<li><!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor issues resolved.</li>
</ul>
</td>
- <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>
+ <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>
+ <!-- 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-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 -->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-2898 -->stop_gained variants not shown correctly on peptide sequence</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>
+ <!-- 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 -->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-2898 -->stop_gained variants not shown correctly on
+ peptide sequence
+ </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>
- </ul><em>New Known Defects</em>
- <ul>
- <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>
+ </ul>
+ <em>New Known Defects</em>
+ <ul>
+ <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
create a Score filter instead.
</li>
</ul>
- </td>
- </tr>
+ </td>
+ </tr>
<tr>
<td width="60" nowrap>
<div align="center">
<!-- JAL-2593 -->Improved performance when rendering lots
of features (particularly when transparency is disabled)
</li>
- <li>
- <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
- exchange of Jalview features and Chimera attributes made
- generally available
- </li>
- </ul>
+ <li>
+ <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
+ exchange of Jalview features and Chimera attributes made
+ generally available
+ </li>
+ </ul>
</div>
</td>
<td><div align="left">
<!-- JAL-2589 -->User defined gap colour not shown in
overview when features overlaid on alignment
</li>
- <li>
- <!-- JAL-2567 -->Feature settings for different views not
- recovered correctly from Jalview project file
- </li>
- <li>
- <!-- JAL-2256 -->Feature colours in overview when first opened
- (automatically via preferences) are different to the main
- alignment panel
- </li>
- </ul>
+ <li>
+ <!-- JAL-2567 -->Feature settings for different views not
+ recovered correctly from Jalview project file
+ </li>
+ <li>
+ <!-- JAL-2256 -->Feature colours in overview when first opened
+ (automatically via preferences) are different to the main
+ alignment panel
+ </li>
+ </ul>
<em>Data import/export</em>
<ul>
<li>
git://source.jalview.org / jalview.git / commitdiff