From bceeb43df6587f5b9bf33660c1f4992f8ed4cc8c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 30 Mar 2010 17:49:49 +0000
Subject: [PATCH] group autoannotation and consensus display, annotation label
 scale to width, etc.

---
 help/html/releases.html |  351 +++++++++++++++++++++++++++++------------------
 1 file changed, 220 insertions(+), 131 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index 19c6d53..dd90b65 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -17,156 +17,231 @@
 		</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 &quot;View in full application&quot;)</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
@@ -175,9 +250,10 @@
 			<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>
@@ -202,7 +278,8 @@
 			<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>
@@ -211,9 +288,10 @@
 			<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
@@ -226,25 +304,36 @@
 			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>
-- 
1.7.10.2