- <li>Group-associated consensus, sequence logos and conservation
- plots</li>
- <li>Symbol distributions for each column can be exported and
- visualized as sequence logos</li>
- <li>Optionally scale multi-character column labels to fit within
- each column of annotation row<!-- todo for applet --></li>
- <li>Optional automatic sort of associated alignment view when a
- new tree is opened.</li>
- <li>Jalview Java Console</li>
- <li>Better placement of desktop window when moving between
- different screens.</li>
- <li>New preference items for sequence ID tooltip and consensus
- annotation</li>
- <li>Client to submit sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a> Workflows</li>
- <li><em>Vamsas Capabilities</em>
- <ul>
- <li>Improved VAMSAS synchronization (Jalview archive used to
- preserve views, structures, and tree display settings)</li>
- <li>Import of vamsas documents from disk or URL via command
- line</li>
- <li>Sharing of selected regions between views and with other
- VAMSAS applications (Experimental feature!)</li>
- <li>Updated API to VAMSAS version 0.2</li>
- </ul>
- </li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>Middle button resizes annotation row height</li>
- <li>New Parameters
- <ul>
- <li>sortByTree (true/false) - automatically sort the associated
- alignment view by the tree when a new tree is opened.</li>
- <li>showTreeBootstraps (true/false) - show or hide branch
- bootstraps (default is to show them if available)</li>
- <li>showTreeDistances (true/false) - show or hide branch
- lengths (default is to show them if available)</li>
- <li>showUnlinkedTreeNodes (true/false) - indicate if
- unassociated nodes should be highlighted in the tree view</li>
- <li>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.</li>
- </ul>
- </li>
- <li>Non-positional features displayed in sequence ID tooltip</li>
- </ul>
- <em>Other</em>
- <ul>
- <li>Features format: graduated colour definitions and
- specification of feature scores</li>
- <li>Alignment Annotations format: new keywords for group
- associated annotation (GROUP_REF) and annotation row display
- properties (ROW_PROPERTIES)</li>
- <li>XML formats extended to support graduated feature
- colourschemes, group associated annotation, and profile visualization
- settings.</li>
- </td>
- <td>
- <ul>
- <li>Source field in GFF files parsed as feature source rather
- than description</li>
- <li>Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).</li>
- <li>URL links generated for all feature links (bugfix)</li>
- <li>Added URL embedding instructions to features file
- documentation.</li>
- <li>Codons containing ambiguous nucleotides translated as 'X' in
- peptide product</li>
- <li>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.</li>
- <li>AMSA files only contain first column of multi-character
- column annotation labels</li>
- <li>Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)</li>
- <li>PDB files without embedded PDB IDs given a friendly name</li>
- <li>Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.</li>
- <li>Application:
- <ul>
- <li>Better handling of exceptions during sequence retrieval</li>
- <li>Dasobert generated non-positional feature URL link text
- excludes the start_end suffix</li>
- <li>DAS feature and source retrieval buttons disabled when
- fetch or registry operations in progress.</li>
- <li>PDB files retrieved from URLs are cached properly</li>
- <li>Sequence description lines properly shared via VAMSAS</li>
- <li>Sequence fetcher fetches multiple records for all data
- sources</li>
- <li>Ensured that command line das feature retrieval completes
- before alignment figures are generated.</li>
- <li>Reduced time taken when opening file browser for first
- time.</li>
- <li>isAligned check prior to calculating tree, PCA or
- submitting an MSA to JNet now excludes hidden sequences.</li>
- <li>User defined group colours properly recovered from Jalview
- projects.</li>
- </ul>
- </li>
- </ul>
- </td>
+ <li>Group-associated consensus, sequence logos and
+ conservation plots</li>
+ <li>Symbol distributions for each column can be exported
+ and visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit
+ within each column of annotation row<!-- todo for applet -->
+ </li>
+ <li>Optional automatic sort of associated alignment view
+ when a new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving
+ between different screens.</li>
+ <li>New preference items for sequence ID tooltip and
+ consensus annotation</li>
+ <li>Client to submit sequences and IDs to Envision2
+ Workflows</li>
+ <li><em>Vamsas Capabilities</em>
+ <ul>
+ <li>Improved VAMSAS synchronization (Jalview archive
+ used to preserve views, structures, and tree display
+ settings)</li>
+ <li>Import of vamsas documents from disk or URL via
+ command line</li>
+ <li>Sharing of selected regions between views and
+ with other VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul></li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the
+ associated alignment view by the tree when a new tree is
+ opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide
+ branch bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide
+ branch lengths (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if
+ unassociated nodes should be highlighted in the tree
+ view</li>
+ <li>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.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID
+ tooltip</li>
+ </ul> <em>Other</em>
+ <ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display
+ properties (ROW_PROPERTIES)</li>
+ <li>XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile
+ visualization settings.</li></td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source
+ rather than description</li>
+ <li>Non-positional features are now included in sequence
+ feature and gff files (controlled via non-positional feature
+ visibility in tooltip).</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as
+ 'X' in peptide product</li>
+ <li>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.</li>
+ <li>AMSA files only contain first column of
+ multi-character column annotation labels</li>
+ <li>Jalview Annotation File generation/parsing consistent
+ with documentation (e.g. Stockholm annotation can be
+ exported and re-imported)</li>
+ <li>PDB files without embedded PDB IDs given a friendly
+ name</li>
+ <li>Find incrementally searches ID string matches as well
+ as subsequence matches, and correctly reports total number
+ of both.</li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence
+ retrieval</li>
+ <li>Dasobert generated non-positional feature URL
+ link text excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled
+ when fetch or registry operations in progress.</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via
+ VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ <li>Ensured that command line das feature retrieval
+ completes before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for
+ first time.</li>
+ <li>isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered
+ from Jalview projects.</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.4.0.b2</strong><br> 28/10/2009
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Experimental support for google analytics usage
+ tracking.</li>
+ <li>Jalview privacy settings (user preferences and docs).</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Race condition in applet preventing startup in
+ jre1.6.0u12+.</li>
+ <li>Exception when feature created from selection beyond
+ length of sequence.</li>
+ <li>Allow synthetic PDB files to be imported gracefully</li>
+ <li>Sequence associated annotation rows associate with
+ all sequences with a given id</li>
+ <li>Find function matches case-insensitively for sequence
+ ID string searches</li>
+ <li>Non-standard characters do not cause pairwise
+ alignment to fail with exception</li>
+ </ul> <em>Application Issues</em>
+ <ul>
+ <li>Sequences are now validated against EMBL database</li>
+ <li>Sequence fetcher fetches multiple records for all
+ data sources</li>
+ </ul> <em>InstallAnywhere Issues</em>
+ <ul>
+ <li>Dock icon works for Mac OS X java (Mac 1.6 update
+ issue with installAnywhere mechanism)</li>
+ <li>Command line launching of JARs from InstallAnywhere
+ version (java class versioning error fixed)</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+
+ <div align="center">
+ <strong>2.4</strong><br> 27/8/2008
+ </div>
+ </td>
+ <td><em>User Interface</em>
+ <ul>
+ <li>Linked highlighting of codon and amino acid from
+ translation and protein products</li>
+ <li>Linked highlighting of structure associated with
+ residue mapping to codon position</li>
+ <li>Sequence Fetcher provides example accession numbers
+ and 'clear' button</li>
+ <li>MemoryMonitor added as an option under Desktop's
+ Tools menu</li>
+ <li>Extract score function to parse whitespace separated
+ numeric data in description line</li>
+ <li>Column labels in alignment annotation can be centred.</li>
+ <li>Tooltip for sequence associated annotation give name
+ of sequence</li>
+ </ul> <em>Web Services and URL fetching</em>
+ <ul>
+ <li>JPred3 web service</li>
+ <li>Prototype sequence search client (no public services
+ available yet)</li>
+ <li>Fetch either seed alignment or full alignment from
+ PFAM</li>
+ <li>URL Links created for matching database cross
+ references as well as sequence ID</li>
+ <li>URL Links can be created using regular-expressions</li>
+ </ul> <em>Sequence Database Connectivity</em>
+ <ul>
+ <li>Retrieval of cross-referenced sequences from other
+ databases</li>
+ <li>Generalised database reference retrieval and
+ validation to all fetchable databases</li>
+ <li>Fetch sequences from DAS sources supporting the
+ sequence command</li>
+ </ul> <em>Import and Export</em>
+ <li>export annotation rows as CSV for spreadsheet import</li>
+ <li>Jalview projects record alignment dataset associations,
+ EMBL products, and cDNA sequence mappings</li>
+ <li>Sequence Group colour can be specified in Annotation
+ File</li>
+ <li>Ad-hoc colouring of group in Annotation File using RGB
+ triplet as name of colourscheme</li>
+ </ul> <em>VAMSAS Client capabilities (Experimental)</em>
+ <ul>
+ <li>treenode binding for VAMSAS tree exchange</li>
+ <li>local editing and update of sequences in VAMSAS
+ alignments (experimental)</li>
+ <li>Create new or select existing session to join</li>
+ <li>load and save of vamsas documents</li>
+ </ul> <em>Application command line</em>
+ <ul>
+ <li>-tree parameter to open trees (introduced for passing
+ from applet)</li>
+ <li>-fetchfrom command line argument to specify nicknames
+ of DAS servers to query for alignment features</li>
+ <li>-dasserver command line argument to add new servers
+ that are also automatically queried for features</li>
+ <li>-groovy command line argument executes a given groovy
+ script after all input data has been loaded and parsed</li>
+ </ul> <em>Applet-Application data exchange</em>
+ <ul>
+ <li>Trees passed as applet parameters can be passed to
+ application (when using "View in full
+ application")</li>
+ </ul> <em>Applet Parameters</em>
+ <ul>
+ <li>feature group display control parameter</li>
+ <li>debug parameter</li>
+ <li>showbutton parameter</li>
+ </ul> <em>Applet API methods</em>
+ <ul>
+ <li>newView public method</li>
+ <li>Window (current view) specific get/set public methods</li>
+ <li>Feature display control methods</li>
+ <li>get list of currently selected sequences</li>
+ </ul> <em>New Jalview distribution features</em>
+ <ul>
+ <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <li>RELEASE file gives build properties for the latest
+ Jalview release.</li>
+ <li>Java 1.1 Applet build made easier and donotobfuscate
+ property controls execution of obfuscator</li>
+ <li>Build target for generating source distribution</li>
+ <li>Debug flag for javacc</li>
+ <li>.jalview_properties file is documented (slightly) in
+ jalview.bin.Cache</li>
+ <li>Continuous Build Integration for stable and
+ development version of Application, Applet and source
+ distribution</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>selected region output includes visible annotations
+ (for certain formats)</li>
+ <li>edit label/displaychar contains existing label/char
+ for editing</li>
+ <li>update PDBEntries when DBRefEntries change (vamsas)</li>
+ <li>shorter peptide product names from EMBL records</li>
+ <li>Newick string generator makes compact representations</li>
+ <li>bootstrap values parsed correctly for tree files with
+ comments</li>
+ <li>pathological filechooser bug avoided by not allowing
+ filenames containing a ':'</li>
+ <li>Fixed exception when parsing GFF files containing
+ global sequence features</li>
+ <li>Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero</li>
+ <li>Close of tree branch colour box without colour
+ selection causes cascading exceptions</li>
+ <li>occasional negative imgwidth exceptions</li>
+ <li>better reporting of non-fatal warnings to user when
+ file parsing fails.</li>
+ <li>Save works when Jalview project is default format</li>
+ <li>Save as dialog opened if current alignment format is
+ not a valid output format</li>
+ <li>UniProt canonical names introduced for both das and
+ vamsas</li>
+ <li>Histidine should be midblue (not pink!) in Zappo</li>
+ <li>error messages passed up and output when data read
+ fails</li>
+ <li>edit undo recovers previous dataset sequence when
+ sequence is edited</li>
+ <li>allow PDB files without pdb ID HEADER lines (like
+ those generated by MODELLER) to be read in properly</li>
+ <li>allow reading of JPred concise files as a normal
+ filetype</li>
+ <li>Stockholm annotation parsing and alignment properties
+ import fixed for PFAM records</li>
+ <li>Structure view windows have correct name in Desktop
+ window list</li>
+ <li>annotation consisting of sequence associated scores
+ can be read and written correctly to annotation file</li>
+ <li>Aligned cDNA translation to aligned peptide works
+ correctly</li>
+ <li>Fixed display of hidden sequence markers and
+ non-italic font for representatives in Applet</li>
+ <li>Applet Menus are always embedded in applet window on
+ Macs.</li>
+ <li>Newly shown features appear at top of stack (in
+ Applet)</li>
+ <li>Annotations added via parameter not drawn properly
+ due to null pointer exceptions</li>
+ <li>Secondary structure lines are drawn starting from
+ first column of alignment</li>
+ <li>UniProt XML import updated for new schema release in
+ July 2008</li>
+ <li>Sequence feature to sequence ID match for Features
+ file is case-insensitive</li>
+ <li>Sequence features read from Features file appended to
+ all sequences with matching IDs</li>
+ <li>PDB structure coloured correctly for associated views
+ containing a sub-sequence</li>
+ <li>PDB files can be retrieved by applet from Jar files</li>
+ <li>feature and annotation file applet parameters
+ referring to different directories are retrieved correctly</li>
+ <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
+ <li>Fixed application hang whilst waiting for
+ splash-screen version check to complete</li>
+ <li>Applet properly URLencodes input parameter values
+ when passing them to the launchApp service</li>
+ <li>display name and local features preserved in results
+ retrieved from web service</li>
+ <li>Visual delay indication for sequence retrieval and
+ sequence fetcher initialisation</li>
+ <li>updated Application to use DAS 1.53e version of
+ dasobert DAS client</li>
+ <li>Re-instated Full AMSA support and .amsa file
+ association</li>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ sequences
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.3</strong><br> 9/5/07
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Jmol 11.0.2 integration</li>
+ <li>PDB views stored in Jalview XML files</li>
+ <li>Slide sequences</li>
+ <li>Edit sequence in place</li>
+ <li>EMBL CDS features</li>
+ <li>DAS Feature mapping</li>
+ <li>Feature ordering</li>
+ <li>Alignment Properties</li>
+ <li>Annotation Scores</li>
+ <li>Sort by scores</li>
+ <li>Feature/annotation editing in applet</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Headless state operation in 2.2.1</li>
+ <li>Incorrect and unstable DNA pairwise alignment</li>
+ <li>Cut and paste of sequences with annotation</li>
+ <li>Feature group display state in XML</li>
+ <li>Feature ordering in XML</li>
+ <li>blc file iteration selection using filename # suffix</li>
+ <li>Stockholm alignment properties</li>
+ <li>Stockhom alignment secondary structure annotation</li>
+ <li>2.2.1 applet had no feature transparency</li>
+ <li>Number pad keys can be used in cursor mode</li>
+ <li>Structure Viewer mirror image resolved</li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.2.1</strong><br> 12/2/07
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Non standard characters can be read and displayed
+ <li>Annotations/Features can be imported/exported to the
+ applet via textbox
+ <li>Applet allows editing of sequence/annotation/group
+ name & description
+ <li>Preference setting to display sequence name in
+ italics
+ <li>Annotation file format extended to allow
+ Sequence_groups to be defined
+ <li>Default opening of alignment overview panel can be
+ specified in preferences
+ <li>PDB residue numbering annotation added to associated
+ sequences
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Applet crash under certain Linux OS with Java 1.6
+ installed
+ <li>Annotation file export / import bugs fixed
+ <li>PNG / EPS image output bugs fixed
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong>2.2</strong><br> 27/11/06
+ </div>
+ </td>
+ <td>
+ <ul>
+ <li>Multiple views on alignment
+ <li>Sequence feature editing
+ <li>"Reload" alignment
+ <li>"Save" to current filename
+ <li>Background dependent text colour
+ <li>Right align sequence ids
+ <li>User-defined lower case residue colours
+ <li>Format Menu
+ <li>Select Menu
+ <li>Menu item accelerator keys
+ <li>Control-V pastes to current alignment
+ <li>Cancel button for DAS Feature Fetching
+ <li>PCA and PDB Viewers zoom via mouse roller
+ <li>User-defined sub-tree colours and sub-tree selection
+
+
+
+
+
+
+ <li>'New Window' button on the 'Output to Text box'
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>New memory efficient Undo/Redo System
+ <li>Optimised symbol lookups and conservation/consensus
+ calculations
+ <li>Region Conservation/Consensus recalculated after
+ edits
+ <li>Fixed Remove Empty Columns Bug (empty columns at end
+ of alignment)
+ <li>Slowed DAS Feature Fetching for increased robustness.
+
+
+
+
+
+
+ <li>Made angle brackets in ASCII feature descriptions
+ display correctly
+ <li>Re-instated Zoom function for PCA
+ <li>Sequence descriptions conserved in web service
+ analysis results
+ <li>UniProt ID discoverer uses any word separated by
+ ∣
+ <li>WsDbFetch query/result association resolved
+ <li>Tree leaf to sequence mapping improved
+ <li>Smooth fonts switch moved to FontChooser dialog box.
+