+
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* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
<title>Release History</title>
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+<body>
+ <p>
+ <strong>Release History</strong>
+ </p>
+ <table border="1">
+ <tr>
+ <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
+ <th><em>New Features</em></th>
+ <th><em>Issues Resolved</em></th>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
+ <em>10/03/2022</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3616 JAL-3551 JAL-2322 -->Support for viewing 3D
+ structures with ChimeraX and Pymol in addition to Jmol and
+ Chimera.
+ </li>
+ <li>
+ <!-- JAL-3829 -->Discover 3D structure data for sequences
+ with Uniprot references via 3D-Beacons
+ </li>
+ <li>
+ <!-- JAL-3391 -->Rank and select available structures for
+ Uniprot sequences according to number of residues in
+ structure mapped to positions involved in the alignment
+ </li>
+ <li>
+ <!-- JAL-2226 -->Structure annotation rows for all mapped
+ chains in 3D structures are included in the 'Reference
+ Annotation' for a sequence
+ </li>
+ <li>
+ <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
+ </li>
+ <li>
+ <!-- JAL-3821 -->ENA record's mol_type honoured so RNA
+ molecules imported from ENA records are shown as RNA
+ <li>
+ <!-- JAL-3863 -->Support for Canonical Uniprot IDs
+ </li>
+ <li>
+ <!-- JAL-3503 -->New Preferences tab for adjusting Jalview's
+ memory settings at launch
+ </li>
+ <li>
+ <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
+ non-alphanumerics when discovering database references with
+ 'Fetch DB Refs'
+ </li>
+ <li>
+ <!-- JAL-3884 -->Suppressed harmless exceptions output to
+ Console whilst discovering database references for a
+ sequence
+ </li>
+ <li>
+ <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
+ schema
+ </li>
+ <li>
+ <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
+ disabled by default
+ </li>
+ <li>
+ <!-- JAL-3144 -->Reverted to Jalview 'classic' drop-down
+ menu for selecting which database to fetch from in sequence
+ fetcher dialog.
+ </li>
+ <li>
+ <!-- JAL-3018 -->Updated Ensembl REST Client compatibility
+ to 15.2 and revised model organism names (rat, xenopus,
+ dmelanogaster now rattus_norvegicus, xenopus_tropicalis,
+ drosophila_melanogaster)
+ </li>
+ <li>
+ <!-- JAL-3530 -->-nowebservicediscovery command line
+ argument to prevent automatic discovery of analysis
+ webservices on launch
+ </li>
+ <li>
+ <!-- JAL-3618 -->Allow 'App' directories to be opened when
+ locating Chimera, ChimeraX or Pymol binaries via filechooser
+ opened by double clicking the Structure Preferences' path
+ textbox
+ </li>
+ <li>
+ <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
+ proxies that require authentication
+ </li>
+ <li>
+ <!-- JAL-3103 -->New mechanism for opening URLs with system
+ default browser (works on OSX and Linux as well as Windows)
+ </li>
+ <li>
+ <!-- JAL-3871 JAL-3874 -->Upgraded bundled version of Jmol
+ to 14.31.53
+ </li>
+ <li>
+ <!-- JAL-3837 -->GPL license info on splash screen and About
+ text
+ </li>
+ </ul> <em>Jalview Native App</em>
+ <ul>
+ <li>
+ <!-- JAL-3830 -->New command line launcher scripts (.sh,
+ .ps1, .bat) usable on macOS, Linux/Unix, Windows and
+ documentation in Help. Installer wizard has option to add
+ this to PATH, or link to it in your PATH.<br /> <em>This
+ is the recommended workaround for known issue about
+ working directory preservation when running native
+ application from command line. <!-- JAL-3523 -->
+ </em>
+ </li>
+ <li>Notarized MacOS installer for compliance with
+ latest OSX releases (Monterey)</li>
+ <li>
+ <!-- JAL-3805 -->Uninstaller application for old
+ (InstallAnywhere based) Jalview installations removed from
+ the OSX disk image
+ </li>
+ <li>
+ <!-- JAL-3608 -->Options to allow user to choose the (Swing)
+ Look and Feel (LaF) used by Jalview
+ </li>
+ <li>
+ <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved
+ operation on Linux Ubuntu with HiDPI display in Java 11
+ (still known issues with HiDPI screens in java 8 and 11. see
+ <a href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
+ </li>
+ <li>
+ <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
+ configuration from jalview_properties
+ </li>
+ <li>
+ <!-- JAL- -->New Jalview Develop app - making it even easier
+ to get at Jalview's development builds
+ </li>
+ <li>
+ <!-- JAL-3594 -->New splashscreens for Jalview, Jalview Test
+ and Jalview Develop applications.
+ </li>
+ <li>
+ <!-- JAL-3728 -->Jalview logos shown for Jalview Java
+ Console and other window widgets in taskbar and dock rather
+ than anonymous 'Java' icons
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul>
+ <li>
+ <!-- JAL-3624 -->PDB structures mapped to Uniprot Sequences
+ with SIFTS
+ </li>
+ <li>
+ <!-- JAL-3208 -->setprop commandline argument reinstated for
+ JalviewJS only
+ </li>
+ <li>
+ <!-- JAL-3163 -->Missing message bundle keys are only
+ reported once per key (avoids excessive log output in js
+ console)
+ </li>
+ <li>
+ <!-- JAL-3168 -->Feature type is included in the title of
+ the Feature Settings' Colour Chooser dialog
+ </li>
+ <li>
+ <!-- JAL-3279 -->Build details reported in About window
+ </li>
+ <li>
+ <!-- JAL-3038 JAL-3071 JAL-3263 JAL-3084 -->Numerous minor
+ GUI additions and improvements in sync with Java
+ application.
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>
+ <!-- -->First integrated JalviewJS and Jalview release
+ </li>
+ <li><!-- JAL-3841,JAL-3248 -->Updated README and doc/building.md</li>
+ <li>
+ <!-- JAL-3789, JAL-3679 -->Improved JalviewJS/Jalview build
+ process, added support for system package provided eclipse
+ installs on linux
+ </li>
+ <li>Install4j 9.0.x used for installer packaging</li>
+ <li>
+ <!-- JAL-3930 -->Improved use of installers for unattended
+ installation with a customizedId of "JALVIEW" in install4j's
+ Jalview Launcher
+ </li>
+ <li>
+ <!-- JAL-3907 -->Improved compatibility of Jalview build
+ with Java 17 (next LTS target)
+ </li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>
+ <!-- JAL-3674 -->Slow structure commands can block Jalview
+ execution
+ </li>
+ <li>
+ <!-- JAL-3904 -->Structure window's viewer-specific menu
+ disappears when only one structure is shown (and many
+ sequences:one chain mappings are present)
+ </li>
+ <li>
+ <!-- JAL-3779 -->Annotation file: PROPERTIES apply only to
+ the first SEQUENCE_GROUP defined
+ </li>
+
+ <li>
+ <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not
+ propagated between Linked CDS - Protein alignments and their
+ trees (known defect from 2.11.1.3)
+ </li>
+ <li>
+ <!-- JAL-3761 -->Not all codon positions highlighted for
+ overlapping exon splice sites (e.g due to RNA slippage)
+ </li>
+ <li>
+ <!-- JAL-3794 -->X was not being recognised as the unknown
+ base in DNA sequences
+ </li>
+ <li>
+ <!-- JAL-3915 -->Removed RNAview checkbox and logic from
+ Structure Preferences
+ </li>
+ <li>
+ <!-- JAL-3583 -->Tooltip behaviour improved (slightly)
+ </li>
+ <li>
+ <!-- JAL-3162 -->Can edit a feature so that start > end
+ </li>
+ <li>
+ <!-- JAL-2848 -->Cancel from Amend Features doesn't reset a
+ modified graduated colour
+ </li>
+ <li>
+ <!-- JAL-3788 -->New View with automatic 'Show Overview'
+ preference enabled results in Null Pointer Exceptions when
+ clustal colouring is enabled
+ </li>
+ <li>
+ <!-- JAL-3275 -->Can open multiple Preferences panels
+ </li>
+ <li>
+ <!-- JAL-3633 -->Properly configure HTTPS proxy settings
+ from Preferences
+ </li>
+ <li>
+ <!-- JAL-3949 -->Standard out logging broken: messages only
+ routing to stderr and appear as a raw template
+ </li>
+ <li>
+ <!-- JAL-3739 -->Entering web service parameter values in
+ numerical field doesn't update the value of the parameter
+ until return is pressed.
+ </li>
+ <li>
+ <!-- JAL-3749 -->Resolved known issue (from 2.11.1.1)
+ concerning duplicate CDS sequences generated when protein
+ products for certain ENA records are repeatedly shown via
+ Calculate->Show Cross Refs
+ </li>
+ </ul> <em>JalviewJS</em>
+ <ul>
+ <li>
+ <!-- JAL-3202 -->Consensus profile may include zero (rounded
+ down) percentage values causing a divide by zero
+ </li>
+ <li>
+ <!-- JAL-3762 -->JalviewJS doesn't honour arguments passed
+ via Info.args when there are arguments on the URL
+ </li>
+ <li>
+ <!-- JAL-3602 -->gradle closure-compiler not using UTF-8
+ </li>
+ <li>
+ <!-- JAL-3603 -->Annotation file fails to load from URL in
+ JalviewJS
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Gradle
+ <ul>
+ <li>Fixed non-fatal gradle errors during build</li>
+ <li>
+ <!-- JAL-3745 -->Updated build.gradle for use with
+ Gradle v.6.6+
+ </li>
+ </ul>
+ </li>
+
+ </ul> <em>Known Issues</em>
+ <ul>
+ <li>
+ <!-- JAL-3764 -->Display of RESNUM sequence features are not
+ suppressed when structures associated with a sequence are
+ viewed with an external viewer (Regression from 2.11.1
+ series)
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
+ <em>18/01/2022</em></strong></td>
+ <td></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
+ updated by Jalview or other applications (Windows, other non
+ Unix/BSD OSs)
+ </li>
+ </ul> <em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
+ certificates.
+ </li>
+ </ul>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
+ <em>6/01/2022</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3934 -->Version bump library dependency: Log4j
+ 2.16.0 to 2.17.0.
+ </li>
+ </ul></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
+ <em>20/12/2021</em></strong></td>
+
+ <td align="left" valign="top"><em>Security</em>
+ <ul>
+ <li>
+ <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
+ (was log4j 1.2.x).
+ </ul> <em>Development</em>
+ <ul>
+ <li>Updated building instructions</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>
+ <!-- JAL-3840 -->Occupancy calculation is incorrect for
+ alignment columns with over -1+2^32 gaps (breaking filtering
+ and display)
+ </li>
+ <li>
+ <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
+ scale factors being set with buggy window-managers (linux
+ only)
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>Fixed non-fatal gradle errors during build</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
+ <em>09/03/2021</em></strong></td>
+ <td align="left" valign="top"><em>Improved control of
+ Jalview's use of network services via jalview_properties</em>
+ <ul>
+ <li>
+ <!-- JAL-3814 -->New .jalview_properties token controlling
+ launch of the news browser (like -nonews argument)
+ </li>
+ <li>
+ <!-- JAL-3813 -->New .jalview_properties token controlling
+ download of linkout URLs from
+ www.jalview.org/services/identifiers
+ </li>
+ <li>
+ <!-- JAL-3812 -->New .jalview_properties token controlling
+ download of BIOJSHTML templates
+ </li>
+ <li>
+ <!-- JAL-3811 -->New 'Discover Web Services' option to
+ trigger a one off JABAWS discovery if autodiscovery was
+ disabled
+ </li>
+ </ul></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3818 -->Intermittent deadlock opening structure in
+ Jmol
+ </li>
+ </ul> <em>New Known defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
+ always restored from project (since 2.10.3)
+ </li>
+ <li>
+ <!-- JAL-3806 -->Selections from tree built from CDS aren't
+ propagated to Protein alignment (since 2.11.1.3)
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
+ <em>29/10/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3765 -->Find doesn't always highlight all matching
+ positions in a sequence (bug introduced in 2.11.1.2)
+ </li>
+ <li>
+ <!-- JAL-3760 -->Alignments containing one or more protein
+ sequences can be classed as nucleotide
+ </li>
+ <li>
+ <!-- JAL-3748 -->CDS alignment doesn't match original CDS
+ sequences after alignment of protein products (known defect
+ first reported for 2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3725 -->No tooltip or popup menu for genomic
+ features outwith CDS shown overlaid on protein
+ </li>
+ <li>
+ <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
+ correctly mapped by Jalview (e.g. affects viral CDS with
+ ribosomal slippage, since 2.9.0)
+ </li>
+ <li>
+ <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
+ CDS features
+ </li>
+ <li>
+ <!-- JAL-3700 -->Selections in CDS sequence panel don't
+ always select corresponding protein sequences
+ </li>
+ <li>
+ <!-- JAL-3759 --> <em>Make groups from selection</em> for a
+ column selection doesn't always ignore hidden columns
+ </li>
+ </ul> <em>Installer</em>
+ <ul>
+ <li>
+ <!-- JAL-3611 -->Space character in Jalview install path on
+ Windows prevents install4j launching getdown
+ </li>
+ </ul> <em>Development</em>
+ <ul>
+ <li>
+ <!-- JAL-3248 -->Fixed typos and specified compatible gradle
+ version numbers in doc/building.md
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
+ <em>25/09/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
+ "Encountered problems opening
+ https://www.jalview.org/examples/exampleFile_2_7.jvp"
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
+ <em>17/09/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
+ residue in cursor mode
+ </li>
+ <li>
+ <!-- JAL-3695 -->Support import of VCF 4.3 by updating
+ HTSJDK from 2.12 to 2.23
+ </li>
+ <li>
+ <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
+ optimisations and improvements suggested by Bob Hanson and
+ improved compatibility with JalviewJS
+ </li>
+ <li>
+ <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
+ alignments from Pfam and Rfam
+ </li>
+ <li>
+ <!-- JAL-2656 -->Recognise GZipped content for URLs and File
+ import (no longer based on .gz extension)
+ </li>
+ <li>
+ <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
+ </li>
+ <li>
+ <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
+ ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
+ EMBL flat file
+ </li>
+ <li>
+ <!-- JAL-3667 -->Improved warning messages, debug logging
+ and fixed Retry action when Jalview encounters errors when
+ saving or making backup files.
+ </li>
+ <li>
+ <!-- JAL-3676 -->Enhanced Jalview Java Console:
+ <ul>
+ <li>Jalview's logging level can be configured</li>
+ <li>Copy to Clipboard Buttion</li>
+ </ul>
+ </li>
+ <li>
+ <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
+ when running on Linux (Requires Java 11+)
+ </li>
+ <li>
+ <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
+ green ones) are not automatically displayed when associated
+ structures are displayed or for sequences retrieved from the
+ PDB.
+ </li>
+ </ul> <em>Launching Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
+ through a system property
+ </li>
+ <li>
+ <!-- JAL-3477 -->Improved built-in documentation and command
+ line help for configuring Jalview's memory
+ </li>
+ </ul>
+ </td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3691 -->Conservation and Quality tracks are shown
+ but not calculated and no protein or DNA score models are
+ available for tree/PCA calculation when launched with
+ Turkish language locale
+ </li>
+ <li>
+ <!-- JAL-3493 -->Escape does not clear highlights on the
+ alignment (Since Jalview 2.10.3)
+ </li>
+ <li>
+ <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
+ doesn't slide selected sequences, just sequence under cursor
+ </li>
+ <li>
+ <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
+ sequence under the cursor
+ </li>
+ <li>
+ <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
+ multiple EMBL gene products shown for a single contig
+ </li>
+ <li>
+ <!-- JAL-3696 -->Errors encountered when processing variants
+ from VCF files yield "Error processing VCF: Format specifier
+ '%s'" on the console
+ </li>
+ <li>
+ <!-- JAL-3697 -->Count of features not shown can be wrong
+ when there are both local and complementary features mapped
+ to the position under the cursor
+ </li>
+ <li>
+ <!-- JAL-3673 -->Sequence ID for reference sequence is
+ clipped when Right align Sequence IDs enabled
+ </li>
+ <li>
+ <!-- JAL-2983 -->Slider with negative range values not
+ rendered correctly in VAqua4 (Since 2.10.4)
+ </li>
+ <li>
+ <!-- JAL-3685 -->Single quotes not displayed correctly in
+ internationalised text for some messages and log output
+ </li>
+ <li>
+ <!-- JAL-3490 -->Find doesn't report matches that span
+ hidden gapped columns
+ </li>
+ <li>
+ <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
+ panels, Alignment viewport and annotation renderer.
+ </li>
+ <li>
+ <!-- JAL-3561 -->Jalview ignores file format parameter
+ specifying output format when exporting an alignment via the
+ command line
+ </li>
+ <li>
+ <!-- JAL-3667 -->Windows 10: For a minority of users, if
+ backups are not enabled, Jalview sometimes fails to
+ overwrite an existing file and raises a warning dialog. (in
+ 2.11.0, and 2.11.1.0, the workaround is to try to save the
+ file again, and if that fails, delete the original file and
+ save in place.)
+ </li>
+ <li>
+ <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
+ sequence features displayed causes displayed features to be
+ hidden.
+ </li>
+ <li>
+ <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
+ via command line
+ </li>
+ <li>
+ <!-- JAL-3741 -->References to http://www.jalview.org in
+ program and documentation
+ </li>
+ </ul> <em>Launching Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3718 -->Jalview application fails when launched the
+ first time for a version that has different jars to the
+ previous launched version.
+ </li>
+ </ul> <em>Developing Jalview</em>
+ <ul>
+ <li>
+ <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
+ data, causing cloverReport gradle task to fail with an
+ OutOfMemory error.
+ </li>
+ <li>
+ <!-- JAL-3280 -->Migrated the Jalview Version Checker to
+ monitor the release channel
+ </li>
+ </ul> <em>New Known defects</em>
+ <ul>
+ <li>
+ <!-- JAL-3748 -->CDS shown in result of submitting proteins
+ in a CDS/Protein alignment to a web service is wrong when
+ proteins share a common transcript sequence (e.g. genome of
+ RNA viruses)
+ </li>
+ <li>
+ <!-- JAL-3576 -->Co-located features exported and
+ re-imported are ordered differently when shown on alignment
+ and in tooltips. (Also affects v2.11.1.0)
+ </li>
+ <li>
+ <!-- JAL-3702 -->Drag and drop of alignment file onto
+ alignment window when in a HiDPI scaled mode in Linux only
+ works for the top left quadrant of the alignment window
+ </li>
+ <li>
+ <!-- JAL-3701 -->Stale build data in jalview standalone jar
+ builds (only affects 2.11.1.1 branch)
+ </li>
+ <li>
+ <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
+ when alignment view restored from project (since Jalview
+ 2.11.0)
+ </li>
+ <li>
+ <!-- JAL-3749 -->Duplicate CDS sequences are generated when
+ protein products for certain ENA records are repeatedly
+ shown via Calculate->Show Cross Refs
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" align="center" nowrap><strong><a
+ id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
+ <em>22/04/2020</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li>
+ <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
+ 'virtual' codon features shown on protein (or vice versa)
+ for display in alignments, on structure views (including
+ transfer to UCSF chimera), in feature reports and for
+ export.
+ </li>
+ <li>
+ <!-- JAL-3121 -->Feature attributes from VCF files can be
+ exported and re-imported as GFF3 files
+ </li>
+ <li>
+ <!-- JAL-3376 -->Capture VCF "fixed column" values
+ POS, ID, QUAL, FILTER as Feature Attributes
+ </li>
+ <li>
+ <!-- JAL-3375 -->More robust VCF numeric data field
+ validation while parsing
+ </li>
+ <li>
+ <!-- JAL-3533 -->Feature Settings dialog keeps same screen
+ position if reopened
+ </li>
+ <li>
+ <!-- JAL-3535 -->Feature Settings dialog title includes name
+ of associated view
+ </li>
+ <li>
+ <!-- JAL-3538 -->Font anti-aliasing in alignment views
+ enabled by default
+ </li>
+ <li>
+ <!-- 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>
+
-li:before {
- /* doesnt get processed in javahelp */
- content: '\00b7 ';
- padding: 3px;
- margin-left: -14px;
-}
-</style>
-</head>
-<body>
- <p>
- <strong>Release History</strong>
- </p>
- <table border="1">
- <tr>
- <th nowrap><em>Release</em></th>
- <th><em>New Features</em></th>
- <th><em>Issues Resolved</em></th>
- </tr>
- <tr>
- <td width="60" align="center" nowrap>
- <strong><a name="Jalview.2.11.1">2.11.1</a><br />
- <em>19/11/2019</em></strong>
- </td>
- <td align="left" valign="top">
- <ul>
- <li><!-- -->
+ </ul></li>
+ <li>
+ <!-- JAL-3232 -->Jalview Groovy Scripting Console updated to
+ Groovy v2.5
</li>
- </ul>
- <em>Deprecations</em>
- </td>
- <td align="left" valign="top">
- <ul>
- </ul>
- <em>Java 11 Compatibility issues</em>
+ <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-2987 -->OSX - Can't view results in PDB/Uniprot FTS
+ <!-- JAL-3035 -->DAS sequence retrieval and annotation
+ capabilities removed from the Jalview Desktop
</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
+ <!-- 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-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>)
+ <!-- JAL-3311 -->Disable VAMSAS menu in preparation for
+ removal
</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>
+ <!-- -->Jalview Desktop no longer distributed via Java Web
+ Start
+ </li>
+ </ul> <em>Documentation</em>
+ <ul>
<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>
+ <!-- JAL-3003 -->Added remarks about transparent rendering
+ effects not supported in EPS figure export
+ </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
+ <!-- JAL-2903 -->Typos in documentation for Preferences
+ dialog
</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>
- <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>
- <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
- </ul> <em>Development and Release Processes</em>
- <ul>
- <li>
- <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
- </li>
- <li>
- <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
- <li>
- <!-- JAL-3225 -->Eclipse project configuration managed with
+ </ul> <em>Development and Release Processes</em>
+ <ul>
+ <li>
+ <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated
+ from Ant to Gradle
+ </li>
+ <li>
+ <!-- JAL-1424 -->Enhanced checks for missing and duplicated
+ keys in Message bundles
+ </li>
+ <li>
+ <!-- JAL-3225 -->Eclipse project configuration managed with
gradle-eclipse
</li>
<li>
- <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
- Bamboo continuous integration for unattended Test Suite
- execution
+ <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian Bamboo
+ continuous integration for unattended Test Suite execution
</li>
<li>
- <!-- JAL-2864 -->Memory test suite to detect leaks in common
+ <!-- JAL-2864 -->Memory test suite to detect leaks in common
operations
</li>
<li>
- <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+ <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
issues resolved
</li>
<li>
- <!-- JAL-3248 -->Developer documentation migrated to
+ <!-- JAL-3248 -->Developer documentation migrated to
markdown (with HTML rendering)
</li>
<li>
- <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+ <!-- JAL-3287 -->HelpLinksChecker runs on Windows
</li>
<li>
- <!-- JAL-3289 -->New URLs for publishing development
+ <!-- JAL-3289 -->New URLs for publishing development
versions of Jalview
</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>
- <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>
+ <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> <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-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>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em></em>
+ </ul> <em>Java 11 Specific defects</em>
<ul>
+ <li>
+ <!-- JAL-3235 -->Jalview Properties file is not sorted
+ alphabetically when saved
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
<li>
<!-- JAL-3101 -->Default memory for Jalview webstart and
InstallAnywhere increased to 1G.
</li>
</ul>
</div></td>
- <td><div align="left">
- <em></em>
- <ul>
+ <td><div align="left">
+ <em></em>
+ <ul>
<li>
<!-- JAL-3104 -->Poorly scaled bar in quality annotation
row shown in Feredoxin Structure alignment view of example
latest version of OSX.
</li>
</ul>
- </div>
- </td>
+ </div></td>
</tr>
<tr>
<td width="60" nowrap>
</ul>
<em>New Known Defects</em>
<ul>
- <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
+ <li>
+ <!-- JAL-3083 -->Cancel option doesn't reset Colour by
+ Annotation
+ </li>
</ul>
</div></td>
</tr>
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
+ <!-- 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>
+ </div></td>
<td><div align="left">
<ul>
<li>
columns in annotation row
</li>
<li>
- <!-- JAL-2913 -->Preferences panel's ID Width control is not
- honored in batch mode
+ <!-- JAL-2913 -->Preferences panel's ID Width control is
+ not honored in batch mode
</li>
<li>
<!-- JAL-2945 -->Linked sequence highlighting doesn't work
with negative residue numbers or missing residues fails
</li>
<li>
- <!-- JAL-2952 -->Exception when shading sequence with negative
- Temperature Factor values from annotated PDB files (e.g.
- as generated by CONSURF)
+ <!-- JAL-2952 -->Exception when shading sequence with
+ negative Temperature Factor values from annotated PDB
+ files (e.g. as generated by CONSURF)
</li>
<li>
<!-- JAL-2920 -->Uniprot 'sequence variant' features
structure and/or overview windows are also shown
</li>
<li>
- <!-- JAL-2954 -->Selecting columns from highlighted regions
- very slow for alignments with large numbers of sequences
+ <!-- JAL-2954 -->Selecting columns from highlighted
+ regions very slow for alignments with large numbers of
+ sequences
</li>
<li>
<!-- JAL-2925 -->Copy Consensus fails for group consensus
with 'StringIndexOutOfBounds'
</li>
<li>
- <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
- platforms running Java 10
+ <!-- JAL-2976 -->VAqua(4) provided as fallback Look and
+ Feel for OSX platforms running Java 10
</li>
<li>
<!-- JAL-2960 -->Adding a structure to existing structure
- view appears to do nothing because the view is hidden behind the alignment view
+ view appears to do nothing because the view is hidden
+ behind the alignment view
</li>
</ul>
<em>Applet</em>
</ul>
<em>Batch Mode</em>
<ul>
- <li>
- <!-- JAL-2913 -->Fixed ID width preference is not respected
- </li>
+ <li>
+ <!-- JAL-2913 -->Fixed ID width preference is not
+ respected
+ </li>
</ul>
<em>New Known Defects</em>
<ul>
Sequences' enabled) or Ensembl isoforms (Workaround in
2.10.4 is to fail back to N&W mapping)
</li>
- <li>
- <!-- JAL-2990 -->Export Annotations from File Menu with CSV
- option gives blank output
- </li>
- </ul>
- </div>
- </td>
+ <li>
+ <!-- JAL-2990 -->Export Annotations from File Menu with
+ CSV option gives blank output
+ </li>
+ </ul>
+ </div></td>
</tr>
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
+ <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br />
+ <em>24/1/2018</em></strong>
</div>
</td>
<td><div align="left">
- <ul><li>Updated Certum Codesigning Certificate
- (Valid till 30th November 2018)</li></ul></div></td>
- <td><div align="left">
- <em>Desktop</em><ul>
<ul>
- <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
- <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
- <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
- <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
- <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
- <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
- <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
+ <li>Updated Certum Codesigning Certificate (Valid till
+ 30th November 2018)</li>
</ul>
- </div>
- </td>
+ </div></td>
+ <td><div align="left">
+ <em>Desktop</em>
+ <ul>
+ <ul>
+ <li>
+ <!-- JAL-2859-->Only one structure is loaded when
+ several sequences and structures are selected for
+ viewing/superposing
+ </li>
+ <li>
+ <!-- JAL-2851-->Alignment doesn't appear to scroll
+ vertically via trackpad and scrollwheel
+ </li>
+ <li>
+ <!-- JAL-2842-->Jalview hangs if up/down arrows pressed
+ in cursor mode when cursor lies in hidden region at
+ start of alignment
+ </li>
+ <li>
+ <!-- JAL-2827-->Helix annotation has 'notches' when
+ scrolled into view if columns are hidden
+ </li>
+ <li>
+ <!-- JAL-2740-->Annotation column filter can be slow to
+ reset (ie after hitting cancel) for large numbers of
+ hidden columns
+ </li>
+ <li>
+ <!-- JAL-2849-->User preference for disabling inclusion
+ of sequence limits when exporting as flat file has no
+ effect
+ </li>
+ <li>
+ <!-- JAL-2679-->Reproducible cross-reference
+ relationships when retrieving sequences from
+ EnsemblGenomes
+ </li>
+ </ul>
+ </div></td>
</tr>
<tr>
<td width="60" nowrap>
<em>New features in Jalview Desktop</em>
<ul>
<li>
- <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
+ <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API
+ at uniprot.org
</li>
- <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
+ <li>
+ <!-- JAL-2745 -->HTTPS used for all connections to
+ ebi.ac.uk
</li>
</ul>
</div></td>
- <td><div align="left">
- </div></td>
+ <td><div align="left"></div></td>
</tr>
<tr>
<td width="60" nowrap>
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
+ <!-- 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>
column.
</li>
<li>
- <!-- JAL-1980 -->Null Pointer Exception raised when
+ <!-- JAL-1980 -->Null Pointer Exception raised when
pressing Add on an orphaned cut'n'paste window.
</li>
<!-- may exclude, this is an external service stability issue JAL-1941
<ul>
<li>URL links generated from description line for
regular-expression based URL links (applet and application)
+
<li>Non-positional feature URL links are shown in link
menu</li>
<li>Cancel button for DAS Feature Fetching
<li>PCA and PDB Viewers zoom via mouse roller
<li>User-defined sub-tree colours and sub-tree selection
+
<li>'New Window' button on the 'Output to Text box'
</ul>
<li>Fixed Remove Empty Columns Bug (empty columns at end
of alignment)
<li>Slowed DAS Feature Fetching for increased robustness.
+
<li>Made angle brackets in ASCII feature descriptions
display correctly
<li>WsDbFetch query/result association resolved
<li>Tree leaf to sequence mapping improved
<li>Smooth fonts switch moved to FontChooser dialog box.
+
</ul>
</td>
git://source.jalview.org / jalview.git / blobdiff