- <li>
- <!-- JAL-2060 -->'Graduated colour' option not offered for
- manually created features (where if feature score is Float.NaN)
- </li>
- <li>
- <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
- when columns are hidden
- </li>
- <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-3075 -->Column selection incorrect after scrolling out of
- scale panel
- </li>
- <li>
- <!-- JAL-3074 -->Left/right drag in annotation can scroll
- alignment down
- </li>
- <li>
- <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
- scale panel
- </li>
- <li>
- <!-- JAL-3002 -->Column display is out by one after Page Down,
- Page Up in wrapped mode
- </li>
- <li>
- <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
- </li>
- <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>
- <li>
- <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
- Colour menu
- </li>
- <li>
- <!-- 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-3313 -->Codon consensus incorrectly scaled when shown
- without normalisation
- </li>
- <li>
- <!-- JAL-3021 -->Sequence Details report should open positioned at top
- of report
- </li>
- <li>
- <!-- JAL-914 -->Help page can be opened twice
- </li>
- <li>
- <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
- </li>
- </ul> <em>Editing</em>
- <ul>
- <li>
- <!-- JAL-2822 -->Start and End should be updated when sequence
- data at beginning or end of alignment added/removed via 'Edit'
- sequence
- </li>
- <li>
- <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
- relocate sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
- </li>
- <li>
- <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
- dialog corrupts dataset sequence
- </li>
- <li>
- <!-- JAL-868 -->Structure colours not updated when associated tree
- repartitions the alignment view (Regression in 2.10.5)
- </li>
- </ul>
- <em>Datamodel</em>
- <ul>
- <li>
- <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
- sequence's End is greater than its length
- </li>
- <li><strong>Bugs fixed for Java 11 Support (not
- yet on general release)</strong>
- <ul>
- <li>
- <!-- JAL-3288 -->Menus work properly in split-screen
- </li>
- </ul></li>
- </ul> <em>New Known Defects</em>
- <ul>
- <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
- </li>
- <li>
- <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
- regions of protein alignment.
- </li>
- <li>
- <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
- is restored from a Jalview 2.11 project
- </li>
- <li>
- <!-- JAL-3213 -->Alignment panel height can be too small after
- 'New View'
- </li>
- <li>
- <!-- JAL-3240 -->Display is incorrect after removing gapped
- columns within hidden columns
- </li>
- <li>
- <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
- window after dragging left to select columns to left of visible
- region
- </li>
- <li>
- <!-- JAL-2876 -->Features coloured according to their description
- string and thresholded by score in earlier versions of Jalview are
- not shown as thresholded features in 2.11. To workaround please
- create a Score filter instead.
- </li>
- <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
- <li>
- <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
- </li>
- <li>
- <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
- alignments with multiple views can close views unexpectedly
- </li>
- <li><strong>Java 11 Specific defects</strong>
- <ul>
- <li>
- <!-- JAL-3235 -->Jalview Properties file is not sorted
- alphabetically when saved
- </li>
- </ul>