X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6469c5f804ae3ee891947f75d7db644328ddb7e2;hb=731df4f556602bdfffb0127953c525a38feb0438;hp=0c6a131516bd92835bf4aafa3fe3352e0e3d9b47;hpb=3b68920e3494f2dd066844893e5fb0a9472ab8f7;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 0c6a131..6469c5f 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -48,22 +48,63 @@
2.10.1
- 22/11/2016
+ 24/11/2016
|
- General
-
- - Improved memory usage: sparse arrays used for all consensus calculations
-
+ General
+
+ -
+ Improved memory usage: sparse arrays used
+ for all consensus calculations
+
+ -
+ Updated Jmol shipped with applet and
+ desktop to 14.6.4
+
+ -
+
+
+
Application
- - 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
-
-
+ -
+ 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
@@ -71,36 +112,103 @@
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
+ -
+ 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 invalid 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
-
-
-
+ -
+ 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'
+
+ -
+ Export as PNG or SVG is
+ corrupted when annotation panel vertical scroll is not at
+ first annotation row
+
+ -
+
+
Applet
Build and deployment
- - Failing/passing unit tests
+ -
+ Failing/passing unit tests
+
New Known Issues
@@ -616,6 +724,14 @@
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.
+
@@ -684,6 +800,9 @@
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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