<tr>
<td width="60" align="center" nowrap>
<strong><a name="Jalview.2.11">2.11</a><br />
- <em>tbc/06/2019</em></strong>
+ <em>20/06/2019</em></strong>
</td>
<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
+ <!-- JAL-2620 -->Alternative genetic code tables 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>
+ <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
+ <ul>
+ <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 window to show full report for 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-3049,JAL-3054 -->Improved tooltips in Feature Settings
+ dialog
+ </li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3141 -->Backup files created when saving Jalview project
+ or alignment files
+ </li>
+ <li><strong>Principal Components Analysis Viewer</strong>
+ <ul>
+ <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>
<em>Deprecations</em>
<ul>
<li>
<!-- JAL-3035 -->DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
</li>
- </ul>
- <em>Release Processes</em>
- <ul>
<li>
- Atlassian Bamboo continuous integration server for
+ <!-- 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>
+ <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
+ <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
+ </ul> <em>Documentation</em>
+ <ul>
+ <li>
+ <!-- JAL-3003 -->Added remarks about transparent rendering effects
+ not supported in EPS figure export
+ </li>
+ </ul> <em>Development and Release Processes</em>
+ <ul>
+ <li>
+ <!-- JAL-3196,JAL-3007 -->Jalview Native Application and
+ Installers built with Install4j (licensed to the Jalview open
+ source project) rather than InstallAnywhere
+ </li>
+ <li>
+ <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
+ settings, receive over the air updates and launch specific
+ versions via (<a href="https://github.com/threerings/getdown">Three
+ Rings' GetDown</a>)
+ </li>
+ <li>
+ <!-- JAL-3196,JAL-3179 -->Build system migrated from Ant to Gradle
+ </li>
+ <li>
+ <!-- JAL-3225 -->Eclipse project configuration managed with
+ gradle-eclipse
+ </li>
+ <li>
+ Atlassian Bamboo continuous integration 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>
+ <!-- JAL-3140 -->IntervalStoreJ (NCList
+ implementation that alows updates) used for Sequence Feature collections</li>
</ul>
</td>
<td align="left" valign="top">
<!-- 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>
+ <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>
<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>
<!-- JAL-2541 -->Delete/Cut selection doesn't relocate
sequence features correctly when start of sequence is
removed (Known defect since 2.10)</li>
- </ul>
- <em>New Known Defects</em>
+ </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</li>
- </ul>
+ <!-- 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>
+ </ul>
</td>
</tr>
<tr>
<!-- JAL-2593 -->Improved performance when rendering lots
of features (particularly when transparency is disabled)
</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">
git://source.jalview.org / jalview.git / blobdiff