</p>
<table border="1">
<tr>
- <td width="60" nowrap>
- <div align="center">
- <em><strong>Release</strong></em>
- </div>
- </td>
- <td>
- <div align="center">
- <em><strong>New Features</strong></em>
- </div>
- </td>
- <td>
- <div align="center">
- <em><strong>Issues Resolved</strong></em>
- </div>
- </td>
+ <th nowrap><em>Release</em></th>
+ <th><em>New Features</em></th>
+ <th><em>Issues Resolved</em></th>
</tr>
-
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.11.0">2.11.0</a><br />
- <em>29/01/2019</em></strong>
- </div>
+ <tr>
+ <td width="60" align="center" nowrap>
+ <strong><a name="Jalview.2.11">2.11</a><br />
+ <em>14/05/2019 (final due date !)</em></strong>
</td>
- <td><div align="left">
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
+ <li>
+ <!-- JAL-3141 -->Optional automatic backups when saving
+ Jalview project or alignment files</li>
+ <li>
+ <!-- JAL-1767,JAL-2647 -->Principal Components Analysis and
+ Viewer state is saved in Jalview Project<br />The 'Change
+ parameters' option has also been removed from the PCA viewer</li>
+ <li>
+ <!-- JAL-3127 -->New 'Colour by Sequence ID' (subgroup) option</li>
+ <li>
+ <!-- JAL-2620 -->Alternative genetic code tables supported for
+ 'Translate as cDNA'</li>
+ <li>
+ <!-- JAL-2933 -->Finder panel remembers last position in each view</li>
+ <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>
+ <li>
+ <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
+ <li>
+ <!-- JAL-2808,JAL-2069 -->Sequence features can be filtered and
+ shaded according to any associated attributes (e.g. variant
+ 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>
+ <!-- JAL-2527 -->Alignment Overview now by default shows
+ only visible region of alignment (this can be changed in
+ user preferences)</li>
+ <li>
+ <!-- JAL-3169 -->File Chooser stays open after Cancel overwrite</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 -->Show annotation tooltips and popup menus in wrapped mode</li>
+ <li>
+ <!-- JAL-3073 -->Can select columns by dragging left/right in annotations</li>
+ <li>
+ <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings dialog</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-3203 -->Overview panel default changed to not show hidden regions</li>
+ <li>
+ <!-- JAL-3181 -->Consistent ordering of links in sequence id popup menu</li>
+ <li>
+ <!-- JAL-3021 -->Sequence Details report opens positioned to top of report</li>
+ <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 cueing with graduated colours</li>
+ </ul>
<em>Deprecations</em>
<ul>
<li>
</ul>
<em>Release Processes</em>
<ul>
- <li>Atlassian Bamboo continuous integration server for unattended Test Suite execution</li>
- <li><!-- JAL-2864 -->Memory test suite to detect leaks in common operations</li>
+ <li>
+ Atlassian Bamboo continuous integration server for
+ unattended Test Suite execution</li>
+ <li>
+ <!-- JAL-2864 -->Memory test suite to detect leaks in common
+ operations</li>
+ <li>
+ <!-- JAL-3140 -->IntervalStoreJ (new updatable NCList
+ implementation) used for Sequence Feature collections</li>
+ <li>
+ <!-- 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>
- </div></td>
- <td><div align="left">
- <em></em>
+ </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>
+ <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>
+ 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>
+ and the mouse moved to the left of the first column</li>
<li>
<!-- JAL-2846 -->Error message for trying to load in invalid
- URLs doesn't tell users the invalid URL
- </li>
+ 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-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-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>
+ via 'Edit' sequence</li>
<li>
<!-- JAL-2541 -->Delete/Cut selection doesn't relocate
sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
- </li>
- <li>
- <!-- JAL- -->
- </li>
+ removed (Known defect since 2.10)</li>
</ul>
<em>New Known Defects</em>
<ul>
<li>
- <!-- JAL-3178 -->Nonpositional features lose feature group
- on export as jalview features file
- </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>
</ul>
- </div></td>
+ </td>
</tr>
<tr>
<td width="60" nowrap>