<td>
<div align="center">
<strong><a name="Jalview2.7">2.7</a>
- </strong><br> <em>20/09/2011</em>
+ </strong><br> <em>27/09/2011</em>
</div></td>
<td><em>Application</em>
<ul>
- <li>tweaked default layout of web services menu</li>
- <li>view/alignment association menu to enable user to easily
+ <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
+ <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
+ <li>Annotation row column label formatting attributes stored
in project file</li>
- <li>annotation row order for auto-calculated annotation rows
+ <li>Annotation row order for auto-calculated annotation rows
preserved in jalview project file</li>
- <li>visual progress indication when Jalview state is saved
+ <li>Visual progress indication when Jalview state is saved
using Desktop window menu</li>
- <li>visual indication that command line arguments are still
+ <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
+ <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
+ <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>Update JGoogleAnalytics to latest release (0.3)</li>
<li>'view structures' 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
+ <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>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>'automaticScrolling' parameter</li>
- <li>allow sequences with partial ID string matches to be
+ <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>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>JalviewLite.js javascript library</li>
<li>Javascript callbacks for
<ul>
- <li>applet initialisation</li>
- <li>sequence/alignment mouse-overs and selections</li>
+ <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>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
+ <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>
<ul>
- <li>enable Jmol displays to be associated with multiple
+ <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
+ <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
+ <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>Add groovy test harness for bulk load testing to examples
</li>
- <li>groovy script to load and align a set of sequences using a
+ <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>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
+ <li>User defined colourscheme throws exception when current
built in colourscheme is saved as new scheme</li>
<li>AlignFrame->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
+ <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
+ <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>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
+ <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
+ <li>Visibility status of autocalculated annotation row not
preserved when project is loaded</li>
- <li>tree bootstraps are not preserved when saved as a jalview
+ <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
+ <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
+ <li>Duplicate group associated conservation or consensus
created on new view</li>
- <li>annotation scrollbar not displayed after 'show all
+ <li>Annotation scrollbar not displayed after 'show all
hidden annotation rows' option selected</li>
- <li>alignment quality not updated after alignment annotation
+ <li>Alignment quality not updated after alignment annotation
row is hidden then shown</li>
- <li>preserve colouring of structures coloured by sequences in pre
+ <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 'reset
+ <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>structures imported from file and saved in project get
+ <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
+ <li>Alignment height set incorrectly when lots of annotation
rows are displayed</li>
- <li>relative URLs in feature HTML text not resolved to
+ <li>Relative URLs in feature HTML text not resolved to
codebase</li>
- <li>view follows highlighting does not work for positions in
+ <li>View follows highlighting does not work for positions in
sequences</li>
<li><= 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
+ <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
+ <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
+ <li>Relative URLs for datasources assumed to be relative to
applet's codebase</li>
- <li>status bar not updated after finished searching and search
+ <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
+ <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
+ <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
+ <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>
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
+ <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>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>Sequence numbering not preserved in MSF alignment output</li>
<li>Jalview PDB file reader does not extract sequence from
nucleotide chains correctly</li>
- <li>annotation row height and visibility attributes not stored
- in jalview project</li>
- <li>structure colours not updated when tree partition changed
+ <li>Structure colours not updated when tree partition changed
in alignment</li>
- <li>sequence associated secondary structure not correctly
+ <li>Sequence associated secondary structure not correctly
parsed in interleaved stockholm</li>
- <li>colour by annotation dialog does not restore current state
+ <li>Colour by annotation dialog does not restore current state
</li>
<li>Hiding (nearly) all sequences doesn't work properly</li>
- <li>sequences containing lowercase letters are not properly
+ <li>Sequences containing lowercase letters are not properly
associated with their pdb files</li>
</ul> <em>Documentation and Development</em>
<ul>
<title>What's new ?</title>
</head>
<body>
-<p><strong>What's new ?</strong></p>
-<p>The Jalview 2.6.1 release fixes a number of minor bugs affecting
-Jalview operation, including issues affecting the import and export of
-PIR files and working with multiple multiple structure superpositions.
-For full details see the <a href="releases.html#Jalview2.6.1">Jalview
-2.6.1 release history</a>.</p>
-<p><strong>Highlights in Jalview Version 2.6</strong></p>
-<ul>
- <li><a href="webServices/JABAWS.html">JABA Web Services</a> for
- multiple alignment using:
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ The Jalview 2.7 release features new web services, and important
+ improvements to the way in which Jalview handles alignments and
+ associated PDB structures, as well as numerous minor improvements and
+ bug fixes. Version 2.7 of the JalviewLite applet also features a
+ significantly enhanced Javascript API enabling it to be more easily
+ integrated with javascript based web applications. <br /> For full
+ details see the <a href="releases.html#Jalview2.7">Jalview 2.7
+ release history</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview Desktop Version 2.7</strong>
+ </p>
<ul>
- <li>ClustalW</li>
- <li>MAFFT</li>
- <li>Muscle</li>
- <li>ProbCons</li>
- <li>T-COFFEE</li>
+ <li>New <a href="features/viewingpdbs.html">structure viewer
+ options</a>:
+ <ul>
+ <li>Colour and superimpose 3D structures of complexes and
+ multi-domain chains using several different alignments</li>
+ <li>Drag and drop to associate PDB files with sequences that
+ have the same name</li>
+ <li>Open and superimpose all associated structures for the
+ current selection</li>
+ </ul>
+ <li>New web services for <a href="webServices/shmr.html">alignment
+ analysis</a></li>
+ <li>Improved graphical user interface for <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>services.
+ </li>
+ <li>Sort associated alignment views option in tree viewer</li>
+ <li>Default colours for <a
+ href="colourSchemes/annotationColouring.html">shading alignment
+ by quantitative annotation</a>.
+ </li>
+ <li><a href="webServices/newsreader.html">Jalview Desktop RSS
+ reader</a> - following important updates at <a
+ href="http://www.jalview.org/feeds/desktop/rss">http://www.jalview.org/feeds/desktop/rss</a>
</ul>
- </li>
- <li>User modifiable alignment service parameters</li>
- <li>Visualization of superposed structures associated with protein
- or nucleotide sequence alignments.</li>
- <li>Export coordinates and projection as CSV from PCA viewer</li>
-</ul>
-<p><strong>Issues Resolved (a select list - see release
-history for details)</strong></p>
-<ul>
-
-</ul>
-<p>See the <a href="releases.html">Release History</a> page for
-details of all new features and resolved issues.</p>
+ <p>
+ <strong>Issues Resolved (a select list - see the <a
+ href="releases.html#Jalview2.7">release history</a> for full details)
+ </strong>
+ </p>
+ <p>
+ <strong>Issues in the Jalview Desktop</strong>
+ <ul>
+ <li>Problems viewing associated structures for sequences
+ retrieved from UNIPROT</li>
+ <li>Problems viewing Jalview projects from older versions in
+ version 2.6</li>
+ <li>Preservation of hidden annotation rows and tree bootstrap
+ values in projects</li>
+ <li>Newly added JABAWS servers not always visible in web services
+ menu</li>
+ </ul>
+ <strong>Issues specific to the JalviewLite Applet</strong>
+ <ul>
+ <li>Layout problems when lots of annotation rows are displayed</li>
+ <li><= shown as = in annotation row tooltip</li>
+ <li>export features raises exception when no features exist</li>
+ <li>relative URLs not handled properly when used in parameters
+ and annotation files</li>
+ </ul>
+ <strong>Issues affecting both applet and application</strong>
+ <ul>
+ <li>sequence numbering not preserved in MSF alignment output</li>
+ <li>sequence associated secondary structure not correctly parsed
+ in interleaved stockholm</li>
+ <li>sequences containing lowercase letters are not properly
+ associated with their pdb files</li>
+ <li>Jalview PDB file reader does not extract sequence from deoxy
+ nucleotide chains correctly</li>
+ <li>Sequence length given in alignment properties window is off
+ by 1</li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff