X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=3599194881d07cbfeb1bbddef9d91fb371fc32d1;hb=8a33c09bdd60c4b0f1c85136d1f8596240151c67;hp=dc199d513573589f01cc47671921c07884cf87da;hpb=abdbbc1e70434680cc1e9237260354422f80ff15;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index dc199d5..3599194 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,4 +1,21 @@
+
Release History
@@ -17,577 +34,802 @@
-
|
- 2.4.1
- Not Yet Released
+
|
+ |
- - Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
-
- - URL links generated from description line for regular-expression based URL links (applet and application)
-
- - Non-positional features displayed in sequence ID tooltip on applet
-
- - Non-positional feature URL links are shown in link menu (applet and application)
-
-
- |
-
-
- - URL links generated for all feature links (bugfix)
- - Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)
- - Added URL embedding instructions to features file documentation.
-
- |
-
-
-
- |
- 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
+
- Alignment prettyprinter doesn't cope with long sequence IDs
- - 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)
+ clustalx colourscheme colours Ds preferentially when both
+ D+E are present in over 50% of the column
+ nucleic acid structures retrieved from PDB do not import
+ correctly
+ More columns get selected than were clicked on when a number
+ of columns are hidden
+ annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are present
+
+ Applet
+
+ - annotation panel disappears when annotation is
+ hidden/removed
+
+ Application
+
+ - Alignment view not redrawn properly when new alignment
+ opened where annotation panel is visible but no annotations are
+ present on alignment
+ - pasted region containing hidden columns is incorrectly
+ displayed in new alignment window
+ - Jalview slow to complete operations when stdout is flooded
+ (fix is to close the Jalview console)
+ - CSV output of consensus only includes the percentage of all
+ symbols if sequence logo display is enabled
+ - typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.
+ - inconsistent group submenu and Format submenu entry 'Un' or
+ 'Non'conserved
+ - Sequence feature settings are being shared by multiple
+ distinct alignments
+ - group annotation not recreated when tree partition is
+ changed
+ - double click on group annotation to select sequences does
+ not propagate to associated trees
+ - Mac OSX specific issues:
- - 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
+ - exception raised when mouse clicked on desktop window
+ background
+ - Desktop menu placed on menu bar and application name set
+ correctly
+ - sequence feature settings not wide enough for the save
+ feature colourscheme button
- 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
+
+ |
+
+ 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
+ - Better placement of desktop window when moving between different screens.
+ - 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.
+ - Application:
+
+ - Better handling of exceptions during sequence retrieval
+ - Dasobert generated non-positional feature URL link text
+ excludes the start_end suffix
+ - DAS feature and source retrieval buttons disabled when fetch
+ or registry operations in progress.
+ - 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.
+ - User defined group colours properly recovered from Jalview projects.
- |
+
+
+
+
|
- 2.04
- 24/8/05
+ 2.4.0.b2
+ 28/10/2009
|
- - Hold down mouse wheel & scroll to change font size
+ - Experimental support for google analytics usage tracking.
+ - Jalview privacy settings (user preferences and docs).
|
- - Improved JPred client reliability
- - Improved loading of Jalview files
+ - 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
- |
-
-
- |
- 2.03
- 18/8/05
- |
-
+ Application Issues
- - 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
+ - Sequences are now validated against EMBL database
+ - Sequence fetcher fetches multiple records for all data
+ sources
- |
-
+ InstallAnywhere Issues
- - InstallAnywhere download for Sparc Solaris
+ - 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)
|
|
- 2.02
- 18/7/05
+
+ 2.4
+ 27/8/2008
|
- |
-
+ | User Interface
- - Copy & Paste order of sequences maintains alignment
- order.
+ - 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
- |
-
-
- |
- 2.01
- 12/7/05
- |
-
+ Web Services and URL fetching
- - 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.
+ - 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
- - 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.
+ - Retrieval of cross-referenced sequences from other databases
-
- |
-
-
- |
- 2.0
- 20/6/05
- |
-
-
- |
- |
-
+ 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
+ |
+
+
+ |
+ |
+