme throws exception when current +
    • User defined colourscheme throws exception when current built in colourscheme is saved as new scheme
    • AlignFrame->Save in application pops up save dialog for valid filename/format
    • -
    • cannot view associated structure for uniprot sequence
    • -
    • pdb file association breaks for Uniprot sequence P37173
    • -
    • associate PDB from file dialog does not tell you which +
    • Cannot view associated structure for Uniprot sequence
    • +
    • PDB file association breaks for Uniprot sequence P37173
    • +
    • Associate PDB from file dialog does not tell you which sequence is to be associated with the file
    • -
    • find All raises null pointer exception when query only +
    • Find All raises null pointer exception when query only matches sequence IDs
    • -
    • pre 2.6 jalview project cannot be loaded into v2.6
    • +
    • Pre 2.6 Jalview project cannot be loaded into v2.6
    • Jalview project with Jmol views created with Jalview 2.4 cannot be loaded
    • -
    • filetype associations not installed for webstart launch
    • -
    • two or more chains in a single PDB file associated with +
    • Filetype associations not installed for webstart launch
    • +
    • Two or more chains in a single PDB file associated with sequences in different alignments do not get coloured by their associated sequence
    • -
    • visibility status of autocalculated annotation row not +
    • Visibility status of autocalculated annotation row not preserved when project is loaded
    • -
    • tree bootstraps are not preserved when saved as a jalview +
    • Annotation row height and visibility attributes not stored + in jalview project
    • +
    • Tree bootstraps are not preserved when saved as a jalview project
    • -
    • envision2 workflow tooltips are corrupted
    • -
    • enabling show group conservation also enables colour by +
    • Envision2 workflow tooltips are corrupted
    • +
    • Enabling show group conservation also enables colour by conservation
    • -
    • duplicate group associated conservation or consensus +
    • Duplicate group associated conservation or consensus created on new view
    • -
    • annotation scrollbar not displayed after 'show all +
    • Annotation scrollbar not displayed after 'show all hidden annotation rows' option selected
    • -
    • alignment quality not updated after alignment annotation +
    • Alignment quality not updated after alignment annotation row is hidden then shown
    • -
    • preserve colouring of structures coloured by sequences in pre +
    • Preserve colouring of structures coloured by sequences in pre jalview 2.7 projects
    • Web service job parameter dialog is not laid out properly
    • -
    • web services menu not refreshed after 'reset +
    • Web services menu not refreshed after 'reset services' button is pressed in preferences
    • -
    • annotation off by one in jalview v2_3 example project
    • -
    • structures imported from file and saved in project get +
    • Annotation off by one in jalview v2_3 example project
    • +
    • Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded
    • Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
    Applet
      -
    • alignment height set incorrectly when lots of annotation +
    • Alignment height set incorrectly when lots of annotation rows are displayed
    • -
    • relative URLs in feature HTML text not resolved to +
    • Relative URLs in feature HTML text not resolved to codebase
    • -
    • view follows highlighting does not work for positions in +
    • View follows highlighting does not work for positions in sequences
    • <= shown as = in tooltip
    • -
    • export features raises exception when no features exist
    • -
    • separator string used for serialising lists of ids for +
    • Export features raises exception when no features exist
    • +
    • Separator string used for serialising lists of IDs for javascript api is modified when separator string provided as parameter
    • -
    • null pointer exception when selecting tree leaves for +
    • Null pointer exception when selecting tree leaves for alignment with no existing selection
    • -
    • relative URLs for datasources assumed to be relative to +
    • Relative URLs for datasources assumed to be relative to applet's codebase
    • -
    • status bar not updated after finished searching and search +
    • Status bar not updated after finished searching and search wraps around to first result
    • StructureSelectionManager instance shared between several jalview applets causes race conditions and memory leaks
    • -
    • hover tooltip and mouseover of position on structure not +
    • Hover tooltip and mouseover of position on structure not sent from Jmol in applet
    • -
    • certain sequences of javascript method calls to applet API +
    • Certain sequences of javascript method calls to applet API fatally hang browser
    General
      -
    • view follows structure mouseover scrolls beyond position +
    • View follows structure mouseover scrolls beyond position with wrapped view and hidden regions
    • Find sequence position moves to wrong residue with/without hidden columns
    • @@ -201,24 +204,22 @@ off by 1
    • InvalidNumberFormat exceptions thrown when trying to import PDB like structure files
    • -
    • positional search results are only highlighted between +
    • Positional search results are only highlighted between user-supplied sequence start/end bounds
    • -
    • end attribute of sequence is not validated
    • +
    • End attribute of sequence is not validated
    • Find dialog only finds first sequence containing a given sequence position
    • -
    • sequence numbering not preserved in MSF alignment output
    • +
    • Sequence numbering not preserved in MSF alignment output
    • Jalview PDB file reader does not extract sequence from nucleotide chains correctly
    • -
    • annotation row height and visibility attributes not stored - in jalview project
    • -
    • structure colours not updated when tree partition changed +
    • Structure colours not updated when tree partition changed in alignment
    • -
    • sequence associated secondary structure not correctly +
    • Sequence associated secondary structure not correctly parsed in interleaved stockholm
    • -
    • colour by annotation dialog does not restore current state +
    • Colour by annotation dialog does not restore current state
    • Hiding (nearly) all sequences doesn't work properly
    • -
    • sequences containing lowercase letters are not properly +
    • Sequences containing lowercase letters are not properly associated with their pdb files
    Documentation and Development
      diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 44e0961..88e8ee9 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -20,36 +20,84 @@ What's new ? -

      What's new ?

      -

      The Jalview 2.6.1 release fixes a number of minor bugs affecting -Jalview operation, including issues affecting the import and export of -PIR files and working with multiple multiple structure superpositions. -For full details see the Jalview -2.6.1 release history.

      -

      Highlights in Jalview Version 2.6

      -
        -
      • JABA Web Services for - multiple alignment using: +

        + What's new ? +

        +

        + The Jalview 2.7 release features new web services, and important + improvements to the way in which Jalview handles alignments and + associated PDB structures, as well as numerous minor improvements and + bug fixes. Version 2.7 of the JalviewLite applet also features a + significantly enhanced Javascript API enabling it to be more easily + integrated with javascript based web applications.
        For full + details see the Jalview 2.7 + release history. +

        +

        + Highlights in Jalview Desktop Version 2.7 +

        -
      • -
      • User modifiable alignment service parameters
      • -
      • Visualization of superposed structures associated with protein - or nucleotide sequence alignments.
      • -
      • Export coordinates and projection as CSV from PCA viewer
      • -
      -

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

      -
        - -
      -

      See the Release History page for -details of all new features and resolved issues.

      +

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

      +

      + Issues in the Jalview Desktop +

        +
      • Problems viewing associated structures for sequences + retrieved from UNIPROT
      • +
      • Problems viewing Jalview projects from older versions in + version 2.6
      • +
      • Preservation of hidden annotation rows and tree bootstrap + values in projects
      • +
      • Newly added JABAWS servers not always visible in web services + menu
      • +
      + Issues specific to the JalviewLite Applet +
        +
      • Layout problems when lots of annotation rows are displayed
      • +
      • <= shown as = in annotation row tooltip
      • +
      • export features raises exception when no features exist
      • +
      • relative URLs not handled properly when used in parameters + and annotation files
      • +
      + Issues affecting both applet and application +
        +
      • sequence numbering not preserved in MSF alignment output
      • +
      • sequence associated secondary structure not correctly parsed + in interleaved stockholm
      • +
      • sequences containing lowercase letters are not properly + associated with their pdb files
      • +
      • Jalview PDB file reader does not extract sequence from deoxy + nucleotide chains correctly
      • +
      • Sequence length given in alignment properties window is off + by 1
      • +