X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=4077a838b970ce88dfcc7f05167ea4e4b101f463;hb=dc4e35ab621a97c049f89ea9aa6d19737179139e;hp=30aa7f2ffeb89a133d38777e22cc860d9b99ffd0;hpb=f3210a53ff0c7fcb833319ce6dfd322ac8d2ee23;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 30aa7f2..4077a83 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -52,78 +52,147 @@
- 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
- - 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
+ General
+ -
+ Improved memory usage: sparse arrays used
+ for all consensus calculations
+
+ -
+ Jmol updated to version 14.6.4 (released 3rd Oct 2016)
+
+ - Updated Jalview's Certum code signing certificate
+ for 2016-2017
- Build and deployment
+ Application
-
+ -
+ Sequence ID tool tip presents abridged
+ set of database cross-references, sorted alphabetically
+
+ -
+ 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
+
+ -
+ New keystroke (B) and Select highlighted
+ columns menu item to mark columns containing
+ highlighted regions (e.g. 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
+
- |
+
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
-
-
- 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
- -
- 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
-
- - Rename UI components for running JPred predictions from 'JNet' to 'JPred'
+ -
+ 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
+
+ -
+ Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+
-
-
-
-
- Applet
-
- Build and deployment
+ Application
- - Failing/passing unit tests
+ -
+ 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
+
- New Known Issues
+
|