From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 18 Apr 2019 14:17:45 +0000 (+0100)
Subject: JAL-3111 additional release notes
X-Git-Tag: Release_2_11_0~17^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4992ecae64d0c987c217e8c584161706188f9d52;p=jalview.git

JAL-3111 additional release notes
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 067363a..b58cb31 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -90,6 +90,10 @@ li:before {
             attributes from VCF file, or key-value pairs imported from
             column 9 of GFF file)</li>
           <li>
+            <!-- JAL-2897 -->Show synonymous codon variants on peptide sequences</li>
+          <li>
+            <!-- JAL-2792 -->Popup report of a selected sequence feature's details</li>
+          <li>
             <!-- JAL-3139,JAL-2816 -->More efficient sequence feature render
             algorithm (Z-sort/transparency and filter aware)</li>
           <li>
@@ -125,6 +129,10 @@ li:before {
           <li>
             <!-- JAL-3218 -->Scale panel popup menu allows Hide selected columns adjacent 
             to a hidden column marker</li>
+          <li>
+            <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image incrementally</li>
+          <li>
+            <!-- JAL-2965 -->PCA depth queuing with graduated colours</li>
         </ul>
         <em>Deprecations</em>
         <ul>
@@ -145,7 +153,7 @@ li:before {
             <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
             implementation) used for Sequence Feature collections</li>
           <li>
-            <!-- JAL-3063 -->Castor library for XML marshalling and
+            <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
             unmarshalling has been replaced by JAXB for Jalview projects
             and XML based data retrieval clients</li>
         </ul>
@@ -175,7 +183,7 @@ li:before {
             <!-- JAL-2865 -->Jalview hangs when closing windows
             or the overview updates with large alignments</li>
           <li>
-            <!-- JAL-2865 -->Tree and PCA calculation fails for selected
+            <!-- JAL-2750 -->Tree and PCA calculation fails for selected
             region if columns were selected by dragging right-to-left
             and the mouse moved to the left of the first column</li>
           <li>
@@ -185,25 +193,25 @@ li:before {
             <!-- JAL-3178 -->Nonpositional features lose feature group
             on export as Jalview features file</li>
           <li>
-            <!-- JAL-3161 -->Status bar updates beyond visible columns</li>
-          <li>
             <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or 
             printed when columns are hidden</li>
           <li>
-            <!-- JAL-3082 -->Regular expression error in Select Columns by Annotation description</li>
+            <!-- JAL-3082 -->Regular expression error for '(' in Select Columns by Annotation description</li>
           <li>
             <!-- JAL-3072 -->Scroll doesn't stop on mouse up after 
             dragging out of Scale or Annotation Panel</li>
           <li>
-            <!-- JAL-3002 -->Display is incorrect after Page Down and Up in wrapped mode</li>
+            <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
           <li>
-            <!-- JAL-914 -->Help page can be opened twice</li>
+            <!-- JAL-3074 -->Left/right drag in annotation can scroll alignment down</li>
           <li>
-            <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
+            <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in scale panel</li>
           <li>
-            <!-- JAL-3075 -->Column selection incorrect after scrolling out of scale panel</li>
+            <!-- JAL-3002 -->Column display is out by one after Page Down, Page Up in wrapped mode</li>
+          <li>
+            <!-- JAL-2839 -->Finder doesn't skip hidden regions</li>
           <li>
-            <!-- JAL-2750 -->Tree calculation fails on a selection dragged to left of alignment</li>
+            <!-- JAL-2932 -->Finder searches in minimised alignments</li>
           <li>
             <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected on
             opening an alignment</li>
@@ -213,7 +221,27 @@ li:before {
             <!-- JAL-3201 -->Per-group Clustal colour scheme changes when 
             different groups in the alignment are selected</li>
           <li>
+            <!-- JAL-2717 -->Internationalised colour scheme names not shown correctly in menu</li>
+          <li>
+            <!-- JAL-3206 -->Colour by Annotation can go black at min/max threshold limit</li>
+          <li>
             <!-- JAL-3125 -->Value input for graduated feature colour threshold gets 'unrounded'</li>
+          <li>
+            <!-- JAL-2982 -->PCA image export doesn't respect background colour</li>
+          <li>
+            <!-- JAL-2963 -->PCA points don't dim when rotated about y axis</li>
+          <li>
+            <!-- JAL-2959 -->PCA Print dialog continues after Cancel</li>
+          <li>
+            <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not Tree font</li>
+          <li>
+            <!-- JAL-2964 -->Associate Tree with All Views not restored from project file</li>
+          <li>
+            <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview shown in complementary view</li>
+          <li>
+            <!-- JAL-2898 -->stop_gained variants not shown correctly on peptide sequence</li>
+          <li>
+            <!-- JAL-914 -->Help page can be opened twice</li>
         </ul>
         <em>Editing</em>
         <ul>