X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_10_1.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_10_1.md;h=ae4c29e89f516f9eaff1d6b3f314d0103433a976;hb=9949854f4c2dc75980f15acdee69594ca6b22631;hp=0000000000000000000000000000000000000000;hpb=cfba86992cd64bb0df6105bbf5dfc076ba8a93b2;p=jalview.git diff --git a/help/markdown/releases/release-2_10_1.md b/help/markdown/releases/release-2_10_1.md new file mode 100644 index 0000000..ae4c29e --- /dev/null +++ b/help/markdown/releases/release-2_10_1.md @@ -0,0 +1,52 @@ +--- +channel: release +version: 2.10.1 +date: 2016-11-29 +--- + +## New Features + + + +### 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 + + +### 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](webServices/urllinks.html#warning) 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 + + +## Issues Resolved + + + +### 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 + - Custom URL links for database cross-references are matched to database name regardless of case + + +### 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 + - Structure View's mapping report switched ranges for PDB and sequence for SIFTS