X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=b9a27ff9e02f0fb2d53a8e01f25f195229692221;hp=93c126781374f333b0988d7e5b4126cdc9f11816;hb=639c433bf1162d8219b12813753c9ba38446b52e;hpb=e4a1d321196af18049444db25ce0e2b142cdd984 diff --git a/help/help/html/releases.html b/help/help/html/releases.html index 93c1267..b9a27ff 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -24,25 +24,25 @@ Release History @@ -58,9 +58,349 @@ li:before { 2.11.2.0
+ 10/03/2022 + + Jalview Native App + JalviewJS + Development + + + + JalviewJS + Development + Known Issues + + + + + 2.11.1.7
+ 18/01/2022 + + + Security + + + + 2.11.1.6
+ 6/01/2022 + + Security + + + + + 2.11.1.5
- 22/06/2021 - Development + 20/12/2021 + + Security + Development @@ -256,6 +596,12 @@ li:before { Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+) +
  • + RESNUM sequence features (the + green ones) are not automatically displayed when associated + structures are displayed or for sequences retrieved from the + PDB. +
    • Launching Jalview @@ -336,6 +682,11 @@ li:before { save in place.)
  • + Dragging a PDB file onto an alignment with + sequence features displayed causes displayed features to be + hidden. +
    • +
  • Cannot process alignments from HTTPS urls via command line
    • @@ -366,13 +717,13 @@ li:before {
  • CDS shown in result of submitting proteins in a CDS/Protein alignment to a web service is wrong when - proteins share a common transcript sequence (e.g. - genome of RNA viruses) + proteins share a common transcript sequence (e.g. genome of + RNA viruses)
  • - Co-located features exported and re-imported - are ordered differently when shown on alignment and in - tooltips. (Also affects v2.11.1.0) + Co-located features exported and + re-imported are ordered differently when shown on alignment + and in tooltips. (Also affects v2.11.1.0)
  • Drag and drop of alignment file onto @@ -385,7 +736,8 @@ li:before {
  • Sequence ID colourscheme not re-applied - when alignment view restored from project (since Jalview 2.11.0) + when alignment view restored from project (since Jalview + 2.11.0)
  • Duplicate CDS sequences are generated when @@ -441,32 +793,42 @@ li:before { with no feature types visible
  • - Improved support for filtering feature attributes with large integer values + Improved support for filtering feature + attributes with large integer values +
    • + + Jalview Installer + Jalview Installer - Release processes Build System - Groovy Scripts - Groovy Scripts + - - 2.11.0
    - 04/07/2019     - + 2.11.0
    04/07/2019
  • - Symmetric score matrices for faster - tree and PCA calculations + Symmetric score matrices for faster tree + and PCA calculations
  • Principal Components Analysis Viewer -
    • +
  • New 'Colour by Sequence ID' option
  • Speed and Efficiency - Deprecations Documentation Development and Release Processes @@ -843,16 +1243,17 @@ li:before { superposition in Jmol fail on Windows
  • - Blank error dialog is displayed when discovering - structures for sequences with lots of PDB structures + Blank error dialog is displayed when + discovering structures for sequences with lots of PDB + structures
  • - Text misaligned in EPS or SVG image export with - monospaced font + Text misaligned in EPS or SVG image export + with monospaced font
  • - Warning of 'Duplicate entry' when saving Jalview - project involving multiple views + Warning of 'Duplicate entry' when saving + Jalview project involving multiple views
  • Overview for complementary view in a linked @@ -860,79 +1261,81 @@ li:before { Annotation dialog hides columns
  • - Selection highlighting in the complement of a - CDS/Protein alignment stops working after making a selection in - one view, then making another selection in the other view + Selection highlighting in the complement of + a CDS/Protein alignment stops working after making a + selection in one view, then making another selection in the + other view
  • Annotations tooltip changes beyond visible columns
  • - Table Columns could be re-ordered in Feature - Settings and Jalview Preferences panels + Table Columns could be re-ordered in + Feature Settings and Jalview Preferences panels
  • - Jalview hangs when closing windows, or redrawing the - overview with large alignments + Jalview hangs when closing windows, or + redrawing the overview with large alignments
  • Tree and PCA calculation fails for selected - region if columns were selected by dragging right-to-left and the - mouse moved to the left of the first column + region if columns were selected by dragging right-to-left + and the mouse moved to the left of the first column
  • - Couldn't hide selected columns adjacent to a - hidden column marker via scale popup menu + Couldn't hide selected columns adjacent to + a hidden column marker via scale popup menu
  • - Error message for trying to load in invalid URLs - doesn't tell users the invalid URL + Error message for trying to load in invalid + URLs doesn't tell users the invalid URL
  • Tooltips displayed for features filtered by score from view
  • - Sequence Variants retrieved from Ensembl during - show cross references or Fetch Database References are shown in - red in original view + Sequence Variants retrieved from Ensembl + during show cross references or Fetch Database References + are shown in red in original view
  • - stop_gained variants not shown correctly on - peptide sequence (computed variant shown as p.Res.null) + stop_gained variants not shown + correctly on peptide sequence (computed variant shown as + p.Res.null)
  • 'Graduated colour' option not offered for manually created features (where feature score is Float.NaN)
  • - Blank extra columns drawn or printed - when columns are hidden + Blank extra columns drawn or + printed when columns are hidden
  • Regular expression error for '(' in Select Columns by Annotation description
  • - Scroll doesn't stop on mouse up after dragging - out of Scale or Annotation Panel + Scroll doesn't stop on mouse up after + dragging out of Scale or Annotation Panel
  • - Column selection incorrect after scrolling out of - scale panel + Column selection incorrect after scrolling + out of scale panel
  • Left/right drag in annotation can scroll alignment down
  • - Error if mouse moved before clicking Reveal in - scale panel + Error if mouse moved before clicking Reveal + in scale panel
  • - Column display is out by one after Page Down, - Page Up in wrapped mode + Column display is out by one after Page + Down, Page Up in wrapped mode
  • Finder doesn't skip hidden regions @@ -941,24 +1344,24 @@ li:before { Finder searches in minimised alignments
  • - 'Apply Colour to All Groups' not always selected - on opening an alignment + 'Apply Colour to All Groups' not always + selected on opening an alignment
  • - 'Colour by Annotation' not marked selected in - Colour menu + 'Colour by Annotation' not marked selected + in Colour menu
  • - Per-group Clustal colour scheme changes when - different groups in the alignment are selected + Per-group Clustal colour scheme changes + when different groups in the alignment are selected
  • - Internationalised colour scheme names not shown - correctly in menu + Internationalised colour scheme names not + shown correctly in menu
  • - Colour by Annotation can go black at min/max - threshold limit + Colour by Annotation can go black at + min/max threshold limit
  • Value input for graduated feature colour @@ -969,56 +1372,59 @@ li:before { colour
  • - PCA points don't dim when rotated about y axis + PCA points don't dim when rotated about y + axis
  • PCA Print dialog continues after Cancel
  • - Cancel in Tree Font dialog resets alignment, not - Tree font + Cancel in Tree Font dialog resets + alignment, not Tree font
  • - Associate Tree with All Views not restored from - project file + Associate Tree with All Views not restored + from project file
  • - Scrolling of split frame is sluggish if Overview - shown in complementary view + Scrolling of split frame is sluggish if + Overview shown in complementary view
  • - Codon consensus incorrectly scaled when shown - without normalisation + Codon consensus incorrectly scaled when + shown without normalisation
  • - Sequence Details report should open positioned at top - of report + Sequence Details report should open + positioned at top of report
  • Help page can be opened twice
  • - Fuzzy text in web service status menu on OSX Mojave + Fuzzy text in web service status menu on + OSX Mojave
    • Editing Datamodel Bugs fixed for Java 11 Support (not yet on - general release) + Bugs fixed for Java 11 Support (not yet on general + release) New Known Defects - Java 11 Specific defects - Java 11 Specific defects + - -
    - 2.10.5
    10/09/2018     -
    - -
    - - New Known Defects
    @@ -1293,13 +1704,12 @@ li:before { of features (particularly when transparency is disabled)
  • - Experimental features in 2.10.2 for - exchange of Jalview features and Chimera attributes made - generally available + Experimental features in 2.10.2 + for exchange of Jalview features and Chimera attributes + made generally available
    • - - +
    Applet @@ -1397,9 +1809,10 @@ li:before { Batch Mode New Known Defects -
    - +
    - 2.10.3b1
    24/1/2018     + 2.10.3b1
    + 24/1/2018
    -
    -
    - Desktop
    - + +
    + Desktop +
    @@ -1703,14 +2145,16 @@ li:before { New features in Jalview Desktop -
    -
    +
    @@ -2179,9 +2623,9 @@ li:before { recovered correctly from Jalview project file
  • - Feature colours in overview when first opened - (automatically via preferences) are different to the main - alignment panel + Feature colours in overview when first + opened (automatically via preferences) are different to + the main alignment panel
    • Data import/export @@ -3057,7 +3501,7 @@ li:before { column.
  • - Null Pointer Exception raised when + Null Pointer Exception raised when pressing Add on an orphaned cut'n'paste window.