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 --> 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 preferences for height, width and scale factor
22 - <!-- JAL-4307 --> Show or hide ligands in a Jmol structure view via View Ligands submenu
24 ### Improved support for working with structures and computationally determined models
25 - <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
26 - <!-- JAL-4095 --> Interactive picking of low pAE score regions
27 - <!-- JAL-4027 --> contact matrix datatype in Jalview
28 - <!-- JAL-4033 --> Selections with visual feedback via contact matrix annotation
29 - <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
30 - <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
31 - <!-- JAL-4123 --> GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted
32 - <!-- JAL-3914 --> Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
33 - <!-- JAL-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
34 - <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
35 - <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
36 - <!-- JAL-4281 --> Store and restore adjustable ID margin and annotation panel height in Jalview projects
37 - <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
38 - <!-- 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.
41 ### Jalview on the command line
42 - <!-- 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.
43 - <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
44 - <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output
45 - <!-- JAL-244 --> Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs
46 - <!-- JAL-901 --> Specify alignment title on import via --title argument
47 - <!-- JAL-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
48 - Add a command line option to set Jalview properties for this session only
49 - Add a command line option to suppress opening the startup file for this session
51 ### Other improvements
52 - <!-- JAL-4250 --> Secondary structure annotation glyphs are rendered anti-aliasing when enabled
53 - <!-- JAL-325 --> Helix and Sheet glyphs vertically centered with respect to grey coil secondary structure annotation track
54 - <!-- JAL-4317 --> feature should be displayed when its rendering and filtering settings are adjusted
55 - <!-- JAL-4250 --> Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3
56 - <!-- JAL-3119 --> Name of alignment and view included in overview window's title
57 - <!-- JAL-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
58 - <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
59 - <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
60 - <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
61 - <!-- JAL-4206 --> Relative files added to recent files list via import from command line are selected when Jalview opened from same location
62 - <!-- JAL-4308 --> Reduce number of database crossreferences shown in tooltip
63 - <!-- JAL-4315 --> Drag and drop feature colours file on an alignment to quickly apply feature settings
64 - <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
65 - <!-- JAL-4304,JAL-4305 --> Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly.
67 ### Development and Deployment
68 - <!-- JAL-4054 --> Installers built with install4j10
69 - <!-- JAL-4167 --> Create separate gradle test task for some tests
70 - <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
71 - <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
72 - <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
73 - <!-- JAL-4110 --> Output stderr and stdout when running tests via gradle
74 - <!-- JAL-3599 --> New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress)
77 - <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
78 - <!-- JAL-3776 --> Cancelling interactive calculation leaves empty progress bar.
79 - <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
80 - <!-- JAL-1988 --> Can quit Jalview while 'save project' is in progress
81 - <!-- JAL-4126 --> 'Use original colours' option of colour by annotation not honoured when restoring view from project
82 - <!-- JAL-4116 --> PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch)
83 - <!-- JAL-3784 --> Multiple overview windows can be opened for a particular alignment view when multiple views are present
84 - <!-- JAL-3785 --> Overview windows opened automatically (due to preferences settings) lack title
85 - <!-- 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
86 - <!-- JAL-4184 --> Stockholm export does not include sequence descriptions
87 - <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
88 - <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
89 - <!-- JAL-4177 --> Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
90 - <!-- JAL-4311 --> 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models
91 - <!-- JAL-4133 --> Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
92 - <!-- JAL-4253,JAL-4293 --> Lower line of the sequence group border does not align with vertical and background residue box
93 - <!-- JAL-4128 --> Resizing overview quickly with solid-drags enabled causes exception
94 - <!-- JAL-4150 --> Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window
95 - <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
96 - <!-- JAL-4153 --> JvCacheableInputBoxTest flaky on build server
97 - <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
98 - <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running
99 - <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
100 - <!-- 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
101 - <!-- JAL-4310 --> Don't offer View model page for sources that do not have model pages
102 - <!-- JAL-4298 --> Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang
103 - <!-- 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)
104 - <!-- JAL-4223 --> RNAML import missing terminal residue
105 - <!-- JAL-4218 --> Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
108 - <!-- 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.
109 - <!-- JAL-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
110 - <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
111 - <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
112 - <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
113 - <!-- JAL-4325 --> Overview shown and then closed when importing legacy jalview projects without overview store/restore information
114 - <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
115 - <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
116 - <!-- JAL-3024 --> Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
117 - <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
118 - <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line
119 - <!-- JAL-4290 --> Headless alignment export with structure annotations doesn't include secondary structure and temperature factor
git://source.jalview.org / jalview.git / blob