From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 1 Jul 2022 12:44:40 +0000 (+0100)
Subject: JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and... 
X-Git-Tag: Release_2_11_2_6~42^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=00a0552110d2d6a9f4e4da584b28d53fc3bfffd0;ds=sidebyside

JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new
---

diff --git a/help/help/html/features/uniprotsequencefetcher.html b/help/help/html/features/uniprotsequencefetcher.html
index 72e7649..25d1a17 100644
--- a/help/help/html/features/uniprotsequencefetcher.html
+++ b/help/help/html/features/uniprotsequencefetcher.html
@@ -32,6 +32,14 @@
   allows sequences to be located via gene name, keywords, or even
   <em>via</em> manual cross-referencing from UniProt or other
   bioinformatics websites.
+  <br/>
+  <br />
+  <strong>Please Note:</strong>Versions of Jalview older than 2.11.2.3 may need a configuration change
+  in order to access freetext search. Please see this post:
+  <a
+    href="https://discourse.jalview.org/t/uniprot-free-text-search-not-working-in-jalview-2-11-2-2-and-earlier/1825">https://discourse.jalview.org/t/uniprot-free-text-search-not-working-in-jalview-2-11-2-2-and-earlier/1825</a>
+  in Jalview's discussion forum for a workaround.
+  <br />
   <p>
     To open the UniProt Sequence Fetcher, select UniProt as the database
     from any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened
diff --git a/help/markdown/releases/release-2_11_2_3.md b/help/markdown/releases/release-2_11_2_3.md
index 6f4ce26..52c81d2 100644
--- a/help/markdown/releases/release-2_11_2_3.md
+++ b/help/markdown/releases/release-2_11_2_3.md
@@ -12,10 +12,12 @@ channel: "release"
 - <!-- JAL-3989 --> Release process generates Hugo friendly JSON metadata to use when publishing releases on www.jalview.org
 - <!-- JAL-3553 --> New gradle tasks for publishing to the Jalview version archive
 - <!-- JAL-4023 --> Tree branch labels shown using Scientific notation for very small or large lengths
+- <!-- JAL-4036 --> Uniprot Free Text Search redirected to legacy.uniprot.org
 
 
 ## Issues Resolved
 
+- <!-- JAL-4036 --> Uniprot Free Text Search in Jalview 2.11.2.2 and earlier stopped working on 29th June 2022
 - <!-- JAL-4008 --> Validation fails when trying to configure custom JABAWS server
 - <!-- JAL-4020 --> Jalview doesn't call PymolWIN.exe correctly - improved recognition of binaries on Windows
 - <!-- JAL-4024 --> Jumping from left to far right via rapid drag of scroll bar or clicking the overview window can cause Jalview to temporarily hang when working with alignments with more than 10 thousand columns
diff --git a/help/markdown/whatsnew/whatsnew-2_11_2_3.md b/help/markdown/whatsnew/whatsnew-2_11_2_3.md
index cda0ff2..f911062 100644
--- a/help/markdown/whatsnew/whatsnew-2_11_2_3.md
+++ b/help/markdown/whatsnew/whatsnew-2_11_2_3.md
@@ -1 +1 @@
-Jalview 2.11.2.3 is the third patch release in the 2.11.2 series. It addresses a critical bugs affecting users working with very wide alignments and those needing to use alternate JABAWS servers, support for display of very small and large tree lengths with scientific notation, and essential improvements to the build and release notes documentation system.
+Jalview 2.11.2.3 is the third patch release in the 2.11.2 series. It addresses a critical bugs affecting Uniprot free text search, users working with very wide alignments and those needing to use alternate JABAWS servers, support for display of very small and large tree lengths with scientific notation, and essential improvements to the build and release notes documentation system.