From 8a3915baf2a22618346a5a2ecd38f7fbca5d4a44 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 30 Jan 2014 15:48:13 +0000 Subject: [PATCH] JAL-1432 'whats new' and release history --- help/helpTOC.xml | 19 +----- help/html/releases.html | 98 ++++++++++++++++++++++++++++++ help/html/whatsNew.html | 153 +++++++++++++++-------------------------------- 3 files changed, 148 insertions(+), 122 deletions(-) diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 5a92936..3c5b9c2 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -20,22 +20,9 @@ - - - - - - - - - - - - - - - - + + + diff --git a/help/html/releases.html b/help/html/releases.html index e091da0..d436b34 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -34,6 +34,104 @@
Issues Resolved
+ +
+ 2.8.0b1
30/1/2014 +
+ + +
    +
  • Trusted certificates for JalviewLite applet and + Jalview Desktop application
    Certificate was donated by + Certum to the Jalview + open source project). +
    • +
  • Jalview SRS links replaced by Uniprot and EBI-search +
    • +
  • Output in Stockholm format
    • +
  • Allow import of data from gzipped files
    • +
  • Export/import group and sequence associated line + graph thresholds
    • +
  • Nucleotide substitution matrix that supports RNA and + ambiguity codes
    • +
  • Allow disorder predictions to be made on the current + selection (or visible selection) in the same way that JPred + works
    • +
  • Groovy scripting for headless jalview operation
    • +
Other improvements +
    +
  • Upgrade desktop installer to InstallAnywhere 2013
    • +
  • COMBINE statement uses current SEQUENCE_REF and + GROUP_REF scope to group annotation rows
    • +
  • Support '' style escaping of quotes in Newick + files
    • +
  • Group options for JABAWS service by command line name
    • +
  • Empty tooltip shown for JABA service options with a + link but no description
    • +
  • Select primary source when selecting authority in + database fetcher GUI
    • +
  • Add .mfa to FASTA file extensions recognised by + Jalview
    • +
  • Annotation label tooltip text wrap
    • +
+ + +
    +
  • Slow scrolling when lots of annotation rows are + displayed
    • +
  • Lots of NPE (and slowness) after creating RNA + secondary structure annotation line
    • +
  • Sequence database accessions not imported when + fetching alignments from Rfam
    • +
  • Incorrect SHMR submission for sequences with + identical IDs
    • +
  • View all structures does not always superpose + structures
    • +
  • Option widgets in service parameters not updated to + reflect user or preset settings
    • +
  • Null pointer exceptions for some services without + presets or adjustable parameters
    • +
  • Discover PDB IDs entry in structure menu doesn't + discover PDB xRefs
    • +
  • Exception encountered while trying to retrieve + features with DAS
    • +
  • Lowest value in annotation row isn't coloured + when colour by annotation (per sequence) is coloured
    • +
  • Keyboard mode P jumps to start of gapped region when + residue follows a gap
    • +
  • Jalview appears to hang importing an alignment with + Wrap as default or after enabling Wrap
    • +
  • 'Right click to add annotations' message + shown in wrap mode when no annotations present
    • +
  • Disorder predictions fail with NPE if no automatic + annotation already exists on alignment
    • +
  • oninit javascript function should be called after + initialisation completes
    • +
  • Remove redundancy after disorder prediction corrupts + alignment window display
    • +
  • Example annotation file in documentation is invalid
    • +
  • Grouped line graph annotation rows are not exported + to annotation file
    • +
  • Multi-harmony analysis cannot be run when only two + groups created
    • +
  • Cannot create multiple groups of line graphs with + several 'combine' statements in annotation file
    • +
  • Pressing return several times causes Number Format + exceptions in keyboard mode
    • +
  • Multi-harmony (SHMMR) method doesn't submit + correct partitions for input data
    • +
  • Translation from DNA to Amino Acids fails
    • +
  • Jalview fail to load newick tree with quoted label
    • +
  • --headless flag isn't understood
    • +
  • ClassCastException when generating EPS in headless + mode
    • +
  • Adjusting sequence-associated shading threshold only + changes one row's threshold
    • +
  • Preferences and Feature settings panel panel + doesn't open
    • +
+ +
2.8
12/11/2012 diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b81031d..79cf7c9 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -21,111 +21,52 @@ What's new ? -

- What's new ?
- Jalview 2.8 includes a number of enhancements and new features that - have been in development since July 2010. It is also the first Jalview - release to incorporate RNA visualization features developed by Lauren - Lui and Jan Engelhart during their Google Summer of Code projects - (http://code.google.com/soc/). As usual you can find the highlights - below, but to see the comprehensive list take a look at the look at - the Jalview 2.8 Release Notes. -

- Highlights in Jalview Version 2.8 -
    -
  • Improved JABAWS - client and new JABAWS 2.0 Services - -
    • -
  • RNA -
      -
    • Import sequence and alignment associated WUSS or VIENNA - dot-bracket notation from files and the RFAM - database -
      • -
    • Interactive editing of RNA secondary structure annotation
      • -
    • Colour scheme for purine/pyrimidine and to highlight RNA - helices
      • -
    • RNA canonical base pair consensus - score and sequence logo -
      • -
    • Embedded VARNA RNA - secondary structure viewer in the Desktop -
      • -
    • -
  • Parse and display T-COFFEE - alignment quality scores (thanks to Paolo di Tomasso of the Notredame - Group) -
    • -
  • Per - sequence alignment annotation shading
    • -
  • Enhanced PCA viewer: more - export options, and switch between different PCA modes and residue - score models -
    • -
  • New Jalview Desktop database - fetcher GUI -
    • -
  • Support for DAS 1.6 and DAS 2.0 sources (thanks to the new - JDAS Distributed Annotation client library (see - http://code.google.com/p/jdas))
    • -
  • Export sequence database annotation as an HTML report
    • -
  • Normalised Sequence - Logo Display
    • -
-

- Issues resolved in the Jalview Desktop -

-
    -
  • PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch - REST service
    • -
  • Stop windows being moved outside desktop on OSX
    • -
  • Jnet job queues forever if a very short sequence is submitted - for prediction
    • -
  • Structure view highlighting doesn't work on windows 7
    • -
  • Jalview desktop fails to launch with exception when using - proxy
    • -
  • DAS Sequence retrieval with range qualification results in - sequence xref which includes range qualification
    • -
  • Cannot close news reader when JABAWS server warning dialog is - shown
    • -
  • Edited sequence not submitted to web service
    • -
  • Jalview 2.7 InstallAnywhere installer doesn't unpack and run - on OSX Mountain Lion -
      -
    • If you use webstart then you may need to go into the - Security panel (a.k.a the gatekeeper) in your System - Settings, and select the 'allow any code to run' option. -
      • -
    -
    • -
-

- Issues specific to the JalviewLite Applet -

-
    -
  • Sequence features are momentarily displayed before they are - hidden using hidefeaturegroups applet parameter
    • -
  • loading features via javascript API automatically enables - feature display
    • -
  • scrollToColumnIn javascript API method doesn't work
    • -
-

- Issues affecting both applet and application -

-
    -
  • Redundancy removal fails for rna alignment
    • -
  • PCA window shows grey box when first opened on OSX
    • -
  • Letters coloured pink in sequence logo when alignment - coloured with clustalx
    • -
+

+ What's new ?
Jalview 2.8.0b1 is a bugfix + release for Jalview version 2.8.
As usual you can find the + highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes. +

+

+ This bug fix release includes numerous minor enhancements made over + the last 12 months. Importantly, it is also the first release that + provides Jalview as a trusted application, signed with a certificate + donated to us by Certum. +

+ Enhancements and new features +
    +
  • Allow disorder predictions to be made on the current + selection (or visible selection) in the same way that JPred works
    • +
  • allow import of data from gzipped files
    • +
  • Improved per-sequence 'colour-by-annotation' performance
    • +
  • Support '' style escaping of quotes in Newick files
    • +
  • group options for JABAWS service by command line name
    • +
  • Select primary source when selecting authority in database + fetcher GUI
    • +
  • COMBINE statement uses current SEQUENCE_REF and GROUP_REF + scope to group annotation rows
    • +
  • add .mfa to FASTA file extensions recognised by Jalview
    • +
  • groovy scripting for headless jalview operation
    • +
  • Output in Stockholm format
    • +
+ Bug fixes +
    +
  • Uniprot and PDB database cross-reference fetching works + properly
    • +
  • 'View all structures' in the desktop is more reliable
    • +
  • Web services parameter dialog box shows the options enabled + for different presets
    • +
  • Interactive creation of RNA secondary structure works more + smoothly
    • +
  • Keyboard mode 'P' command jumps to the right place
    • +
  • Improved support for parsing database cross-references via + Stockholm and Rfam database
    • +
  • Improved semantics in annotation files for grouping + annotation rows associated with particular sequences and groups
    • +
  • More robust DNA->Amino acid translation
    • +
  • Improved Headless-mode operation for DAS annotation + retrieval, groovy script execution and alignment figure generation
    • +
  • annotation label tooltip text needs to be wrapped
    • +
-- 1.7.10.2