X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Freleases.html;h=a37729664005d9f7279ba4da55dff518cd377bd8;hb=7bb369b2c881f59430db9c6eba292bf93663e240;hp=c88d13d5ce6978c9d6ce2b6af579523275e73eca;hpb=d29dadac0e5d78bbe5b683a1042c0c10a916cada;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index c88d13d..a377296 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,12 +47,247 @@
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+ |
+
+ General
+
+ -
+ Improved memory usage: sparse arrays used
+ for all consensus calculations
+
+ -
+ Updated Jmol shipped with applet and
+ desktop to 14.6.4
+
+ -
+
+
+
+
+ Application
+
+ -
+ Sequence ID tool tips have been tamed
+ (databases sorted alphabetically, abridged ID sets)
+
+ -
+ New replacement token for creating URLs just
+ from database cross references. Users with custom links
+ will receive a warning
+ dialog asking them to update their preferences.
+
+ -
+ Cancel button and escape listener on
+ dialog warning user about disconnecting Jalview from a
+ Chimera session
+
+ -
+ Jalview's chimera control window closes if
+ the Chimera it is connected to is shut down
+
+ -
+ Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+
+ -
+ Select highlighted columns menu item and
+ keystroke (B) to mark columns containing highlighted
+ regions from structure selections or results of a Find
+ operation
+
+ -
+ Command line option for batch-generation
+ of HTML pages rendering alignment data with the BioJS
+ MSAviewer
+
+
+
+
+ Applet
+
+ Build and deployment
+
+ - Updated Jalview's Certum code signing certificate
+ for 2016-2017
+
+ |
+
+
+ General
+
+ -
+ Columns with more than one modal residue
+ are not coloured or thresholded according to percent
+ identity (first observed in Jalview 2.8.2)
+
+ -
+ Threonine incorrectly reported as not
+ hydrophobic
+
+ -
+ Updates to documentation pages (above PID
+ threshold, amino acid properties)
+
+ -
+ Lower case residues in sequences are not
+ reported as mapped to residues in a structure file in the
+ View Mapping report
+
+ -
+ Identical features with non-numeric scores
+ could be added multiple times to a sequence
+
+ -
+ Disulphide
+ bond features shown as two highlighted residues rather
+ than a range in linked structure views, and treated
+ correctly when selecting and computing trees from features
+
+
+
+ Application
+
+ -
+ Custom URL links for specific database
+ names without regular expressions also offer links from
+ Sequence ID
+
+ -
+ Removing a single configured link in the
+ URL links pane in Connections preferences doesn't actually
+ update Jalview configuration
+
+ -
+ CTRL-Click on a selected region to open
+ the alignment area popup menu doesn't work on El-Capitan
+
+ -
+ Jalview doesn't offer to associate mmCIF
+ files with similarly named sequences if dropped onto the
+ alignment
+
+ -
+ Additional mappings are shown for PDB
+ entries where more chains exist in the PDB accession than
+ are reported in the SIFTS file
+
+ -
+ Certain structures do not get mapped to
+ the structure view when displayed with Chimera
+
+ -
+ No chains shown in the Chimera view
+ panel's View->Show Chains submenu
+
+ -
+ Export as HTML with embedded SVG doesn't
+ work for wrapped alignment views
+
+ -
+ Rename UI components for running JPred
+ predictions from 'JNet' to 'JPred'
+
+ -
+ Export as PNG or SVG is
+ corrupted when annotation panel vertical scroll is not at
+ first annotation row
+
+ -
+ Attempting to view structure for Hen
+ lysozyme results in a PDB Client error dialog box
+
+
+ Applet
+
+ Build and deployment
+
+ -
+ Failing/passing unit tests
+
+
+ New Known Issues
+
+ |
+
+
+
+ |
+ Application
+
+ - 3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded
+ - Progress bar reports models as they are loaded to
+ structure views
+ |
+
+
+ General
+
+ - Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied
+ - FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees
+
+ Application
+
+ - Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX
+ - Multiple structure views can be opened and
+ superposed without timeout for structures with multiple
+ models or multiple sequences in alignment
+ - Cannot import or associated local PDB files without
+ a PDB ID HEADER line
+ - RMSD is not output in Jmol console when
+ superposition is performed
+ - Drag and drop of URL from Browser fails for Linux
+ and OSX versions earlier than El Capitan
+ - ENA client ignores invalid content from ENA server
+ - Exceptions are not raised in console when ENA
+ client attempts to fetch non-existent IDs via Fetch DB
+ Refs UI option
+ - Exceptions are not raised in console when a new
+ view is created on the alignment
+ - OSX right-click fixed for group selections:
+ CMD-click to insert/remove gaps in groups and CTRL-click
+ to open group pop-up menu
+
+ Build and deployment
+
+ - URL link checker now copes with multi-line anchor
+ tags
+
+ New Known Issues
+
+ - Drag and drop from URL links in browsers do not
+ work on Windows
+
+ |
+
+
+ |
+
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General
-
+ Updated Spanish translations.
+
+ -
Jmol now primary parser
for importing structure data to Jalview. Enables mmCIF and
better PDB parsing.
@@ -208,7 +443,11 @@
Ref Fetcher fails to match, or otherwise updates sequence
data from external database records.
-
+ -
+ Revised Jalview Project format for
+ efficient recovery of sequence coding and alignment
+ annotation relationships.
+
Quality and Conservation are now shown on
load even when Consensus calculation is disabled
+
+ Remove right on penultimate column of
+ alignment does nothing
+
Application
@@ -421,7 +664,7 @@
-
Enable 'Get Cross-References' in menu
- after fetching cross-references
+ after fetching cross-references, and restoring from project
-
Mouseover of a copy of a sequence is not
@@ -482,6 +725,14 @@
Incorrect start and end reported for PDB
to sequence mapping in 'View Mappings' report
+ -
+ Unable to read old Jalview projects that
+ contain non-XML data added after Jalvew wrote project.
+
+ - Newly created annotation row reorders
+ after clicking on it to create new annotation for a
+ column.
+
@@ -550,6 +801,9 @@
Applet
- Split frame example added to applet examples page
+ Build and Deployment
+
+ - New ant target for running Jalview's test suite
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