<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>16/2/2020</em></strong>
- </td>
+ <td width="60" align="center" nowrap><strong><a
+ name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
+ <em>16/2/2020</em></strong></td>
<td align="left" valign="top">
<ul>
- <li><!-- -->
+ <li>
+ <!-- -->
</li>
- </ul>
- <em>Deprecations</em>
+ </ul> <em>Release processes</em>
+ <ul>
+ <li>
+ <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
+ </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>Deprecations</em>
</td>
<td align="left" valign="top">
<ul>
- </ul>
- <em>Java 11 Compatibility issues</em>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- -->
+ </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 causing
+ IllegalArgumentException in some circumstances
+ </li>
+ <li>
+ <!-- JAL-3406 -->Credits missing some authors in Jalview
+ help documentation for 2.11.0 release
+ </li>
+ </ul> <em>Java 11 Compatibility issues</em>
<ul>
<li>
<!-- JAL-2987 -->OSX - Can't view results in PDB/Uniprot FTS
</li>
- </ul>
-
- <em>Repository and Source Release</em>
+ </ul> <em>Repository and Source Release</em>
<ul>
<li>
<!-- JAL-3474 -->removed redundant .gitignore files from
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-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>
+ <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>
'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>
+ <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>
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>
+ <!-- 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>
+ <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
<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>
+ <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
gradle-eclipse
</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>
+ <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>
+ <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
</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>
</td>
- </tr>
+ </tr>
<tr>
<td width="60" nowrap>
<div align="center">
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>
+ <li>
+ <!-- JAL-2990 -->Export Annotations from File Menu with CSV
+ option gives blank output
+ </li>
+ </ul>
</div>
</td>
</tr>
git://source.jalview.org / jalview.git / commitdiff