X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=fc054dc81b7a95b01c117f4fbe7f0f98b7694fba;hb=27c23832c62a8ceb981973d72b1652d464efa096;hp=3d20be5986ed6b0d3ec1d335d63aa59e3753b266;hpb=3f3f50865b2c7459cb58801d66378001b2e653ac;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 3d20be5..fc054dc 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -33,30 +33,297 @@
 		<div align="center"><em><strong>Issues Resolved</strong></em></div>
 		</td>
 	</tr>
-	<tr>
+		<tr>
+			<td>
+				<div align="center">
+					<strong><a name="Jalview2.7">2.7</a>
+					</strong><br> <em>27/09/2011</em>
+				</div></td>
+			<td><em>Application</em>
+				<ul>
+					<li>Jalview Desktop News Reader</li>
+					<li>Tweaked default layout of web services menu</li>
+					<li>View/alignment association menu to enable user to easily
+						specify which alignment a multi-structure view takes its
+						colours/correspondences from</li>
+					<li>Allow properties file location to be specified as URL </li>
+						<li>Extend jalview project to preserve associations between
+							many alignment views and a single Jmol display</li>
+						<li>Store annotation row height in jalview project file</li>
+						<li>Annotation row column label formatting attributes stored
+							in project file</li>
+						<li>Annotation row order for auto-calculated annotation rows
+							preserved in jalview project file</li>
+						<li>Visual progress indication when Jalview state is saved
+							using Desktop window menu</li>
+						<li>Visual indication that command line arguments are still
+							being processed</li>
+						<li>Groovy script execution from URL</li>
+						<li>Colour by annotation default min and max colours in
+							preferences</li>
+						<li>Automatically associate PDB files dragged onto an
+							alignment with sequences that have high similarity and matching
+							IDs</li>
+						<li>Update JGoogleAnalytics to latest release (0.3)</li>
+						<li>&#39;view structures&#39; option to open many structures
+							in same window</li>
+						<li>Sort associated views menu option for tree panel</li>
+						<li>Group all JABA and non-JABA services for a particular
+							analysis function in its own submenu</li>
+				</ul> <em>Applet</em>
+			<ul>
+					<li>Userdefined and autogenerated annotation rows for groups</li>
+					<li>Adjustment of alignment annotation pane height</li>
+					<li>Annotation scrollbar for annotation panel</li>
+					<li>Drag to reorder annotation rows in annotation panel</li>
+					<li>&#39;automaticScrolling&#39; parameter</li>
+					<li>Allow sequences with partial ID string matches to be
+						annotated from GFF/jalview features files</li>
+					<li>Sequence logo annotation row in applet</li>
+					<li>Absolute paths relative to host server in applet
+						parameters are treated as such</li>
+					<li>New in the JalviewLite javascript API:
+						<ul>
+							<li>JalviewLite.js javascript library</li>
+							<li>Javascript callbacks for
+								<ul>
+									<li>Applet initialisation</li>
+									<li>Sequence/alignment mouse-overs and selections</li>
+								</ul>
+							</li>
+							<li>scrollTo row and column alignment scrolling functions</li>
+							<li>Select sequence/alignment regions from javascript</li>
+							<li>javascript structure viewer harness to pass messages
+								between Jmol and Jalview when running as distinct applets</li>
+							<li>sortBy method</li>
+							<li>Set of applet and application examples shipped with
+								documentation</li>
+							<li>New example to demonstrate jalviewLite and Jmol
+								javascript message exchange</li>
+						</ul>
+				</ul> <em>General</em>
+				<ul>
+					<li>Enable Jmol displays to be associated with multiple
+						multiple alignments</li>
+					<li>Option to automatically sort alignment with new tree</li>
+					<li>User configurable link to enable redirects to a
+						www.jalview.org mirror</li>
+					<li>Jmol colours option for Jmol displays</li>
+					<li>Configurable newline string when writing alignment and
+						other flat files</li>
+					<li>Allow alignment annotation description lines to contain
+						html tags</li>
+				</ul> <em>Documentation and Development</em>
+				<ul>
+					<li>Add groovy test harness for bulk load testing to examples
+					</li>
+					<li>Groovy script to load and align a set of sequences using a
+						web service before displaying the result in the Jalview desktop</li>
+					<li>Restructured javascript and applet api documentation</li>
+					<li>Ant target to publish example html files with applet archive</li>
+					<li>Netbeans project for building jalview from source</li>
+					<li>ant task to create online javadoc for jalview source</li>
+				</ul></td>
+			<td><em>Application</em>
+				<ul>
+					<li>User defined colourscheme throws exception when current
+						built in colourscheme is saved as new scheme</li>
+					<li>AlignFrame-&gt;Save in application pops up save dialog for
+						valid filename/format</li>
+					<li>Cannot view associated structure for Uniprot sequence</li>
+					<li>PDB file association breaks for Uniprot sequence P37173</li>
+					<li>Associate PDB from file dialog does not tell you which
+						sequence is to be associated with the file</li>
+					<li>Find All raises null pointer exception when query only
+						matches sequence IDs</li>
+					<li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
+					<li>Jalview project with Jmol views created with Jalview 2.4
+						cannot be loaded</li>
+					<li>Filetype associations not installed for webstart launch</li>
+					<li>Two or more chains in a single PDB file associated with
+						sequences in different alignments do not get coloured by their
+						associated sequence</li>
+					<li>Visibility status of autocalculated annotation row not
+						preserved when project is loaded</li>
+					<li>Annotation row height and visibility attributes not stored
+						in jalview project</li>
+					<li>Tree bootstraps are not preserved when saved as a jalview
+						project</li>
+					<li>Envision2 workflow tooltips are corrupted</li>
+					<li>Enabling show group conservation also enables colour by
+						conservation</li>
+					<li>Duplicate group associated conservation or consensus
+						created on new view</li>
+					<li>Annotation scrollbar not displayed after &#39;show all
+						hidden annotation rows&#39; option selected</li>
+					<li>Alignment quality not updated after alignment annotation
+						row is hidden then shown</li>
+					<li>Preserve colouring of structures coloured by sequences in pre
+						jalview 2.7 projects</li>
+					<li>Web service job parameter dialog is not laid out properly
+					</li>
+					<li>Web services menu not refreshed after &#39;reset
+						services&#39; button is pressed in preferences</li>
+					<li>Annotation off by one in jalview v2_3 example project</li>
+					<li>Structures imported from file and saved in project get
+						name like jalview_pdb1234.txt when reloaded</li>
+					<li>Jalview does not always retrieve progress of a JABAWS job
+						execution in full once it is complete</li>
+				</ul> <em>Applet</em>
+				<ul>
+					<li>Alignment height set incorrectly when lots of annotation
+						rows are displayed</li>
+					<li>Relative URLs in feature HTML text not resolved to
+						codebase</li>
+					<li>View follows highlighting does not work for positions in
+						sequences</li>
+					<li>&lt;= shown as = in tooltip</li>
+					<li>Export features raises exception when no features exist</li>
+					<li>Separator string used for serialising lists of IDs for
+						javascript api is modified when separator string provided as
+						parameter</li>
+					<li>Null pointer exception when selecting tree leaves for
+						alignment with no existing selection</li>
+					<li>Relative URLs for datasources assumed to be relative to
+						applet&#39;s codebase</li>
+					<li>Status bar not updated after finished searching and search
+						wraps around to first result</li>
+					<li>StructureSelectionManager instance shared between several
+						jalview applets causes race conditions and memory leaks</li>
+					<li>Hover tooltip and mouseover of position on structure not
+						sent from Jmol in applet</li>
+					<li>Certain sequences of javascript method calls to applet API
+						fatally hang browser</li>
+				</ul> <em>General</em>
+				<ul>
+					<li>View follows structure mouseover scrolls beyond position
+						with wrapped view and hidden regions</li>
+					<li>Find sequence position moves to wrong residue with/without
+						hidden columns</li>
+					<li>Sequence length given in alignment properties window is
+						off by 1</li>
+					<li>InvalidNumberFormat exceptions thrown when trying to
+						import PDB like structure files</li>
+					<li>Positional search results are only highlighted between
+						user-supplied sequence start/end bounds</li>
+					<li>End attribute of sequence is not validated</li>
+					<li>Find dialog only finds first sequence containing a given
+						sequence position</li>
+					<li>Sequence numbering not preserved in MSF alignment output</li>
+					<li>Jalview PDB file reader does not extract sequence from
+						nucleotide chains correctly</li>
+					<li>Structure colours not updated when tree partition changed
+						in alignment</li>
+					<li>Sequence associated secondary structure not correctly
+						parsed in interleaved stockholm</li>
+					<li>Colour by annotation dialog does not restore current state
+					</li>
+					<li>Hiding (nearly) all sequences doesn&#39;t work properly</li>
+					<li>Sequences containing lowercase letters are not properly
+						associated with their pdb files</li>
+				</ul> <em>Documentation and Development</em>
+				<ul>
+					<li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
+						tool</li>
+				</ul></td>
+		</tr>
+		<tr>
+			<td>
+				<div align="center">
+					<strong><a name="Jalview2.6.1">2.6.1</a>
+					</strong><br> <em>15/11/2010</em>
+				</div></td>
+			<td><em>Application</em>
+				<ul>
+					<li>New warning dialog when the Jalview Desktop cannot contact
+						web services</li>
+					<li>JABA service parameters for a preset are shown in service
+						job window</li>
+					<li>JABA Service menu entries reworded</li>
+				</ul></td>
+			<td>
+				<ul>
+					<li>Modeller PIR IO broken - cannot correctly import a pir
+						file emitted by jalview</li>
+					<li>Existing feature settings transferred to new alignment
+						view created from cut'n'paste</li>
+					<li>Improved test for mixed amino/nucleotide chains when
+						parsing PDB files</li>
+					<li>Consensus and conservation annotation rows occasionally
+						become blank for all new windows</li>
+					<li>Exception raised when right clicking above sequences in
+						wrapped view mode</li>
+				</ul> <em>Application</em>
+				<ul>
+					<li>multiple multiply aligned structure views cause cpu usage
+						to hit 100% and computer to hang</li>
+					<li>Web Service parameter layout breaks for long user
+						parameter names</li>
+					<li>Jaba service discovery hangs desktop if Jaba server is
+						down</li>
+				</ul></td>
+		</tr>
+		<tr>
 		<td>
 		<div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
-		<em>X/7/2010</em></div>
+		<em>26/9/2010</em></div>
 		</td>
-		<td>
+		<td><em>Application</em>
 		<ul>
-			<li>Changed minimum Java version required for Jalview<br>
-			When used with Jmol, JalviewLite needs at least Java 1.5<br>
-			The application needs at least 1.6.</li>
-			<li>Updated embedded Jmol to series 12.XX<br><strong>See note about use of applet with Jmol</strong></li>
-			
+			<li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
+			<strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
+			<li>Web Services preference tab</li>
+			<li>Analysis parameters dialog box and user defined preferences</li>
+			<li>Improved speed and layout of Envision2 service menu</li>
+			<li>Superpose structures using associated sequence alignment</li>
+			<li>Export coordinates and projection as CSV from PCA viewer</li>
 		</ul>
 		<em>Applet</em>
 		<ul>
-			<li></li>
+			<li>enable javascript: execution by the applet via the link out
+			mechanism</li>
+		</ul>
+		<em>Other</em>
+		<ul>
+			<li>Updated the Jmol Jalview interface to work with Jmol series
+			12</li>
+			<li>The Jalview Desktop and JalviewLite applet now require Java
+			1.5</li>
+			<li>Allow Jalview feature colour specification for GFF sequence
+			annotation files</li>
+			<li>New 'colour by label' keword in jalview feature file type
+			colour specification</li>
+			<li>New Jalview Desktop Groovy API method that allows a script
+			to check if it being run in an interactive session or in a batch
+			operation from the jalview command line</li>
+		</ul>
+		</td>
+		<td>
+		<ul>
+			<li>clustalx colourscheme colours Ds preferentially when both
+			D+E are present in over 50% of the column</li>
 		</ul>
+
 		<em>Application</em>
 		<ul>
-			<li>Jalview 2 Web Services</li>
-			<li>Web Services configuration tab in preferences</li>
+			<li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
+			selected Regions menu item</li>
+			<li>sequence fetcher replaces ',' for ';' when the ',' is part
+			of a valid accession ID</li>
+			<li>fatal OOM if object retrieved by sequence fetcher runs out
+			of memory</li>
+			<li>unhandled Out of Memory Error when viewing pca analysis
+			results</li>
+			<li>InstallAnywhere builds fail to launch on OS X java 10.5
+			update 4 (due to apple Java 1.6 update)</li>
+			<li>Installanywhere Jalview silently fails to launch</li>
+		</ul>
+		<em>Applet</em>
+		<ul>
+			<li>Jalview.getFeatureGroups() raises an
+			ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
 		</ul>
 		</td>
-		<td></td>
 	</tr>
 	<tr>
 		<td>
