8 - <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
9 - <!-- JAL-3416 --> Jalview now uses a standard 'look and feel' (FlatLaf) on Linux, OSX and everywhere else
10 - <!-- JAL-4019 --> Ambiguous Base Colourscheme
11 - <!-- JAL-4061 --> Find can search sequence features' type and description
12 - <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
13 - <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu
14 - <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
15 - <!-- JAL-4190 --> Pressing escape in tree panel clears any current selection
16 - <!-- JAL-4089 --> Use selected columns for superposition
17 - <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
18 - <!-- JAL-4221 --> sequence descriptions are updated from database reference sources if not already defined
19 - <!-- JAL-4273,JAL-3497 --> Visible adjuster marks to grab and adjust annotation panel height and id width
20 - <!-- JAL-4260 --> Adjustable ID margin when alignment is wrapped
21 - <!-- JAL-4274 --> Command line options and configurable bitmap export (via preferences file) for height, width and scale factor
22 - <!-- JAL-4307 --> Show or hide ligands in a Jmol structure view via View Ligands submenu
23 - <!-- JAL-4252 --> Jmol's display is antialiased by default (smoother, less pixellated)
25 ### Improved support for working with structures and computationally determined models
26 - <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
27 - <!-- JAL-4095 --> Interactive picking of low pAE score regions
28 - <!-- JAL-4027, JAL-3858, JAL-2292 --> Predicted Alignment Error annotation tracks for structures from AlphaFold DB
29 - <!-- JAL-4033 --> Selections with visual feedback via contact matrix annotation
30 - <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
31 - <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
32 - <!-- JAL-4123 --> GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted
33 - <!-- JAL-3914 --> Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
34 - <!-- JAL-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
35 - <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
36 - <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
37 - <!-- JAL-4281 --> Store and restore adjustable ID margin and annotation panel height in Jalview projects
38 - <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
39 - <!-- JAL-4147 --> Per-structure and chain shown when annotation shown sorted by label enabling secondary structure and temperature factor scores from different chains and structures for the same sequence to be visually compared.
40 - <!-- JAL-4216 --> PDB or mmCIF files with chains with negative RESNUMs for their whole sequence extent cannot be linked to alignments
43 ### Jalview on the command line
44 - <!-- JAL-4160,JAL-629,JAL-4262,JAL-4265, --> New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation.
45 - <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
46 - <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output
47 - <!-- JAL-244 --> Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs
48 - <!-- JAL-901 --> Specify alignment title on import via --title argument
49 - <!-- JAL-4195 --> Sensible responses from the CLI when things go wrong during image export
50 - <!-- JAL-4194 --> Add a command line option to set Jalview properties for this session only
51 - <!-- JAL-4193 --> Add a command line option to suppress opening the startup file for this session
53 ### Other improvements
54 - <!-- JAL-4250 --> Secondary structure annotation glyphs are rendered anti-aliasing when enabled
55 - <!-- JAL-325,JAL-4250 --> Helix and Sheet glyphs vertically centred with respect to grey coil secondary structure annotation track
56 - <!-- JAL-4317 --> feature should be displayed when its rendering and filtering settings are adjusted
57 - <!-- JAL-4250 --> Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3
58 - <!-- JAL-3119 --> Name of alignment and view included in overview window's title
59 - <!-- JAL-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
60 - <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
61 - <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
62 - <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
63 - <!-- JAL-4206 --> Relative files added to recent files list via import from command line are selected when Jalview opened from same location
64 - <!-- JAL-4308 --> Reduce number of database crossreferences shown in tooltip
65 - <!-- JAL-4315 --> Drag and drop feature colours file on an alignment to quickly apply feature settings
66 - <!-- JAL-3676 --> Improved startup info in console output: which properties file was being used and slight revisions to the formatting of platform information.
67 - <!-- JAL-4304,JAL-4305 --> Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly.
68 - <!-- JAL-1713,JAL-2528 --> Overview display and hidden region visibility stored in Jalview projects
69 - <!-- JAL-4169 --> Updated faq and documentation urls in splashscreen and help documentation
71 ### Development and Deployment
72 - <!-- JAL-4054 --> Installers built with install4j10
73 - <!-- JAL-4167 --> Create separate gradle test task for some tests
74 - <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
75 - <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
76 - <!-- JAL-4288 --> Update .jvl generation in build.gradle for jalview branch builds
77 - <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
78 - <!-- JAL-4110 --> Output stderr and stdout when running tests via gradle
79 - <!-- JAL-3599 --> New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress)
83 - <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
84 - <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
85 - <!-- JAL-1988 --> Can quit Jalview while 'save project' is in progress
86 - <!-- JAL-4126 --> 'Use original colours' option of colour by annotation not honoured when restoring view from project
87 - <!-- JAL-4116 --> PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch)
88 - <!-- JAL-3784 --> Multiple overview windows can be opened for a particular alignment view when multiple views are present
89 - <!-- JAL-3785 --> Overview windows opened automatically (due to preferences settings) lack title
90 - <!-- JAL-2353 --> Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession
91 - <!-- JAL-4334 --> Uniprot parser fails to import sequences with features that have 'unknown' start or end
92 - <!-- JAL-4184 --> Stockholm export does not include sequence descriptions
93 - <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
94 - <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
95 - <!-- JAL-4177 --> Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
96 - <!-- JAL-4311 --> 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models
97 - <!-- JAL-4133 --> Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
98 - <!-- JAL-4253,JAL-4293 --> Lower line of the sequence group border does not align with vertical and background residue box
99 - <!-- JAL-4128 --> Resizing overview quickly with solid-drags enabled causes exception
100 - <!-- JAL-4150 --> Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window
101 - <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
102 - <!-- JAL-4153 --> JvCacheableInputBoxTest flaky on build server
103 - <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
104 - <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running jalview via the getdown app launcher
105 - <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
106 - <!-- JAL-3783 --> Groovy console does not open when Jalview launched from jalview's Java 11 executable jar (available via conda) for recent versions of groovy
107 - <!-- JAL-4310 --> Don't offer View model page for sources that do not have model pages
108 - <!-- JAL-4298 --> Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang
109 - <!-- JAL-4282 --> automatic positioning of ID width for imported project can fail for certain font size configured in User preferences (affects most versions of Jalview prior to 2.11.3.0)
110 - <!-- JAL-4223 --> RNAML import missing terminal residue
111 - <!-- JAL-3088 --> RNA secondary structure annotation final-ending-solo-brace arrow points the wrong way
112 - <!-- JAL-4218 --> Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
113 - <!-- JAL-3921 --> Jmol sessions involving large molecules may not be fully saved in Jalview project files (known defect in 2.11.2.x)
117 - <!-- JAL-4303 --> EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu.
118 - <!-- JAL-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
119 - <!-- JAL-4338 --> PAE partition not shown in the same place when tree is closed and reopened
120 - <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
121 - <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
122 - <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0)
123 - <!-- JAL-4325 --> Overview shown and then closed when importing legacy jalview projects without overview store/restore information
124 - <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
125 - <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
126 - <!-- JAL-3024 --> Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
127 - <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
128 - <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line
129 - <!-- JAL-4290 --> Headless alignment export with structure annotations doesn't include secondary structure and temperature factor
130 - <!-- JAL-4151 --> Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window
131 - <!-- JAL-4157 --> Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu
132 - <!-- JAL-4327 --> When the Groovy console is open Jalview does not prompt to save before quitting
133 - <!-- JAL-4328 --> Jalview works with but is not fully compatible with latest Ensembl REST API (15.6)
git://source.jalview.org / jalview.git / blob