Release History

From 247b4f59aad27b654fb55268b55645dc6496f12e Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 30 Apr 2010 14:10:29 +0000 Subject: [PATCH 1/1] tidying for 2.5 release --- help/html/releases.html | 763 +---------------------------------------------- 1 file changed, 1 insertion(+), 762 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index 19bd13a..e18e273 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -15,765 +15,4 @@ * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . ---!> - -Release History - - -

Release History

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- Release -	- New Features -	- Issues Resolved -
- 2.5 - 30/4/2010 -	- New Capabilities - - URL links generated from description line for - regular-expression based URL links (applet and application) - Non-positional feature URL links are shown in link menu - Linked viewing of nucleic acid sequences and structures - Automatic Scrolling option in View menu to display the - currently highlighted region of an alignment. - Order an alignment by sequence length, or using the average score or total feature count for each sequence. - Shading features by score or associated description - Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection). - New hide/show options including Shift+Control+H to hide everything but the currently selected region. - - -Application - - Fetch DB References capabilities and UI expanded to support - retrieval from DAS sequence sources - Local DAS Sequence sources can be added via the command line - or via the Add local source dialog box. - DAS Dbref and DbxRef feature types are parsed as database - references and protein_name is parsed as description line (BioSapiens - terms). - Enable or disable non-positional feature and database - references in sequence ID tooltip from View menu in application. - - Group-associated consensus, sequence logos and conservation - plots - Symbol distributions for each column can be exported and - visualized as sequence logos - Optionally scale multi-character column labels to fit within - each column of annotation row - Optional automatic sort of associated alignment view when a - new tree is opened. - Jalview Java Console - New preference items for sequence ID tooltip and consensus - annotation - Client to submit sequences and IDs to Envision2 Workflows - Vamsas Capabilities - - Improved VAMSAS synchronization (jalview archive used to - preserve views, structures, and tree display settings) - Import of vamsas documents from disk or URL via command line - Sharing of selected regions between views and with other - VAMSAS applications (Experimental feature!) - Updated API to VAMSAS version 0.2 - - - -Applet - - Middle button resizes annotation row height - New Parameters - - sortByTree (true/false) - automatically sort the associated - alignment view by the tree when a new tree is opened. - showTreeBootstraps (true/false) - show or hide branch - bootstraps (default is to show them if available) - showTreeDistances (true/false) - show or hide branch lengths - (default is to show them if available) - showUnlinkedTreeNodes (true/false) - indicate if unassociated - nodes should be highlighted in the tree view - heightScale and widthScale (1.0 or more) - increase the - height or width of a cell in the alignment grid relative to the - current font size. - - - Non-positional features displayed in sequence ID tooltip - -Other - - Features format: graduated colour definitions and - specification of feature scores - Alignment Annotations format: new keywords for group - associated annotation (GROUP_REF) and annotation row display properties - (ROW_PROPERTIES) - XML formats extended to support graduated feature - colourschemes, group associated annotation, and profile visualization - settings. -	- - Source field in GFF files parsed as feature source rather - than description - Non-positional features are now included in sequence feature - and gff files (controlled via non-positional feature visibility in - tooltip). - URL links generated for all feature links (bugfix) - Added URL embedding instructions to features file - documentation. - Codons containing ambiguous nucleotides translated as 'X' in - peptide product - Match case switch in find dialog box works for both sequence - ID and sequence string and query strings do not have to be in upper - case to match case-insensitively. - AMSA files only contain first column of multi-character - column annotation labels - Jalview Annotation File generation/parsing consistent with - documentation (e.g. Stockholm annotation can be exported and - re-imported) - PDB files without embedded PDB IDs given a friendly name - Find incrementally searches ID string matches as well as - subsequence matches, and correctly reports total number of both. - Applet: - - - - - Application: - - Better handling of exceptions during sequence retrieval - Dasobert generated non-positional feature URL link text - excludes the start_end suffix (application) - PDB files retrieved from URLs are cached properly - Sequence description lines properly shared via VAMSAS - Sequence fetcher fetches multiple records for all data - sources - Ensured that command line das feature retrieval completes - before alignment figures are generated. - Reduced time taken when opening file browser for first time. - isAligned check prior to calculating tree, PCA or submitting - an MSA to JNet now excludes hidden sequences. - - - -
- 2.4.0.b2 - 28/10/2009 -	- - Experimental support for google analytics usage tracking. - Jalview privacy settings (user preferences and docs). - -	- - Race condition in applet preventing startup in jre1.6.0u12+. - Exception when feature created from selection beyond length - of sequence. - Allow synthetic PDB files to be imported gracefully - Sequence associated annotation rows associate with all - sequences with a given id - Find function matches case-insensitively for sequence ID - string searches - Non-standard characters do not cause pairwise alignment to - fail with exception - - Application Issues - - Sequences are now validated against EMBL database - Sequence fetcher fetches multiple records for all data - sources - - InstallAnywhere Issues - - Dock icon works for Mac OS X java (Mac 1.6 update issue with - installAnywhere mechanism) - Command line launching of JARs from InstallAnywhere version - (java class versioning error fixed) - -
- - 2.4 - 27/8/2008 -	User Interface - - Linked highlighting of codon and amino acid from translation - and protein products - Linked highlighting of structure associated with residue - mapping to codon position - Sequence Fetcher provides example accession numbers and - 'clear' button - MemoryMonitor added as an option under Desktop's Tools menu - Extract score function to parse whitespace separated numeric - data in description line - Column labels in alignment annotation can be centred. - Tooltip for sequence associated annotation give name of - sequence - - Web Services and URL fetching - - JPred3 web service - Prototype sequence search client (no public services - available yet) - Fetch either seed alignment or full alignment from PFAM - URL Links created for matching database cross references as - well as sequence ID - URL Links can be created using regular-expressions - - Sequence Database Connectivity - - Retrieval of cross-referenced sequences from other databases - - Generalised database reference retrieval and validation to - all fetchable databases - Fetch sequences from DAS sources supporting the sequence - command - - Import and Export - export annotation rows as CSV for spreadsheet import - Jalview projects record alignment dataset associations, EMBL - products, and cDNA sequence mappings - Sequence Group colour can be specified in Annotation File - Ad-hoc colouring of group in Annotation File using RGB - triplet as name of colourscheme - -VAMSAS Client capabilities (Experimental) - - 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 - -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 - -Applet-Application data exchange - - Trees passed as applet parameters can be passed to application - (when using "View in full application") - -Applet Parameters - - feature group display control parameter - debug parameter - showbutton parameter - -Applet API methods - - newView public method - Window (current view) specific get/set public methods - Feature display control methods - get list of currently selected sequences - -New Jalview distribution features - - InstallAnywhere Installer upgraded to IA 2008 VP1 - 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 - Continuous Build Integration for stable and development - version of Application, Applet and source distribution - - -	- - 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 - Save as dialog opened if current alignment format is not a - valid output 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 - allow reading of JPred concise files as a normal filetype - Stockholm annotation parsing and alignment properties import - fixed for PFAM records - Structure view windows have correct name in Desktop window - list - 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 - Uniprot XML import updated for new schema release in July 2008 - Sequence feature to sequence ID match for Features file is - case-insensitive - Sequence features read from Features file appended to all - sequences with matching IDs - PDB structure coloured correctly for associated views - containing a sub-sequence - PDB files can be retrieved by applet from Jar files - feature and annotation file applet parameters referring to - different directories are retrieved correctly - - Fixed application hang whilst waiting for splash-screen - version check to complete - Applet properly URLencodes input parameter values when passing - them to the launchApp service - display name and local features preserved in results retrieved - from web service - Visual delay indication for sequence retrieval and sequence - fetcher initialisation - updated Application to use DAS 1.53e version of dasobert DAS - client - Re-instated Full AMSA support and .amsa file association - Fixed parsing of JNet Concise annotation sans - sequences - -
- 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 - -

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