Release History

Release History

Release	New Features	Issues Resolved
2.3 9/5/07	Jmol 11.0.2 integration PDB views stored in Jalview XML files Slide sequences Edit sequence in place EMBL CDS features DAS Feature mapping Feature ordering Alignment Properties Annotation Scores Sort by scores Feature/annotation editing in applet	Headless state operation in 2.2.1 Incorrect and unstable DNA pairwise alignment Cut and paste of sequences with annotation Feature group display state in XML Feature ordering in XML blc file iteration selection using filename # suffix Stockholm alignment properties Stockhom alignment secondary structure annotation 2.2.1 applet had no feature transparency Number pad keys can be used in cursor mode Structure Viewer mirror image 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	New codebase