+ <!-- JAL-3468 -->Very long feature descriptions truncated in
+ tooltips and menus
+ </li>
+ <li>
+ <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
+ with no feature types visible
+ </li>
+ <li>
+ <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
+ </li>
+ </ul><em>Jalview Installer</em>
+ <ul>
+ <li>
+ <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
+ in console (may be null when Jalview launched as executable jar or via conda)
+ </li>
+ <li>
+ <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
+ </li>
+ <li>
+ <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
+ </li>
+ <li>
+ <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
+ <li>
+ <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
+ </ul> <em>Release processes</em>
+ <ul>
+ <li>
+ <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
+ </li>
+ <li>
+ <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
+ </li>
+ </ul> <em>Build System</em>
+ <ul>
+ <li>
+ <!-- JAL-3510 -->Clover updated to 4.4.1
+ </li>
+ <li>
+ <!-- JAL-3513 -->Test code included in Clover coverage
+ report
+ </li>
+ </ul>
+ <em>Groovy Scripts</em>
+ <ul>
+ <li>
+ <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
+ to stdout containing the consensus sequence for each
+ alignment in a Jalview session
+ </li>
+ <li>
+ <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
+ genomic sequence_variant annotation from CDS as
+ missense_variant or synonymous_variant on protein products.
+ </li>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3581 -->Hidden sequence markers still visible when
+ 'Show hidden markers' option is not ticked
+ </li>
+ <li>
+ <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
+ PNG output when 'Automatically set ID width' is set in
+ jalview preferences or properties file
+ </li>
+ <li>
+ <!-- JAL-3571 -->Feature Editor dialog can be opened when
+ 'Show Sequence Features' option is not ticked
+ </li>
+ <li>
+ <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
+ buttons in Feature Settings dialog are clicked when no
+ features are visible
+ </li>
+ <li>
+ <!-- JAL-3412 -->ID margins for CDS and Protein views not
+ equal when split frame is first opened
+ </li>
+ <li>
+ <!-- JAL-3296 -->Sequence position numbers in status bar not
+ correct after editing a sequence's start position
+ </li>
+ <li>
+ <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
+ with annotation and exceptions thrown when only a few
+ columns shown in wrapped mode
+ </li>
+ <li>
+ <!-- JAL-3386 -->Sequence IDs missing in headless export of
+ wrapped alignment figure with annotations
+ </li>
+ <li>
+ <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
+ ID fails with ClassCastException
+ </li>
+ <li>
+ <!-- JAL-3389 -->Chimera session not restored from Jalview
+ Project
+ </li>
+ <li>
+ <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
+ feature settings dialog also selects columns
+ </li>
+ <li>
+ <!-- JAL-3473 -->SpinnerNumberModel causes
+ IllegalArgumentException in some circumstances
+ </li>
+ <li>
+ <!-- JAL-3534 -->Multiple feature settings dialogs can be
+ opened for a view
+ </li>
+ <li>
+ <!-- JAL-2764 -->Feature Settings dialog is orphaned if
+ alignment window is closed
+ </li>
+ <li>
+ <!-- JAL-3406 -->Credits missing some authors in Jalview
+ help documentation for 2.11.0 release
+ </li>
+ <li>
+ <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
+ includes Pfam ID as sequence's accession rather than its
+ Uniprot Accession
+ </li>
+ </ul> <em>Java 11 Compatibility issues</em>
+ <ul>
+ <li>
+ <!-- JAL-2987 -->OSX - Can't view some search results in
+ PDB/Uniprot search panel
+ </li>
+ </ul> <em>Installer</em>
+ <ul>
+ <li>
+ <!-- JAL-3447 -->Jalview should not create file associations
+ for 3D structure files (.pdb, .mmcif. .cif)
+ </li>
+ </ul> <em>Repository and Source Release</em>
+ <ul>
+ <li>
+ <!-- JAL-3474 -->removed obsolete .cvsignore files from
+ repository
+ </li>
+ <li>
+ <!-- JAL-3541 -->Clover report generation running out of
+ memory
+ </li>
+ </ul> <em>New Known Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-3523 -->OSX - Current working directory not
+ preserved when Jalview.app launched with parameters from
+ command line
+ </li>
+ <li>
+ <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
+ clipped in headless figure export when Right Align option
+ enabled
+ </li>
+ <li>
+ <!-- JAL-3542 -->Jalview Installation type always reports
+ 'Source' in console output
+ </li>
+ <li>
+ <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
+ bamboo server but run fine locally.
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap>
+ <strong><a name="Jalview.2.11.0">2.11.0</a><br />
+ <em>04/07/2019</em></strong>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
+ Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (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-1839,JAL-3254,JAL-3260 -->File type associations for
+ formats supported by Jalview (including .jvp project files)
+ </li>
+ <li>
+ <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
+ arguments and switch between different getdown channels
+ </li>
+ <li>
+ <!-- JAL-3141 -->Backup files created when saving Jalview project
+ or alignment files
+ </li>
+
+ <li>
+ <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
+ <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
+ <li>
+ <!-- JAL-2620 -->Alternative genetic code tables for
+ 'Translate as cDNA'</li>
+ <li>
+ <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
+ <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
+ <ul>
+ <li>
+ <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
+ implementation that allows updates) used for Sequence Feature collections</li>
+ <li>
+ <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->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-2879 -->Feature Attributes and shading schemes
+ stored and restored from Jalview Projects
+ </li>
+ <li>
+ <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
+ recognise variant features
+ </li>
+ <li>
+ <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
+ sequences (also coloured red by default)
+ </li>
+ <li>
+ <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
+ details
+ </li>
+ <li>
+ <!-- JAL-3139,JAL-2816,JAL-1117 -->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-3205 -->Symmetric score matrices for faster
+ tree and PCA calculations
+ </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><!-- JAL-2962 -->'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, JAL-1285 -->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-2185,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 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
+ what is shown)<br />Only visible regions of alignment are 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,JAL-437 -->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><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
+ <li><strong>Java 11 Support (not yet on general release)</strong>
+ <ul>
+ <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>
+ <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and