Release |
New Features |
Issues Resolved |
2.2.1
12/2/07 |
- Non standard characters can be read and displayed
- Annotations/Features can be imported/exported to the applet via textbox
- Applet allows editing of sequence/annotation/group name & description
- Preference setting to display sequence name in italics
- Annotation file format extended to allow Sequence_groups
to be defined
- Default opening of alignment overview panel can be specified in
preferences
- PDB residue numbering annotation added to associated sequences
|
- Applet crash under certain Linux OS with Java 1.6 installed
- Annotation file export / import bugs fixed
- PNG / EPS image output bugs fixed
|
2.2
27/11/06 |
- Multiple views on alignment
- Sequence feature editing
- "Reload" alignment
- "Save" to current filename
- Background dependent text colour
- Right align sequence ids
- User-defined lower case residue colours
- Format Menu
- Select Menu
- Menu item accelerator keys
- Control-V pastes to current alignment
- Cancel button for DAS Feature Fetching
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection
- 'New Window' button on the 'Output to Text box'
|
- New memory efficient Undo/Redo System
- Optimised symbol lookups and conservation/consensus calculations
- Region Conservation/Consensus recalculated after edits
- Fixed Remove Empty Columns Bug (empty columns at end of alignment)
- Slowed DAS Feature Fetching for increased robustness.
- Made angle brackets in ASCII feature descriptions display correctly
- Re-instated Zoom function for PCA
- Sequence descriptions conserved in web service analysis results
- Uniprot ID discoverer uses any word separated by ∣
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
|
2.1.1
12/9/06 |
- Copy consensus sequence to clipboard
|
- Image output - rightmost residues are rendered if sequence id panel
has been resized
- Image output - all offscreen group boundaries are rendered
- Annotation files with sequence references - all elements in file are
relative to sequence position
- Mac Applet users can use Alt key for group editing
|
2.1
22/8/06 |
- MAFFT Multiple Alignment in default Web Service list
- DAS Feature fetching
- Hide sequences and columns
- Export Annotations and Features
- GFF file reading / writing
- Associate structures with sequences from local PDB files
- Add sequences to exisiting alignment
- Recently opened files / URL lists
- Applet can launch the full application
- Applet has transparency for features (Java 1.2 required)
- Applet has user defined colours parameter
- Applet can load sequences from parameter "sequencex"
|
- Redundancy Panel reinstalled in the Applet
- Monospaced font - EPS / rescaling bug fixed
- Annotation files with sequence references bug fixed
|
2.08.1
2/5/06 |
- Change case of selected region from Popup menu
- Choose to match case when searching
- Middle mouse button and mouse movement can compress / expand the visible
width and height of the alignment
|
- Annotation Panel displays complete JNet results
|
2.08b
18/4/06 |
|
- Java 1.5 bug - InternalMessageDialog fix for threads
- Righthand label on wrapped alignments shows correct value
|
2.08
10/4/06 |
- Editing can be locked to the selection area
- Keyboard editing
- Create sequence features from searches
- Precalculated annotations can be loaded onto alignments
- Features file allows grouping of features
- Annotation Colouring scheme added
- Smooth fonts off by default - Faster rendering
- Choose to toggle Autocalculate Consensus On/Off
|
- Drag & Drop fixed on Linux
- Jalview Archive file faster to load/save, sequence descriptions saved.
|
2.07
12/12/05 |
- PDB Structure Viewer enhanced
- Sequence Feature retrieval and display enhanced
- Choose to output sequence start-end after sequence name for file output
- Sequence Fetcher WSDBFetch@EBI
- Applet can read feature files, PDB files and can be used for HTML
form input
|
- HTML output writes groups and features
- Group editing is Control and mouse click
- File IO bugs
|
2.06
28/9/05 |
- View annotations in wrapped mode
- More options for PCA viewer
|
- GUI bugs resolved
- Runs with -nodisplay from command line
|
2.05b
15/9/05 |
- Choose EPS export as lineart or text
- Jar files are executable
- Can read in Uracil - maps to unknown residue
|
- Known OutOfMemory errors give warning message
- Overview window calculated more efficiently
- Several GUI bugs resolved
|
2.05
30/8/05 |
- Edit and annotate in "Wrapped" view
|
- Several GUI bugs resolved
|
2.04
24/8/05 |
- Hold down mouse wheel & scroll to change font size
|
- Improved JPred client reliability
- Improved loading of Jalview files
|
2.03
18/8/05 |
- Set Proxy server name and port in preferences
- Multiple URL links from sequence ids
- User Defined Colours can have a scheme name and added to Colour Menu
- Choose to ignore gaps in consensus calculation
- Unix users can set default web browser
- Runs without GUI for batch processing
- Dynamically generated Web Service Menus
|
- InstallAnywhere download for Sparc Solaris
|
2.02
18/7/05 |
|
- Copy & Paste order of sequences maintains alignment order.
|
2.01
12/7/05 |
- Use delete key for deleting selection.
- Use Mouse wheel to scroll sequences.
- Help file updated to describe how to add alignment annotations.
- Version and build date written to build properties file.
- InstallAnywhere installation will check for updates at launch of Jalview.
|
- Delete gaps bug fixed.
- FileChooser sorts columns.
- Can remove groups one by one.
- Filechooser icons installed.
- Finder ignores return character when searching. Return key will initiate
a search.
|
2.0
20/6/05 |
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