- <li>
- <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
- and Viewer state saved in Jalview Project
- </li>
- <li>'Change parameters' option removed from viewer's
- drop-down menus</li>
- <li>
- <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
- incrementally
- </li>
- <li>
- <!-- JAL-2965 -->PCA plot is depth cued
- </li>
- </ul>
- </li>
- <li>
- <!-- JAL-3127 -->New 'Colour by Sequence ID' option
- </li>
- <li><strong>Speed and Efficiency</strong>
- <ul>
- <li>
- <!-- JAL-3198 -->More efficient creation of selections and
- multiple groups when working with large alignments
- </li>
- <li>
- <!-- JAL-3200 -->Speedier import of annotation rows when parsing
- Stockholm files
- </li>
- </ul>
- <li><strong>User Interface</strong>
- <ul>
- <li>
- <!-- JAL-2933 -->Finder panel remembers last position in each
- view
- </li>
- <li>
- <!-- JAL-2527 -->Alignment Overview now WYSIWIS (What you see is
- what is shown)<br />Only visible region of alignment is shown by
- default (can be changed in user preferences)
- </li>
- <li>
- <!-- JAL-3169 -->File Chooser stays open after responding Cancel
- to the Overwrite Dialog
- </li>
- <li>
- <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
- sequences are hidden
- </li>
- <li>
- <!-- JAL-1244 -->Status bar shows bounds when dragging a
- selection region, and gap count when inserting or deleting gaps
- </li>
- <li>
- <!-- JAL-3132 -->Status bar updates over sequence and annotation
- labels
- </li>
- <li>
- <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
- when in wrapped mode
- </li>
- <li>
- <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
- annotation
- </li>
- <li>
- <!-- JAL-2814 -->Help button on Uniprot and PDB search panels
- </li>
- <li>
- <!-- JAL-2621 -->Cursor changes over draggable box in Overview
- panel
- </li>
- <li>
- <!-- JAL-3181 -->Consistent ordering of links in sequence id
- popup menu
- </li>
- <li>
- <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
- <li>
- <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
-
-
- </ul></li>
- <li><strong>Java 11 Support</strong>
- <ul>
- <li>
- <!-- JAL- -->Java 11 Native Desktop installer, standalone JAR
- and getdown release channels
- </li>
- <li>
- <!-- -->OSX GUI integrations for App menu's 'About' entry and
- trapping CMD-Q
- </li>
- </ul></li>
- </ul>
+ <li>
+ <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
+ and Viewer state saved in Jalview Project
+ </li>
+ <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
+ drop-down menus</li>
+ <li>
+ <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
+ incrementally
+ </li>
+ <li>
+ <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
+ </li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3127 -->New 'Colour by Sequence ID' option
+ </li>
+ <li><strong>Speed and Efficiency</strong>
+ <ul>
+ <li>
+ <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
+ multiple groups when working with large alignments
+ </li>
+ <li>
+ <!-- JAL-3200 -->Speedier import of annotation rows when parsing
+ Stockholm files
+ </li>
+ </ul>
+ <li><strong>User Interface</strong>
+ <ul>
+ <li>
+ <!-- JAL-2933 -->Finder panel remembers last position in each
+ view
+ </li>
+ <li>
+ <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
+ what is shown)<br />Only visible regions of alignment are shown by
+ default (can be changed in user preferences)
+ </li>
+ <li>
+ <!-- JAL-3169 -->File Chooser stays open after responding Cancel
+ to the Overwrite Dialog
+ </li>
+ <li>
+ <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
+ sequences are hidden
+ </li>
+ <li>
+ <!-- JAL-1244 -->Status bar shows bounds when dragging a
+ selection region, and gap count when inserting or deleting gaps
+ </li>
+ <li>
+ <!-- JAL-3132 -->Status bar updates over sequence and annotation
+ labels
+ </li>
+ <li>
+ <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
+ when in wrapped mode
+ </li>
+ <li>
+ <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
+ annotation
+ </li>
+ <li>
+ <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
+ </li>
+ <li>
+ <!-- JAL-2621 -->Cursor changes over draggable box in Overview
+ panel
+ </li>
+ <li>
+ <!-- JAL-3181 -->Consistent ordering of links in sequence id
+ popup menu
+ </li>
+ <li>
+ <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
+ <li>
+ <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
+
+
+ </ul></li>
+ <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
+ <li><strong>Java 11 Support (not yet on general release)</strong>
+ <ul>
+ <li>
+ <!-- -->OSX GUI integrations for App menu's 'About' entry and
+ trapping CMD-Q
+ </li>
+ </ul></li>
+ </ul>