From d8e0a824988ef34a5ffdf0bd7347f27f0ec16d46 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 30 Apr 2010 15:51:33 +0000 Subject: [PATCH] 2.5 release notes --- help/html/releases.html | 760 +++++++++++++++++++++++++++++++++++++++++++++++ help/html/whatsNew.html | 109 +++---- 2 files changed, 819 insertions(+), 50 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index e18e273..a866c09 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -16,3 +16,763 @@ * * 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
    • +
  • 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.
      • +
    +
    • +
+
+
2.4.0.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
      • +
    +     		 
    +

     

    + + diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 6b7a758..4723a9a 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -21,60 +21,69 @@

    What's new ?

    -

    Highlights in Jalview Version 2.4

    +

    Highlights in Jalview Version 2.5

    +Jalview Desktop: + +JalviewLite: +

    Issues Resolved (a select list)

     

    -- 1.7.10.2