<title>Release History</title>
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</head>
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-3503 -->New Preferences tab for adjusting Jalview's
memory settings at launch
</li>
Annotation' for a sequence
</li>
<li>
- <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
+ <!-- JAL-1260 -->Import Genbank and EMBL format flatfiles
</li>
<li>
<!-- JAL-3821 -->ENA record's mol_type honoured so RNA
schema
</li>
<li>
- <!-- JAL-3926 -->Uniprot and PDBe autosearch option is disabled by default
+ <!-- JAL-3926 -->Uniprot and PDBe autosearch option is
+ disabled by default
</li>
<li>
<!-- JAL- -->
</li>
- <li>
- </li>
+ <li></li>
</ul> <em>JalviewJS</em>
<ul>
<li>
</td>
<td>
<ul>
- <li>
+ <li>
<!-- JAL-3674 -->Slow structure commands can block Jalview
execution
</li>
- <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)
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
<!-- 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>
+ <!-- JAL-3794 -->X was not being recognised as the unknown
+ base in DNA sequences
</li>
<li>
<!-- JAL-3915 -->Removed RNAview checkbox and logic from
preference enabled results in Null Pointer Exceptions when
clustal colouring is enabled
</li>
- <li><!-- JAL-3275 -->Can open multiple Preferences panels</li>
+ <li>
+ <!-- JAL-3275 -->Can open multiple Preferences panels
+ </li>
<li>
<!-- JAL-3949 -->Standard out logging broken: messages only
routing to stderr and appear as a raw template
<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>
+ <!-- JAL-3934 -->Version bump library dependency: Log4j
+ 2.16.0 to 2.17.0.
+ </li>
</ul></td>
- <td>
- </td>
+ <td></td>
</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
<li>
<!-- JAL-3477 -->Improved built-in documentation and command
line help for configuring Jalview's memory
- </li>
+ </li>
</ul>
</td>
<td align="left" valign="top">
<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)
+ 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)
+ <!-- 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
</li>
<li>
<!-- JAL-3127 -->Sequence ID colourscheme not re-applied
- when alignment view restored from project (since Jalview 2.11.0)
+ when alignment view restored from project (since Jalview
+ 2.11.0)
</li>
<li>
<!-- JAL-3749 -->Duplicate CDS sequences are generated when
with no feature types visible
</li>
<li>
- <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
+ <!-- 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>
- </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)
+ <!-- JAL-3394 -->New installer/application launcher
+ generated with install4j 8.0.4
</li>
<li>
- <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
+ <!-- JAL-3420 -->Jalview File Associations shown for Unix
+ Platforms
</li>
<li>
- <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
+ <!-- JAL-3477 -->Improved defaults for maximum memory
+ setting when running on large memory machines
</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>
+ <!-- JAL-3577 -->'Jalview Test' installers/apps for easier
+ access to test-release channel builds
+ </li>
</ul> <em>Build System</em>
<ul>
<li>
<!-- JAL-3513 -->Test code included in Clover coverage
report
</li>
- </ul>
- <em>Groovy Scripts</em>
- <ul>
+ </ul> <em>Groovy Scripts</em>
+ <ul>
<li>
<!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
to stdout containing the consensus sequence for each
'Source' in console output
</li>
<li>
- <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
- bamboo server but run fine locally.
+ <!-- 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 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-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
+ <!-- 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)
+ <!-- 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
+ <!-- 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
+ <!-- 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>
+ <!-- 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>
+ '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>
+ <!-- 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>
+ <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
stored and restored from Jalview Projects
</li>
<li>
- <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
- recognise variant features
+ <!-- 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)
+ <!-- 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
+ <!-- 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)
+ <!-- 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
+ <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature
+ Settings dialog
</li>
- </ul>
- </li>
+ </ul></li>
<li>
- <!-- JAL-3205 -->Symmetric score matrices for faster
- tree and PCA calculations
+ <!-- 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
+ <!-- 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-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
+ <!-- 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>
+ </ul></li>
<li>
<!-- JAL-3127 -->New 'Colour by Sequence ID' option
</li>
<li><strong>Speed and Efficiency</strong>
- <ul>
+ <ul>
<li>
- <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
- multiple groups when working with large alignments
+ <!-- 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
+ <!-- JAL-3200 -->Speedier import of annotation rows when
+ parsing Stockholm files
</li>
</ul>
<li><strong>User Interface</strong>
- <ul>
+ <ul>
<li>
- <!-- JAL-2933 -->Finder panel remembers last position in each
- view
+ <!-- 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)
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ selection region, and gap count when inserting or
+ deleting gaps
</li>
<li>
- <!-- JAL-3132 -->Status bar updates over sequence and annotation
- labels
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB
+ search panels
</li>
<li>
- <!-- JAL-2621 -->Cursor changes over draggable box in Overview
- panel
+ <!-- JAL-2621 -->Cursor changes over draggable box in
+ Overview panel
</li>
<li>
- <!-- JAL-3181 -->Consistent ordering of links in sequence id
- popup menu
+ <!-- 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>
+ <!-- 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>
-
-
+ <!-- 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>
+ <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
+ <!-- -->OSX GUI integrations for App menu's 'About'
+ entry and trapping CMD-Q
</li>
</ul></li>
- </ul>
- <em>Deprecations</em>
+ </ul> <em>Deprecations</em>
<ul>
- <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
+ <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
- 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>
+ <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>
+ <!-- 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>
- <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
+ <!-- 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
+ <!-- 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>
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
+ <!-- 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
+ <!-- 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
+ <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving
+ Jalview project involving multiple views
</li>
<li>
<!-- JAL-3164 -->Overview for complementary view in a linked
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
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ 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
+ <!-- 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
+ <!-- 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
+ <!-- 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)
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- 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
<!-- JAL-2932 -->Finder searches in minimised alignments
</li>
<li>
- <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
- on opening an alignment
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- JAL-3206 -->Colour by Annotation can go black at
+ min/max threshold limit
</li>
<li>
<!-- JAL-3125 -->Value input for graduated feature colour
colour
</li>
<li>
- <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- 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
+ <!-- JAL-3313 -->Codon consensus incorrectly scaled when
+ shown without normalisation
</li>
<li>
- <!-- JAL-3021 -->Sequence Details report should open positioned at top
- of report
+ <!-- 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
+ <!-- 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
+ <!-- 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)
+ <!-- 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
+ <!-- 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)
+ <!-- JAL-868 -->Structure colours not updated when
+ associated tree repartitions the alignment view (Regression
+ in 2.10.5)
</li>
</ul> <em>Datamodel</em>
<ul>
<!-- 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-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>
+ <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>
+ <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>
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
+ <!-- JAL-2990 -->Export Annotations from File Menu with
+ CSV option gives blank output
</li>
</ul>
- </div>
- </td>
+ </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 / commitdiff