From 908e8e3c1789cf03f50885d75987cf7d0336f748 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 15 Sep 2021 16:17:11 +0100 Subject: [PATCH] =?utf8?q?JAL-3842=202.11.1.5=20what=E2=80=99s=20new,=20rele?= =?utf8?q?ase=20notes,=20and=20version=20bump=20=20Conflicts:=20 RELEASE?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/help/html/releases.html | 100 ++++++++++++++++++++++++++++++------------ help/help/html/whatsNew.html | 42 +++++++----------- 2 files changed, 88 insertions(+), 54 deletions(-) diff --git a/help/help/html/releases.html b/help/help/html/releases.html index 4c72658..353dd46 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -1,3 +1,4 @@ + New .jalview_properties token controlling - launch of the news browser (like -nonews argument) - -

- New .jalview_properties token controlling - download of linkout URLs from - www.jalview.org/services/identifiers -

- New .jalview_properties token controlling - download of BIOJSHTML templates -

- New 'Discover Web Services' option to trigger - a one off JABAWS discovery if autodiscovery was disabled -

- - -

- + + 2.11.1 .5
+ 22/06/2021 + Development +

Updated building instructions

+ +

+ Occupancy calculation is incorrect for + alignment columns with over -1+2^32 gaps (breaking filtering + and display) +
+ Caps on Hi-DPI scaling to prevent crazy + scale factors being set with buggy window-managers (linux + only) +

Development +

Fixed non-fatal gradle errors during build

+ + + + 2.11.1 .4
+ 09/03/2021 + Improved control of + Jalview's use of network services via jalview_properties +

+ New .jalview_properties token controlling + launch of the news browser (like -nonews argument) +
+ New .jalview_properties token controlling + download of linkout URLs from + www.jalview.org/services/identifiers +
+ New .jalview_properties token controlling + download of BIOJSHTML templates +
+ New 'Discover Web Services' option to + trigger a one off JABAWS discovery if autodiscovery was + disabled +

+ +

+ Intermittent deadlock opening structure in + Jmol +

New Known defects +

+ Protein Cross-Refs for Gene Sequence not + always restored from project (since 2.10.3) +
+ Selections from tree built from CDS aren't + propagated to Protein alignment (since 2.11.1.3) +

+
- Jalview 2.11.1.3 + Welcome to Jalview Version $$Version-Rel$$ !!
Please take a + look at the release + notes for this build. +
+
+ Jalview 2.11.1.4 +
+
Jalview 2.11.1.4 is the fourth patch release in the 2.11.1 + series. One critical bug was fixed in this release - when Jalview + would occasionally hang when viewing structures in Jmol. This release + also introduces a number of new configuration options for disabling + web service connections used by the Jalview Debian package.
-
Jalview 2.11.1.3 is the third patch release in the 2.11.1 - series. Critical bugs resolved in this release include:
-
-
Find doesn't highlight all motif matches for a sequence.
-
Mouse over highlighting, CDS reconstruction and problems - with virtual feature popups when working with linked CDS/Protein - alignments.
-
Result of aligning protein sequences linked to CDS results - in incorrect CDS alignment.
-
Jalview installer doesn't correctly install Jalview on - paths containing spaces.
-

For the full release notes, see the Jalview 2.11.1.3 + href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4 release notes.

Known Issues
-
-
We've had reports from a small number of windows 10 users - who see a warning dialog pop up when Jalview tries to save a new - version of an existing file. If you are affected by this bug and - this latest version of Jalview doesn't fix it, please let us know!
-
Co-located features exported and re-imported are ordered - differently when shown on alignment and in tooltips. (Also affects - v2.11.1.0)
-
Drag and drop of alignment file onto alignment window when - in a HiDPI scaled mode in Linux only works for the top left - quadrant of the alignment window.
+
New known issues in this release affect recovery of CDS/Protein + relationships from project files, and interactive selection of + protein sequences from a tree built on linked nucleotide sequences. + We will provide patches for these issues as soon as possible.

-- 1.7.10.2