From: jprocter <Jim Procter>
Date: Mon, 14 Jun 2010 11:43:46 +0000 (+0000)
Subject: add patch for JAL-572 to release history
X-Git-Tag: Release_2_5_1~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c38e0656da581f385c49f712a689232040425b0a;p=jalview.git

add patch for JAL-572 to release history
---

diff --git a/help/html/releases.html b/help/html/releases.html
index 6784640..a968438 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -51,7 +51,11 @@
 			of columns are hidden</li>
 			<li>annotation label popup menu not providing correct
 			add/hide/show options when rows are hidden or none are present</li>
-			<li>Stockholm format shown in list of readable formats.</li>
+			<li>Stockholm format shown in list of readable formats, and
+			parser copes better with alignments from RFAM.</li>
+			<li>CSV output of consensus only includes the percentage of all
+			symbols if sequence logo display is enabled</li>
+
 		</ul>
 		<em>Applet</em>
 		<ul>
@@ -67,8 +71,6 @@
 			displayed in new alignment window</li>
 			<li>Jalview slow to complete operations when stdout is flooded
 			(fix is to close the Jalview console)</li>
-			<li>CSV output of consensus only includes the percentage of all
-			symbols if sequence logo display is enabled</li>
 			<li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 			selected Rregions menu item.</li>
 			<li>inconsistent group submenu and Format submenu entry 'Un' or
@@ -98,8 +100,7 @@
 		<div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
 		<em>30/4/2010</em></div>
 		</td>
-		<td>
-		<em>New Capabilities</em>
+		<td><em>New Capabilities</em>
 		<ul>
 			<li>URL links generated from description line for
 			regular-expression based URL links (applet and application)
@@ -107,125 +108,132 @@
 			<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>Order an alignment by sequence length, or using the average score or total feature count for each sequence.</li>
+			<li>Order an alignment by sequence length, or using the average
+			score or total feature count for each sequence.</li>
 			<li>Shading features by score or associated description</li>
-			<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>
+			<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>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
+		</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>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 <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>
 
 	</tr>
 	<tr>
@@ -314,523 +322,525 @@
 		<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>