From 247b4f59aad27b654fb55268b55645dc6496f12e Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 30 Apr 2010 14:10:29 +0000 Subject: [PATCH] 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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
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
    • -
    -
     
    -

     

    - - +--> -- 1.7.10.2