From: jprocter <Jim Procter>
Date: Fri, 30 Apr 2010 11:52:50 +0000 (+0000)
Subject: doc
X-Git-Tag: Release_2_5~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=de934b6dd40469cccd6298a8de15829233b4fd93;p=jalview.git

doc
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 724996d..19bd13a 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -37,9 +37,10 @@
 
 		<td>
 		<div align="center"><strong>2.5</strong><br>
-		<em>30th April 2010</em></div>
+		<em>30/4/2010</em></div>
 		</td>
 		<td>
+		<em>New Capabilities</em>
 		<ul>
 			<li>URL links generated from description line for
 			regular-expression based URL links (applet and application)
@@ -52,99 +53,121 @@
 			<li>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
 			<li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</li>
 			<!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
-		</ul>
-		<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>
-		<em>Application</em>
-		<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>DAS Dbref and DbxRef feature types are parsed as database
-			references and protein_name is parsed as description line (BioSapiens terms).</li>
-			<li>Enable or disable non-positional feature and database
-			references in sequence ID tooltip from View menu in application.</li>
+</ul>
+<em>Application</em>
+<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>DAS Dbref and DbxRef feature types are parsed as database
+	references and protein_name is parsed as description line (BioSapiens
+	terms).</li>
+	<li>Enable or disable non-positional feature and database
+	references in sequence ID tooltip from View menu in application.</li>
 	<!--			<li>New hidden columns and rows and representatives capabilities
 			in annotations file (in progress - not yet fully implemented)</li> -->
-			<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>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>
-		</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>
-		<li></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>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>
-				<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>
-			</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>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>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>
+			<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>
+		</ul>
+		</li>
+	</ul>
+	</td>
 
 	</tr>
 	<tr>
@@ -233,526 +256,523 @@
 		<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 &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>
-		<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>
+</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 &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>
+<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>
+</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
-			&amp; 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>&quot;Reload&quot; alignment
-			<li>&quot;Save&quot; 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 &#8739;
-			<li>WsDbFetch query/result association resolved
-			<li>Tree leaf to sequence mapping improved
-			<li>Smooth fonts switch moved to FontChooser dialog box.
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.1.1</strong><br>
-		12/9/06</div>
-		</td>
-		<td>
-		<ul>
-			<li>Copy consensus sequence to clipboard</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Image output - rightmost residues are rendered if sequence
-			id panel has been resized</li>
-			<li>Image output - all offscreen group boundaries are rendered</li>
-			<li>Annotation files with sequence references - all elements in
-			file are relative to sequence position</li>
-			<li>Mac Applet users can use Alt key for group editing</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.1</strong><br>
-		22/8/06</div>
-		</td>
-		<td>
-		<ul>
-			<li>MAFFT Multiple Alignment in default Web Service list</li>
-			<li>DAS Feature fetching</li>
-			<li>Hide sequences and columns</li>
-			<li>Export Annotations and Features</li>
-			<li>GFF file reading / writing</li>
-			<li>Associate structures with sequences from local PDB files</li>
-			<li>Add sequences to exisiting alignment</li>
-			<li>Recently opened files / URL lists</li>
-			<li>Applet can launch the full application</li>
-			<li>Applet has transparency for features (Java 1.2 required)</li>
-			<li>Applet has user defined colours parameter</li>
-			<li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Redundancy Panel reinstalled in the Applet</li>
-			<li>Monospaced font - EPS / rescaling bug fixed</li>
-			<li>Annotation files with sequence references bug fixed</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.08.1</strong><br>
-		2/5/06</div>
-		</td>
-		<td>
-		<ul>
-			<li>Change case of selected region from Popup menu</li>
-			<li>Choose to match case when searching</li>
-			<li>Middle mouse button and mouse movement can compress / expand
-			the visible width and height of the alignment</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Annotation Panel displays complete JNet results</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.08b</strong><br>
-		18/4/06</div>
-		</td>
-		<td>&nbsp;</td>
-		<td>
-		<ul>
-			<li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
-			<li>Righthand label on wrapped alignments shows correct value</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.08</strong><br>
-		10/4/06</div>
-		</td>
-		<td>
-		<ul>
-			<li>Editing can be locked to the selection area</li>
-			<li>Keyboard editing</li>
-			<li>Create sequence features from searches</li>
-			<li>Precalculated annotations can be loaded onto alignments</li>
-			<li>Features file allows grouping of features</li>
-			<li>Annotation Colouring scheme added</li>
-			<li>Smooth fonts off by default - Faster rendering</li>
-			<li>Choose to toggle Autocalculate Consensus On/Off</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Drag &amp; Drop fixed on Linux</li>
-			<li>Jalview Archive file faster to load/save, sequence
-			descriptions saved.</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.07</strong><br>
-		12/12/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>PDB Structure Viewer enhanced</li>
-			<li>Sequence Feature retrieval and display enhanced</li>
-			<li>Choose to output sequence start-end after sequence name for
-			file output</li>
-			<li>Sequence Fetcher WSDBFetch@EBI</li>
-			<li>Applet can read feature files, PDB files and can be used for
-			HTML form input</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>HTML output writes groups and features</li>
-			<li>Group editing is Control and mouse click</li>
-			<li>File IO bugs</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.06</strong><br>
-		28/9/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>View annotations in wrapped mode</li>
-			<li>More options for PCA viewer</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>GUI bugs resolved</li>
-			<li>Runs with -nodisplay from command line</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td height="63">
-		<div align="center"><strong>2.05b</strong><br>
-		15/9/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>Choose EPS export as lineart or text</li>
-			<li>Jar files are executable</li>
-			<li>Can read in Uracil - maps to unknown residue</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Known OutOfMemory errors give warning message</li>
-			<li>Overview window calculated more efficiently</li>
-			<li>Several GUI bugs resolved</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.05</strong><br>
-		30/8/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>Edit and annotate in &quot;Wrapped&quot; view</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Several GUI bugs resolved</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.04</strong><br>
-		24/8/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>Hold down mouse wheel &amp; scroll to change font size</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Improved JPred client reliability</li>
-			<li>Improved loading of Jalview files</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.03</strong><br>
-		18/8/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>Set Proxy server name and port in preferences</li>
-			<li>Multiple URL links from sequence ids</li>
-			<li>User Defined Colours can have a scheme name and added to
-			Colour Menu</li>
-			<li>Choose to ignore gaps in consensus calculation</li>
-			<li>Unix users can set default web browser</li>
-			<li>Runs without GUI for batch processing</li>
-			<li>Dynamically generated Web Service Menus</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>InstallAnywhere download for Sparc Solaris</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.02</strong><br>
-		18/7/05</div>
-		</td>
-		<td>&nbsp;</td>
-		<td>
-		<ul>
-			<li>Copy &amp; Paste order of sequences maintains alignment
-			order.</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.01</strong><br>
-		12/7/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>Use delete key for deleting selection.</li>
-			<li>Use Mouse wheel to scroll sequences.</li>
-			<li>Help file updated to describe how to add alignment
-			annotations.</li>
-			<li>Version and build date written to build properties file.</li>
-			<li>InstallAnywhere installation will check for updates at
-			launch of Jalview.</li>
-		</ul>
-		</td>
-		<td>
-		<ul>
-			<li>Delete gaps bug fixed.</li>
-			<li>FileChooser sorts columns.</li>
-			<li>Can remove groups one by one.</li>
-			<li>Filechooser icons installed.</li>
-			<li>Finder ignores return character when searching. Return key
-			will initiate a search.<br>
-			</li>
-		</ul>
-		</td>
-	</tr>
-	<tr>
-		<td>
-		<div align="center"><strong>2.0</strong><br>
-		20/6/05</div>
-		</td>
-		<td>
-		<ul>
-			<li>New codebase</li>
-		</ul>
-		</td>
-		<td>&nbsp;</td>
-	</tr>
+</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 &amp;
+		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>&quot;Reload&quot; alignment
+		<li>&quot;Save&quot; 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 &#8739;
+		<li>WsDbFetch query/result association resolved
+		<li>Tree leaf to sequence mapping improved
+		<li>Smooth fonts switch moved to FontChooser dialog box.
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.1.1</strong><br>
+	12/9/06</div>
+	</td>
+	<td>
+	<ul>
+		<li>Copy consensus sequence to clipboard</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Image output - rightmost residues are rendered if sequence id
+		panel has been resized</li>
+		<li>Image output - all offscreen group boundaries are rendered</li>
+		<li>Annotation files with sequence references - all elements in
+		file are relative to sequence position</li>
+		<li>Mac Applet users can use Alt key for group editing</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.1</strong><br>
+	22/8/06</div>
+	</td>
+	<td>
+	<ul>
+		<li>MAFFT Multiple Alignment in default Web Service list</li>
+		<li>DAS Feature fetching</li>
+		<li>Hide sequences and columns</li>
+		<li>Export Annotations and Features</li>
+		<li>GFF file reading / writing</li>
+		<li>Associate structures with sequences from local PDB files</li>
+		<li>Add sequences to exisiting alignment</li>
+		<li>Recently opened files / URL lists</li>
+		<li>Applet can launch the full application</li>
+		<li>Applet has transparency for features (Java 1.2 required)</li>
+		<li>Applet has user defined colours parameter</li>
+		<li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Redundancy Panel reinstalled in the Applet</li>
+		<li>Monospaced font - EPS / rescaling bug fixed</li>
+		<li>Annotation files with sequence references bug fixed</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.08.1</strong><br>
+	2/5/06</div>
+	</td>
+	<td>
+	<ul>
+		<li>Change case of selected region from Popup menu</li>
+		<li>Choose to match case when searching</li>
+		<li>Middle mouse button and mouse movement can compress / expand
+		the visible width and height of the alignment</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Annotation Panel displays complete JNet results</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.08b</strong><br>
+	18/4/06</div>
+	</td>
+	<td>&nbsp;</td>
+	<td>
+	<ul>
+		<li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+		<li>Righthand label on wrapped alignments shows correct value</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.08</strong><br>
+	10/4/06</div>
+	</td>
+	<td>
+	<ul>
+		<li>Editing can be locked to the selection area</li>
+		<li>Keyboard editing</li>
+		<li>Create sequence features from searches</li>
+		<li>Precalculated annotations can be loaded onto alignments</li>
+		<li>Features file allows grouping of features</li>
+		<li>Annotation Colouring scheme added</li>
+		<li>Smooth fonts off by default - Faster rendering</li>
+		<li>Choose to toggle Autocalculate Consensus On/Off</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Drag &amp; Drop fixed on Linux</li>
+		<li>Jalview Archive file faster to load/save, sequence
+		descriptions saved.</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.07</strong><br>
+	12/12/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>PDB Structure Viewer enhanced</li>
+		<li>Sequence Feature retrieval and display enhanced</li>
+		<li>Choose to output sequence start-end after sequence name for
+		file output</li>
+		<li>Sequence Fetcher WSDBFetch@EBI</li>
+		<li>Applet can read feature files, PDB files and can be used for
+		HTML form input</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>HTML output writes groups and features</li>
+		<li>Group editing is Control and mouse click</li>
+		<li>File IO bugs</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.06</strong><br>
+	28/9/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>View annotations in wrapped mode</li>
+		<li>More options for PCA viewer</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>GUI bugs resolved</li>
+		<li>Runs with -nodisplay from command line</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td height="63">
+	<div align="center"><strong>2.05b</strong><br>
+	15/9/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>Choose EPS export as lineart or text</li>
+		<li>Jar files are executable</li>
+		<li>Can read in Uracil - maps to unknown residue</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Known OutOfMemory errors give warning message</li>
+		<li>Overview window calculated more efficiently</li>
+		<li>Several GUI bugs resolved</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.05</strong><br>
+	30/8/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>Edit and annotate in &quot;Wrapped&quot; view</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Several GUI bugs resolved</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.04</strong><br>
+	24/8/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>Hold down mouse wheel &amp; scroll to change font size</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Improved JPred client reliability</li>
+		<li>Improved loading of Jalview files</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.03</strong><br>
+	18/8/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>Set Proxy server name and port in preferences</li>
+		<li>Multiple URL links from sequence ids</li>
+		<li>User Defined Colours can have a scheme name and added to
+		Colour Menu</li>
+		<li>Choose to ignore gaps in consensus calculation</li>
+		<li>Unix users can set default web browser</li>
+		<li>Runs without GUI for batch processing</li>
+		<li>Dynamically generated Web Service Menus</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>InstallAnywhere download for Sparc Solaris</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.02</strong><br>
+	18/7/05</div>
+	</td>
+	<td>&nbsp;</td>
+	<td>
+	<ul>
+		<li>Copy &amp; Paste order of sequences maintains alignment
+		order.</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.01</strong><br>
+	12/7/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>Use delete key for deleting selection.</li>
+		<li>Use Mouse wheel to scroll sequences.</li>
+		<li>Help file updated to describe how to add alignment
+		annotations.</li>
+		<li>Version and build date written to build properties file.</li>
+		<li>InstallAnywhere installation will check for updates at launch
+		of Jalview.</li>
+	</ul>
+	</td>
+	<td>
+	<ul>
+		<li>Delete gaps bug fixed.</li>
+		<li>FileChooser sorts columns.</li>
+		<li>Can remove groups one by one.</li>
+		<li>Filechooser icons installed.</li>
+		<li>Finder ignores return character when searching. Return key
+		will initiate a search.<br>
+		</li>
+	</ul>
+	</td>
+</tr>
+<tr>
+	<td>
+	<div align="center"><strong>2.0</strong><br>
+	20/6/05</div>
+	</td>
+	<td>
+	<ul>
+		<li>New codebase</li>
+	</ul>
+	</td>
+	<td>&nbsp;</td>
+</tr>
 </table>
 <p>&nbsp;</p>
 </body>