- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
- </li>
- <li>
- <!-- JAL-3244 -->'View [Structure] Mappings' and structure
- superposition in Jmol fail on Windows
- </li>
- <li>
- <!-- JAL-3286 -->Blank error dialog is displayed when discovering
- structures for sequences with lots of PDB structures
- </li>
- <li>
- <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
- monospaced font
- </li>
- <li>
- <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
- project involving multiple views
- </li>
- <li>
- <!-- JAL-3164 -->Overview for complementary view in a linked
- CDS/Protein alignment is not updated when Hide Columns by
- Annotation dialog hides columns
- </li>
- <li>
- <!-- JAL-3158 -->Selection highlighting in the complement of a
- CDS/Protein alignment stops working after making a selection in
- one view, then making another selection in the other view
- </li>
- <li>
- <!-- JAL-3161 -->Annotations tooltip changes beyond visible
- columns
- </li>
- <li>
- <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
- Settings and Jalview Preferences panels
- </li>
- <li>
- <!-- JAL-2865 -->Jalview hangs when closing windows or the
- overview updates with large alignments
- </li>
- <li>
- <!-- 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>
- <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
- hidden column marker via scale popup menu
- </li>
- <li>
- <!-- JAL-2846 -->Error message for trying to load in invalid URLs
- doesn't tell users the invalid URL
- </li>
- <li>
- <!-- JAL-3178 -->Nonpositional features lose feature group on
- export as Jalview features file
- </li>
- <li>
- <!-- JAL-2816 -->Tooltips displayed for features filtered by
- score from view
- </li>
- <li>
- <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
- show cross references or Fetch Database References are shown in
- red in original view
- </li>
- <li>
- <!-- JAL-2898 -->stop_gained variants not shown correctly on
- peptide sequence
- </li>
- <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 opens positioned to top
- of report
- </li>
- <li>
- <!-- JAL-914 -->Help page can be opened twice
- </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>
- </ul> <em>New Known Defects</em>
- <ul>
- <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><strong>Java 11 Specific defects</strong>
- <ul>
- <li>
- <!-- JAL-3235 -->Jalview Properties file is not sorted alphabetically when saved</li>
-
- </ul></li>
-
- </ul>
- </td>
- </tr>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
+ </li>
+ <li>
+ <!-- JAL-3244 -->'View [Structure] Mappings' and structure
+ superposition in Jmol fail on Windows
+ </li>
+ <li>
+ <!-- JAL-3286 -->Blank error dialog is displayed when discovering
+ structures for sequences with lots of PDB structures
+ </li>
+ <li>
+ <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
+ monospaced font
+ </li>
+ <li>
+ <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
+ project involving multiple views
+ </li>
+ <li>
+ <!-- JAL-3164 -->Overview for complementary view in a linked
+ CDS/Protein alignment is not updated when Hide Columns by
+ Annotation dialog hides columns
+ </li>
+ <li>
+ <!-- JAL-3158 -->Selection highlighting in the complement of a
+ CDS/Protein alignment stops working after making a selection in
+ one view, then making another selection in the other view
+ </li>
+ <li>
+ <!-- JAL-3161 -->Annotations tooltip changes beyond visible
+ columns
+ </li>
+ <li>
+ <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
+ Settings and Jalview Preferences panels
+ </li>
+ <li>
+ <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
+ overview with large alignments
+ </li>
+ <li>
+ <!-- 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>
+ <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
+ hidden column marker via scale popup menu
+ </li>
+ <li>
+ <!-- JAL-2846 -->Error message for trying to load in invalid URLs
+ doesn't tell users the invalid URL
+ </li>
+ <li>
+ <!-- JAL-2816 -->Tooltips displayed for features filtered by
+ score from view
+ </li>
+ <li>
+ <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
+ show cross references or Fetch Database References are shown in
+ red in original view
+ </li>
+ <li>
+ <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
+ peptide sequence (computed variant shown as p.Res.null)
+ </li>
+ <li>
+ <!-- JAL-2060 -->'Graduated colour' option not offered for
+ manually created features (where 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>
+ </ul> <em>Bugs fixed for Java 11 Support (not yet on
+ general release)</em>
+ <ul>
+ <li>
+ <!-- JAL-3288 -->Menus work properly in split-screen
+ </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>
+ </ul>
+ <em>Java 11 Specific defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3235 -->Jalview Properties file is not sorted
+ alphabetically when saved
+ </li>
+ </ul>
+ </td>
+ </tr>