</div></td>
<td><em>Application</em>
<li>Support for JABAWS 2.0 Services (AACon alignment
- conservation, protein disorder and Clustal Omega) <!--[<a href='http://issues.jalview.org/browse/JAL-976'>JAL-976</a>] - Enhance Jalview desktop to support to JABAWS v2.0 services -->
- <!--[<a href='http://issues.jalview.org/browse/JAL-974'>JAL-974</a>]-->
- <!--[<a href='http://issues.jalview.org/browse/JAL-975'>JAL-975</a>]-->
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1060'>JAL-1060</a>] - -->JABAWS
- server status indicator in Web Services preferences
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-842'>JAL-842</a>] - -->VARNA
- (http://varna.lri.fr) viewer for RNA structures in Jalview
- alignment window
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1133'>JAL-1133</a>] - -->Updated
- jalview build and deploy framework for OSX mountain lion, windows
- 7, and 8
+ 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 <!--[<a href='http://issues.jalview.org/browse/JAL-1027'>JAL-1027</a>] -->
- </li>
+ 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')<!--[<a href='http://issues.jalview.org/browse/JAL-1061'>JAL-1061</a>], [<a href='http://issues.jalview.org/browse/JAL-1075'>JAL-1075</a>] - GUI elements to select one or several DAS sources to query for sequences or database references-->
- </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>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1109'>JAL-1109</a>] -->Store
- and retrieve the 'belowAlignment' flag for annotation
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1110'>JAL-1110</a>]-->calcId
- attribute to group annotation rows on the alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1136'>JAL-1136</a>] - -->Store
- AACon calculation settings for a view in Jalview project
- </li>
+ <li>Store and retrieve the 'belowAlignment' 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>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1160'>JAL-1160</a>] - -->horizontal
- scrolling gesture support
- </li>
- <li>Visual progress indicator when PCA calculation is running<!--[<a href='http://issues.jalview.org/browse/JAL-1120'>JAL-1120</a>] - -->
- </li>
- <li>Simpler JABA web services menus<!--[<a href='http://issues.jalview.org/browse/JAL-1137'>JAL-1137</a>] - -->
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1165'>JAL-1165</a>] - -->visual
- indication that web service results are still being retrieved from
- server
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1183'>JAL-1183</a>] - -->Serialise
- the dialogs that are shown when jalview starts up for first time
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1188'>JAL-1188</a>] - -->Jalview
- user agent string for interacting with HTTP services
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-972'>JAL-972</a>] - -->DAS
- 1.6 and DAS 2.0 source support using new JDAS client library
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1202'>JAL-1202</a>] - -->Examples
- directory and Groovy library included in InstallAnywhere
- distribution
- </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>
- <!--[<a href='http://issues.jalview.org/browse/JAL-963'>JAL-963</a>] - -->RNA
- alignment and secondary structure annotation visualization applet
- example
- </li>
+ <li>RNA alignment and secondary structure annotation
+ visualization applet example</li>
</ul> <em>General</em>
<ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-958'>JAL-958</a>] - -->Normalise
- option for consensus sequence logo
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1121'>JAL-1121</a>] - -->Reset
- button in PCA window to return dimensions to defaults
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1125'>JAL-1125</a>] - -->Allow
- seqspace or Jalview variant of alignment PCA calculation
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1013'>JAL-1013</a>] -->PCA
- with either nucleic acid and protein substitution matrices
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1157'>JAL-1157</a>] - -->Allow
- windows containing HTML reports to be exported in HTML
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-970'>JAL-970</a>] - -->Interactive
- display and editing of RNA secondary structure contacts
- </li>
+ <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>
- <!--[<a href='http://issues.jalview.org/browse/JAL-878'>JAL-878</a>] - -->Parse
- sequence associated secondary structure information in Stockholm
- files
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1015'>JAL-1015</a>] - -->HTML
- Export database accessions and annotation information presented in
- tooltip for sequences
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1052'>JAL-1052</a>] - -->Import
- secondary structure from LOCARNA clustalw style RNA alignment
- files
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1065'>JAL-1065</a>] - [<a href='http://issues.jalview.org/browse/JAL-1078'>JAL-1078</a>]-->import
- and visualise T-COFFEE quality scores for an alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1066'>JAL-1066</a>] - -->'colour
- by annotation' per sequence option to shade each sequence
- according to its associated alignment annotation
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1130'>JAL-1130</a>] - -->New
- Jalview Logo
- </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>'colour by annotation' 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>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1167'>JAL-1167</a>] - -->documentation
- for score matrices used in Jalview
- </li>
+ <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<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] - -->
- <!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] - -->Stop
- windows being moved outside desktop on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] - -->Filetype
- associations not installed for webstart launch
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] - -->Jalview
- does not always retrieve progress of a JABAWS job execution in
- full once it is complete
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-979'>JAL-979</a>] - -->revise
- SHMR RSBS definition to ensure alignment is uploaded via ali_file
- parameter
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-980'>JAL-980</a>] - -->Jalview
- 2.7 is incompatible with Jmol-12.2.2
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] - -->View
- all structures superposed fails with exception
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] - -->Jnet
- job queues forever if a very short sequence is submitted for
- prediction
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1004'>JAL-1004</a>] - -->Cut
- and paste menu not opened when mouse clicked on desktop window
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1010'>JAL-1010</a>] - -->Putting
- fractional value into integer text box in alignment parameter
- dialog causes jalview to hang
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] - -->Structure
- view highlighting doesn't work on windows 7
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1023'>JAL-1023</a>] - -->View
- all structures fails with exception shown in structure view
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1025'>JAL-1025</a>] - -->Characters
- in filename associated with PDBEntry not escaped in a platform
- independent way
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] - -->Jalview
- desktop fails to launch with exception when using proxy
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] - -->Tree
- calculation reports 'you must have 2 or more sequences
- selected' when selection is empty
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1040'>JAL-1040</a>] - -->Jalview
- desktop fails to launch with jar signature failure when java web
- start temporary file caching is disabled
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] - -->DAS
- Sequence retrieval with range qualification results in sequence
- xref which includes range qualification
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1087'>JAL-1087</a>] - -->Errors
- during processing of command line arguments cause progress bar
- (JAL-898) to be removed
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1097'>JAL-1097</a>] - -->Replace
- comma for semi-colon option not disabled for DAS sources in
- sequence fetcher
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] - -->Cannot
- close news reader when JABAWS server warning dialog is shown
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1127'>JAL-1127</a>] - -->Option
- widgets not updated to reflect user settings
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] - -->Edited
- sequence not submitted to web service
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] - -->Jalview
- 2.7 Webstart does not launch on mountain lion
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1135'>JAL-1135</a>] - -->InstallAnywhere
- installer doesn't unpack and run on OSX Mountain Lion
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] - -->Annotation
- panel not given a scroll bar when sequences with alignment
- annotation are pasted into the alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] - -->Sequence
- associated annotation rows not associated when loaded from jalview
- project
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] - -->Browser
- launch fails with NPE on java 1.7
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1171'>JAL-1171</a>] - -->JABAWS
- alignment marked as finished when job was cancelled or job failed
- due to invalid input
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1185'>JAL-1185</a>] - -->NPE
- with v2.7 example when clicking on Tree associated with all views
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] - -->Exceptions
- when copy/paste sequences with grouped annotation rows to new
- window
+ 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'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 'you must have 2 or more
+ sequences selected' 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'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>
- <!--[<a href='http://issues.jalview.org/browse/JAL-962'>JAL-962</a>] - -->Sequence
- features are momentarily displayed before they are hidden using
- hidefeaturegroups applet parameter
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-965'>JAL-965</a>] - -->loading
- features via javascript API automatically enables feature display
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1170'>JAL-1170</a>] - -->scrollToColumnIn
- javascript API method doesn't work
- </li>
+ <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't work</li>
</ul> <em>General</em>
<ul>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] - -->Redundancy
- removal fails for rna alignment
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1032'>JAL-1032</a>] - -->PCA
- calculation fails when sequence has been selected and then
- deselected
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1033'>JAL-1033</a>] - -->PCA
- window shows grey box when first opened on OSX
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1086'>JAL-1086</a>] - -->Letters
- coloured pink in sequence logo when alignment coloured with
- clustalx
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1099'>JAL-1099</a>] - -->Choosing
- fonts without letter symbols defined causes exceptions and redraw
- errors
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1123'>JAL-1123</a>] - -->Initial
- PCA plot view is not same as manually reconfigured view
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1153'>JAL-1153</a>] - -->Grouped
- annotation graph label has incorrect line colour
- </li>
- <li>
- <!--[<a href='http://issues.jalview.org/browse/JAL-1155'>JAL-1155</a>] - -->Grouped
- annotation graph label display is corrupted for lots of labels
- </li>
+ <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>
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
+ <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>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>
+ 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
<li>Drag to reorder annotation rows in annotation panel</li>
<li>'automaticScrolling' parameter</li>
<li>Allow sequences with partial ID string matches to be
- annotated from GFF/jalview features files</li>
+ 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>sortBy method</li>
<li>Set of applet and application examples shipped with
documentation</li>
- <li>New example to demonstrate jalviewLite and Jmol
+ <li>New example to demonstrate JalviewLite and Jmol
javascript message exchange</li>
</ul>
</ul> <em>General</em>
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>
+ 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>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>
+ <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>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
+ 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
<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>
+ 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 'reset
services' button is pressed in preferences</li>
- <li>Annotation off by one in jalview v2_3 example project</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
<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>
+ 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
<td>
<ul>
<li>Modeller PIR IO broken - cannot correctly import a pir
- file emitted by jalview</li>
+ 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
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>
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>
git://source.jalview.org / jalview.git / commitdiff