X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Freleases.html;h=2d51647148790b1f8d7e7f117e3f2caaee111302;hb=e66bdc1c0086ab56c56979d9dc6635e81503eb84;hp=686940361ec725bb20d9b19a6f01c3570a429638;hpb=a982a778b288f91449c7a3f17d4e245f03479643;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index 6869403..2d51647 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -1,14 +1,14 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -33,7 +33,395 @@
 		<div align="center"><em><strong>Issues Resolved</strong></em></div>
 		</td>
 	</tr>
-	<tr>
+  <tr>
+   <td><div align="center">
+     <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
+    </div></td>
+   <td><em>Application</em>
+    <li>Support for JABAWS 2.0 Services (AACon alignment
+     conservation, protein disorder and Clustal Omega)</li>
+    <li>JABAWS server status indicator in Web Services preferences
+   </li>
+    <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
+     Jalview alignment window</li>
+    <li>Updated Jalview build and deploy framework for OSX mountain
+     lion, windows 7, and 8</li>
+    <li>Nucleotide substitution matrix for PCA that supports RNA
+     and ambiguity codes</li>
+
+    <li>Improved sequence database retrieval GUI</li>
+    <li>Support fetching and database reference look up against
+     multiple DAS sources (Fetch all from in 'fetch db refs')</li>
+    <li>Jalview project improvements
+     <ul>
+      <li>Store and retrieve the &#39;belowAlignment&#39; flag for
+       annotation</li>
+      <li>calcId attribute to group annotation rows on the
+       alignment</li>
+      <li>Store AACon calculation settings for a view in Jalview
+       project</li>
+
+     </ul>
+   </li>
+    <li>horizontal scrolling gesture support</li>
+    <li>Visual progress indicator when PCA calculation is running</li>
+    <li>Simpler JABA web services menus</li>
+    <li>visual indication that web service results are still being
+     retrieved from server</li>
+    <li>Serialise the dialogs that are shown when Jalview starts up
+     for first time</li>
+    <li>Jalview user agent string for interacting with HTTP
+     services</li>
+    <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
+     library</li>
+    <li>Examples directory and Groovy library included in
+     InstallAnywhere distribution</li>
+    </ul> <em>Applet</em>
+    <ul>
+     <li>RNA alignment and secondary structure annotation
+      visualization applet example</li>
+    </ul> <em>General</em>
+    <ul>
+     <li>Normalise option for consensus sequence logo</li>
+     <li>Reset button in PCA window to return dimensions to
+      defaults</li>
+     <li>Allow seqspace or Jalview variant of alignment PCA
+      calculation</li>
+     <li>PCA with either nucleic acid and protein substitution
+      matrices
+     <li>Allow windows containing HTML reports to be exported in
+      HTML</li>
+     <li>Interactive display and editing of RNA secondary structure
+      contacts</li>
+     <li>RNA Helix Alignment Colouring</li>
+     <li>RNA base pair logo consensus</li>
+     <li>Parse sequence associated secondary structure information
+      in Stockholm files</li>
+     <li>HTML Export database accessions and annotation information
+      presented in tooltip for sequences</li>
+     <li>Import secondary structure from LOCARNA clustalw style RNA
+      alignment files</li>
+     <li>import and visualise T-COFFEE quality scores for an
+      alignment</li>
+     <li>&#39;colour by annotation&#39; per sequence option to
+      shade each sequence according to its associated alignment
+      annotation</li>
+     <li>New Jalview Logo</li>
+    </ul> <em>Documentation and Development</em>
+    <ul>
+     <li>documentation for score matrices used in Jalview</li>
+     <li>New Website!</li>
+    </ul></td>
+   <td><em>Application</em>
+    <ul>
+     <li>PDB, Unprot and EMBL (ENA) databases retrieved via
+      wsdbfetch REST service</li>
+     <li>Stop windows being moved outside desktop on OSX</li>
+     <li>Filetype associations not installed for webstart launch</li>
+     <li>Jalview does not always retrieve progress of a JABAWS job
+      execution in full once it is complete</li>
+     <li>revise SHMR RSBS definition to ensure alignment is
+      uploaded via ali_file parameter</li>
+     <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
+     <li>View all structures superposed fails with exception</li>
+     <li>Jnet job queues forever if a very short sequence is
+      submitted for prediction</li>
+     <li>Cut and paste menu not opened when mouse clicked on
+      desktop window</li>
+     <li>Putting fractional value into integer text box in
+      alignment parameter dialog causes Jalview to hang</li>
+     <li>Structure view highlighting doesn&#39;t work on windows 7
+     </li>
+     <li>View all structures fails with exception shown in
+      structure view</li>
+     <li>Characters in filename associated with PDBEntry not
+      escaped in a platform independent way</li>
+     <li>Jalview desktop fails to launch with exception when using
+      proxy</li>
+     <li>Tree calculation reports &#39;you must have 2 or more
+      sequences selected&#39; when selection is empty</li>
+     <li>Jalview desktop fails to launch with jar signature failure
+      when java web start temporary file caching is disabled</li>
+     <li>DAS Sequence retrieval with range qualification results in
+      sequence xref which includes range qualification</li>
+     <li>Errors during processing of command line arguments cause
+      progress bar (JAL-898) to be removed</li>
+     <li>Replace comma for semi-colon option not disabled for DAS
+      sources in sequence fetcher</li>
+     <li>Cannot close news reader when JABAWS server warning dialog
+      is shown</li>
+     <li>Option widgets not updated to reflect user settings</li>
+     <li>Edited sequence not submitted to web service</li>
+     <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
+     <li>InstallAnywhere installer doesn&#39;t unpack and run on
+      OSX Mountain Lion</li>
+     <li>Annotation panel not given a scroll bar when sequences
+      with alignment annotation are pasted into the alignment</li>
+     <li>Sequence associated annotation rows not associated when
+      loaded from Jalview project</li>
+     <li>Browser launch fails with NPE on java 1.7</li>
+     <li>JABAWS alignment marked as finished when job was cancelled
+      or job failed due to invalid input</li>
+     <li>NPE with v2.7 example when clicking on Tree associated
+      with all views</li>
+     <li>Exceptions when copy/paste sequences with grouped
+      annotation rows to new window</li>
+    </ul> <em>Applet</em>
+    <ul>
+     <li>Sequence features are momentarily displayed before they
+      are hidden using hidefeaturegroups applet parameter</li>
+     <li>loading features via javascript API automatically enables
+      feature display</li>
+     <li>scrollToColumnIn javascript API method doesn&#39;t work</li>
+    </ul> <em>General</em>
+    <ul>
+     <li>Redundancy removal fails for rna alignment</li>
+     <li>PCA calculation fails when sequence has been selected and
+      then deselected</li>
+     <li>PCA window shows grey box when first opened on OSX</li>
+     <li>Letters coloured pink in sequence logo when alignment
+      coloured with clustalx</li>
+     <li>Choosing fonts without letter symbols defined causes
+      exceptions and redraw errors</li>
+     <li>Initial PCA plot view is not same as manually reconfigured
+      view</li>
+     <li>Grouped annotation graph label has incorrect line colour</li>
+     <li>Grouped annotation graph label display is corrupted for
+      lots of labels</li>
+    </ul>
+  </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>26/9/2010</em></div>
@@ -61,11 +449,11 @@
 			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
+			<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>
+			operation from the Jalview command line</li>
 		</ul>
 		</td>
 		<td>
@@ -209,7 +597,7 @@
 				href="webServices/index.html#envision2">Envision2</a> Workflows</li>
 			<li><em>Vamsas Capabilities</em>
 			<ul>
-				<li>Improved VAMSAS synchronization (jalview archive used to
+				<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>
