From 7a75fae1d4cc6136494716bfaa2b1edb26ca76be Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 3 Jun 2014 14:35:20 +0100 Subject: [PATCH] JAL-1503 whats new and release history for 2.8.1 (still not complete) --- help/help.jhm | 2 + help/helpTOC.xml | 7 ++- help/html/releases.html | 125 +++++++++++++++++++++++++++++++++-------------- 3 files changed, 93 insertions(+), 41 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index 08d3ca9..cc272e8 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -47,6 +47,7 @@ + @@ -127,6 +128,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 4ff36ba..a65cafe 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -21,10 +21,9 @@ - - - - + + + diff --git a/help/html/releases.html b/help/html/releases.html index b6fb83c..a240a49 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -35,51 +35,100 @@ -
- 2.8.1
20/5/2014 -
- - - -
    -
  • i18n Internationalisation of user interface and translation for Spanish locale
    • -
- Application
    -
  • Define/Undefine group on current selection with Ctrl-G
    • -
  • Select columns containing particular features from Feature Settings dialog
    • -
  • View all 'representative' PDB structures for selected sequences
    • -
  • Interactive consensus RNA secondary structure prediction VIENNA RNAAliFold JABA 2.1 service
    • -
  • -
  • Jalview v2.8.1 project preserves sequence dataset and dataset annotation (e.g. hidden secondary structure annotation rows)
    • -
- Applet
    - -
Other improvements -
    -
- - - Application
    +
    + 2.8.1
    + 20/5/2014     +
    + + +
      +
    • Internationalisation of user interface (usually called i18n support) and + translation for Spanish locale
      • +
    • Define/Undefine group on current selection with + Ctrl-G/Shift Ctrl-G
      • +
    • Improved group creation/removal options in alignment/sequence Popup menu
      • + +
    Application +
      +
    • Interactive consensus RNA secondary structure prediction + VIENNA RNAAliFold JABA 2.1 service
      • +
    • Select columns containing particular features from Feature + Settings dialog
      • +
    • View all 'representative' PDB structures for selected + sequences
      • +
    • Update Jalview project format:
      • + Preserve sequence and annotation dataset (to store secondary structure annotation,etc) +
      • Per group and alignment annotation and RNA helix colouring
      • +
    • New similarity measures for PCA and Tree calculation (PAM250)
      • +
    • Experimental support for retrieval and viewing of flanking + regions for an alignment
      • +
    Applet +
      + +
    Other improvements +
  • Sensible precision for symbol distribution percentages shown in logo tooltip.
    • +
  • Annotation panel height set according to amount of annotation when alignment first opened
    • +
+ + + Application +
    +
  • logo keeps spinning and status remains at queued or + running after job is cancelled
    • +
  • cannot export features from alignments imported from Jalview/VAMSAS projects
    • +
  • buggy slider for web service parameters that take float + values
  • Newly created RNA secondary structure line doesn't have 'display all symbols' flag set
    • -
  • T-COFFEE alignment score shading scheme not saved in +
  • T-COFFEE alignment score shading scheme and other annotation shading not saved in jalview project
  • Local file cannot be loaded in freshly downloaded Jalview
  • ??? unresolved ??? Jalview icon not shown on dock in Mountain Lion/Webstart
  • Load file from desktop file browser fails
  • Occasional NPE thrown when calculating large trees
    • -
- Applet -
    +
  • cannot reorder or slide sequences after dragging an + alignment onto desktop
    • +
  • Colour by annotation dialog throws NPE after using + 'extract scores' function
    • +
  • Loading/cut'n'pasting an empty file leads to a grey + alignment window
    • +
  • Disorder thresholds rendered incorrectly after performing + iupred disorder prediction
    • +
  • Multiple group annotated consensus rows shown when + changing 'normalise logo' display setting
    • +
  • Annotation/RNA Helix colourschemes cannot be applied to alignment + with groups (2.8.0b1)
    • +
  • find shows blank dialog after 'finished searching' if nothing matches query
    • +
  • Null Pointer Exceptions raised when sorting by feature with lots of groups
    • +
  • Errors in Jmol console when structures in alignment don't overlap
    • +
  • Not all working JABAWS services are shown in Jalview's menu
    • +
  • JAVAWS version of jalview fails to launch with 'invalid literal/length code'
    • +
Applet +
    +
  • +
  • Remove group option shown in applet when selection is not a group
  • Apply to all groups ticked but colourscheme changes don't affect groups
    • -
- Other
    -
  • -
- - + Other +
    +
  • Consensus sequence for alignments/groups with a single sequence were not calculated
    • +
  • annotation files that contain only groups imported as + annotation and junk sequences
    • +
  • Fasta files with sequences containing '*' incorrectly + recognised as PFAM or BLC
    • +
  • conservation/PID slider apply all groups option doesn't + affect background (2.8.0b1) +
  • +
  • redundancy highlighting is erratic at 0% and 100%
    • +
  • remove gapped columns fails for sequences with ragged + trailing gaps
    • +
  • AMSA annotation row with leading spaces is not registered correctly on import
    • +
  • Jalview crashes when selecting PCA analysis for certain alignments
    • +
  • Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting
    • +
+ +
2.8.0b1
30/1/2014 @@ -172,10 +221,12 @@
  • ClassCastException when generating EPS in headless mode
  • Adjusting sequence-associated shading threshold only - changes one row's threshold
    • + changes one row's threshold
  • Preferences and Feature settings panel panel doesn't open
    • - +
  • hide consensus histogram also hides conservation and + quality histograms
    • + -- 1.7.10.2