Release History

Release History

Release	New Features	Issues Resolved
2.4 Feb/2008	New VAMSAS capabilities in Jalview treenode binding for VAMSAS tree exchange local editing and update of sequences in VAMSAS alignments (experimental) Create new or select existing session to join load and save of vamsas documents Retrieval of cross-referenced sequences from other databases export annotation rows as CSV for spreadsheet import Jalview projects record alignment dataset associations, EMBL products, and cDNA sequence mappings Linked highlighting of codon and amino acid from translation and protein products JPred3 web service Generalised database reference retrieval and validation to all fetchable databases Application command line -tree parameter to open trees (introduced for passing from applet) -fetchfrom command line argument to specify nicknames of DAS servers to query for alignment features -dasserver command line argument to add new servers that are also automatically queried for features -groovy command line argument executes a given groovy script after all input data has been loaded and parsed Trees passed as applet parameters can be passed to application (when using "View in full application") MemoryMonitor added as an option under Desktop's Tools menu allow reading of JPred concise files as a normal filetype sort sequences by named annotation scores Re-instated Full AMSA support and .amsa file association Stockholm annotation parsing and alignment properties import Applet Parameters feature group display control parameter debug parameter Applet API methods newView public method Window (current view) specific get/set public methods Feature display control methods New Jalview distribution features RELEASE file gives build properties for the latest Jalview release. Java 1.1 Applet build made easier and donotobfuscate property controls execution of obfuscator Build target for generating source distribution Debug flag for javacc .jalview_properties file is documented (slightly) in jalview.bin.Cache	selected region output includes visible annotations (for certain formats) edit label/displaychar contains existing label/char for editing update PDBEntries when DBRefEntries change (vamsas) shorter peptide product names from EMBL records Newick string generator makes compact representations bootstrap values parsed correctly for tree files with comments pathological filechooser bug avoided by not allowing filenames containing a ':' Fixed exception when parsing GFF files containing global sequence features Alignment datasets are finalized only when number of references from alignment sequences goes to zero Close of tree branch colour box without colour selection causes cascading exceptions occasional negative imgwidth exceptions better reporting of non-fatal warnings to user when file parsing fails. Save works when Jalview project is default format Uniprot canonical names introduced for both das and vamsas Histidine should be midblue (not pink!) in Zappo error messages passed up and output when data read fails edit undo recovers previous dataset sequence when sequence is edited allow PDB files without pdb ID HEADER lines (like those generated by MODELLER) to be read in properly annotation consisting of sequence associated scores can be read and written correctly to annotation file Aligned cDNA translation to aligned peptide works correctly Fixed display of hidden sequence markers and non-italic font for representatives in Applet Applet Menus are always embedded in applet window on Macs. Newly shown features appear at top of stack (in Applet) Annotations added via parameter not drawn properly due to null pointer exceptions Secondary structure lines are drawn starting from first column of alignment
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