</td>
</tr>
<tr>
-
+
<td>
<div align="center"><strong>2.4.1</strong><br>
<em>Not Yet Released</em></div>
</td>
<td>
<ul>
- <li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li>
- <li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
- <li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
- </li>
- <li>URL links generated from description line for regular-expression based URL links (applet and application)
- </li>
- <li>Non-positional features displayed in sequence ID tooltip on applet
- </li>
- <li>Non-positional feature URL links are shown in link menu (applet and application)
- </li>
- <li>Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
- </li>
- <li>Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
- </li>
- <li>Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
- </li>
- <li>New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)</li>
- <li>Order an alignment in order of average feature score or total feature count</li>
+ <li>Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the command line
+ or via the Add local source dialog box.</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.</li>
+ <li>Parsing of Dbref and DbxRef feature types as database
+ references</li>
+ <li>URL links generated from description line for
+ regular-expression based URL links (applet and application)
+ <li>Non-positional feature URL links are shown in link menu</li>
+ <li>Linked viewing of nucleic acid sequences and structures</li>
+ <li>Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.</li>
+ <li>Optionally scale multi-character column labels to fit within each column<!-- todo for applet --></li>
+ <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
+ </ul>
+ <em>Vamsas Capabilities</em>
+ <ul>
+ <li>
+ <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>
+ <em>Application</em>
+ <ul>
+ <li>New hidden columns and rows and representatives capabilities
+ in annotations file (in progress - not yet fully implemented)</li>
+ <li>Order an alignment in order of average feature score or
+ total feature count</li>
+ <li>Shading features by score or associated description</li>
+ <li>Group-associated automatic and user-defined alignment
+ annotation</li>
+ <li>Symbol distributions for each column can be exported and
+ visualized as sequence logos</li>
+ <li>Optional automatic sort of associated alignment view when a
+ new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>parameter to enable automatic sort of associated alignment view when a
+ new tree is opened.</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>
+ </td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source rather
+ than description</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>PDB files without embedded PDB IDs given a friendly name</li>
+ <li>Applet:
+ <ul>
+ <li></li>
+ </ul>
+ </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 (application)</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>
+ </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>Better handling of exceptions during sequence retrieval</li>
- <li>URL links generated for all feature links (bugfix)</li>
- <li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
- <li>Added URL embedding instructions to features file documentation.</li>
- <li>Codons containing ambiguous nucleotides translated as 'X' in peptide product</li>
- <li>Sequence description lines properly shared via VAMSAS</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>Sequence fetcher fetches multiple records for all data sources</li>
+ <li>Experimental support for google analytics usage tracking.</li>
+ <li>Jalview privacy settings (user preferences and docs).</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>
+ <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>
+ <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>
+ </td>
</tr>
- <tr>
- <td>
-
+ <tr>
+ <td>
+
<div align="center"><strong>2.4</strong><br>
27/8/2008</div>
</td>
- <td>
- <em>User Interface</em>
- <ul>
+ <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>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>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>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>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 created for matching database cross references as
+ well as sequence ID</li>
<li>URL Links can be created using regular-expressions</li>
- </ul>
+ </ul>
<em>Sequence Database Connectivity</em>
- <ul>
+ <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>
+ <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
+ <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>
+ <em>Applet Parameters</em>
<ul>
- <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <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
<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>
+ <li>Continuous Build Integration for stable and development
+ version of Application, Applet and source distribution</li>
</ul>
-
+
</td>
<td>
<ul>
<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>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>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>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
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>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>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>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>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ sequences</li>
</ul>
</td>
</tr>
<tr>
- <td>
+ <td>
<div align="center"><strong>2.3</strong><br>
9/5/07</div>
</td>
git://source.jalview.org / jalview.git / commitdiff