of memory. A future release of Jalview will be able to avoid this by
executing the calculation via a web service.</p>
-<p><strong>About PCA</strong>Principal components analysis is a technique for examining the
+<p><strong>About PCA</strong></p>
+<p>Principal components analysis is a technique for examining the
structure of complex data sets. The components are a set of dimensions
formed from the measured values in the data set, and the principle
component is the one with the greatest magnitude, or length. The sets of
href="scorematrices.html#simplenucleotide">simple single
nucleotide substitution matrix</a>. The options available for
calculation are given in the
- <strong><em>Change Parameters</em></strong> menu.<br /> Jalview allows
- two types of PCA calculation. The default
- <em><strong>Jalview PCA Calculation</strong></em> mode (indicated when
- that option is ticked in the
- <strong><em>Change Parameters</em></strong> menu) of the viewer
- performs PCA on a matrix where elements in the upper diagonal give the
- sum of scores for mutating in one direction, and the lower diagonal is
- the sum of scores for mutating in the other. For protein substitution
- models like BLOSUM62, this gives an asymmetric matrix, and a different
- PCA to one produced with the method described in the paper by G.
- Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2,
- February 1995 (<a
+ <strong><em>Change Parameters</em></strong> menu.</p>
+ <p>
+ <em>PCA Calculation modes</em><br/>
+ The default Jalview calculation mode
+ (indicated when <em><strong>Jalview PCA Calculation</strong></em> is
+ ticked in the <strong><em>Change Parameters</em></strong> menu) is to
+ perform a PCA on a matrix where elements in the upper diagonal give
+ the sum of scores for mutating in one direction, and the lower
+ diagonal is the sum of scores for mutating in the other. For protein
+ substitution models like BLOSUM62, this gives an asymmetric matrix,
+ and a different PCA to a matrix produced with the method described in the
+ paper by G. Casari, C. Sander and A. Valencia. Structural Biology
+ volume 2, no. 2, February 1995 (<a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
- and implemented at the SeqSpace server at the EBI. The original method
- preconditions the matrix by multiplying it with its transpose, and
- this mode is enabled by unchecking the
- <strong><em>Jalview PCA Calculation</em></strong> option in the
- <strong><em>Change Parameters</em></strong> menu.
+ and implemented at the SeqSpace server at the EBI. This method
+ preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the <strong><em>Jalview
+ PCA Calculation</em></strong> option in the <strong><em>Change
+ Parameters</em></strong> menu.
</p>
-<img src="pcaviewer.gif">
+ <img src="pcaviewer.gif">
<p><strong>The PCA Viewer</strong></p>
<p>This is an interactive display of the sequences positioned within
the similarity space, as points in a rotateable 3D scatterplot. The
<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
- <tr>
+ <tr>
<td><div align="center">
- <strong><a name="Jalview.2.8.1">2.8.1</a><br />
- <em>20/5/2014</em></strong>
+ <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>3/6/2014</em></strong>
</div></td>
<td>
<!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
<ul>
- <li>Internationalisation of user interface (usually called i18n support) and
- translation for Spanish locale</li>
+ <li>Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale</li>
<li>Define/Undefine group on current selection with
Ctrl-G/Shift Ctrl-G</li>
- <li>Improved group creation/removal options in alignment/sequence Popup menu</li>
-
+ <li>Improved group creation/removal options in
+ alignment/sequence Popup menu</li>
+
</ul> <em>Application</em>
- <ul>
+ <ul>
<li>Interactive consensus RNA secondary structure prediction
VIENNA RNAAliFold JABA 2.1 service</li>
<li>Select columns containing particular features from Feature
Settings dialog</li>
<li>View all 'representative' PDB structures for selected
sequences</li>
- <li>Update Jalview project format:<ul><li>
- Preserve sequence and annotation dataset (to store secondary structure annotation,etc)
- </li><li>Per group and alignment annotation and RNA helix colouring</li></ul></li>
- <li>New similarity measures for PCA and Tree calculation (PAM250) </li>
- <li>Experimental support for retrieval and viewing of flanking
- regions for an alignment</li>
+ <li>Update Jalview project format:
+ <ul>
+ <li>Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)</li>
+ <li>Per group and alignment annotation and RNA helix
+ colouring</li>
+ </ul>
+ </li>
+ <li>New similarity measures for PCA and Tree calculation
+ (PAM250)</li>
+ <li>Experimental support for retrieval and viewing of flanking
+ regions for an alignment</li>
</ul> <em>Applet</em>
- <ul>
+ <ul>
</ul> <em>Other improvements</em>
- <li>Sensible precision for symbol distribution percentages shown in logo tooltip.</li>
- <li>Annotation panel height set according to amount of annotation when alignment first opened</li>
+ <li>Sensible precision for symbol distribution percentages
+ shown in logo tooltip.</li>
+ <li>Annotation panel height set according to amount of
+ annotation when alignment first opened</li>
</ul>
</td>
<td>
<!-- issues resolved --> <em>Application</em>
- <ul>
+ <ul>
<li>logo keeps spinning and status remains at queued or
running after job is cancelled</li>
- <li>cannot export features from alignments imported from Jalview/VAMSAS projects</li>
- <li>buggy slider for web service parameters that take float
+ <li>cannot export features from alignments imported from
+ Jalview/VAMSAS projects</li>
+ <li>Buggy slider for web service parameters that take float
values</li>
<li>Newly created RNA secondary structure line doesn't have
'display all symbols' flag set</li>
- <li>T-COFFEE alignment score shading scheme and other annotation shading not saved in
- jalview project</li>
+ <li>T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in jalview project</li>
<li>Local file cannot be loaded in freshly downloaded Jalview</li>
- <li>??? unresolved ??? Jalview icon not shown on dock in
- Mountain Lion/Webstart</li>
+ <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
<li>Load file from desktop file browser fails</li>
<li>Occasional NPE thrown when calculating large trees</li>
- <li>cannot reorder or slide sequences after dragging an
+ <li>Cannot reorder or slide sequences after dragging an
alignment onto desktop</li>
<li>Colour by annotation dialog throws NPE after using
'extract scores' function</li>
<li>Loading/cut'n'pasting an empty file leads to a grey
alignment window</li>
<li>Disorder thresholds rendered incorrectly after performing
- iupred disorder prediction</li>
+ IUPred disorder prediction</li>
<li>Multiple group annotated consensus rows shown when
changing 'normalise logo' display setting</li>
- <li>Annotation/RNA Helix colourschemes cannot be applied to alignment
- with groups (2.8.0b1)</li>
- <li>find shows blank dialog after 'finished searching' if nothing matches query</li>
- <li>Null Pointer Exceptions raised when sorting by feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 --></li>
- <li>Errors in Jmol console when structures in alignment don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol --></li>
- <li>Not all working JABAWS services are shown in Jalview's menu</li>
- <li>JAVAWS version of jalview fails to launch with 'invalid literal/length code'</li>
+ <li>Find shows blank dialog after 'finished searching' if
+ nothing matches query</li>
+ <li>Null Pointer Exceptions raised when sorting by feature
+ with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
+ </li>
+ <li>Errors in Jmol console when structures in alignment don't
+ overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
+ </li>
+ <li>Not all working JABAWS services are shown in Jalview's
+ menu</li>
+ <li>JAVAWS version of jalview fails to launch with 'invalid
+ literal/length code'</li>
+ <li>Annotation/RNA Helix colourschemes cannot be applied to
+ alignment with groups (actually fixed in 2.8.0b1)</li>
+ <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
+
</ul> <em>Applet</em>
<ul>
- <li>
- <li>Remove group option shown in applet when selection is not a group</li>
+ <li>Remove group option is shown even when selection is not a
+ group</li>
<li>Apply to all groups ticked but colourscheme changes don't
affect groups</li>
+ <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
+ <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
+ <li>Increased font size for dropdown menus on OSX and embedded windows</li>
</ul> <em>Other</em>
- <ul>
- <li>Consensus sequence for alignments/groups with a single sequence were not calculated</li>
+ <ul>
+ <li>Consensus sequence for alignments/groups with a single
+ sequence were not calculated</li>
<li>annotation files that contain only groups imported as
annotation and junk sequences</li>
<li>Fasta files with sequences containing '*' incorrectly
affect background (2.8.0b1)
<li></li>
<li>redundancy highlighting is erratic at 0% and 100%</li>
- <li>remove gapped columns fails for sequences with ragged
+ <li>Remove gapped columns fails for sequences with ragged
trailing gaps</li>
- <li>AMSA annotation row with leading spaces is not registered correctly on import</li>
- <li>Jalview crashes when selecting PCA analysis for certain alignments</li>
- <li>Opening the colour by annotation dialog for an existing annotation based 'use original colours' colourscheme loses original colours setting</li>
+ <li>AMSA annotation row with leading spaces is not registered
+ correctly on import</li>
+ <li>Jalview crashes when selecting PCA analysis for certain
+ alignments</li>
+ <li>Opening the colour by annotation dialog for an existing
+ annotation based 'use original colours' colourscheme loses
+ original colours setting</li>
</ul>
</td>
</tr>
- <tr>
+ <tr>
<td><div align="center">
<strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
</div>
</head>
<body>
<p>
- <strong>What's new ?</strong><br /> Jalview 2.8.1 includes a range of new features developed in the last 12 months. <br /> As usual you can find the
+ <strong>What's new ?</strong></p>
+ <p>Jalview 2.8.1 includes a range of new features developed over the last 12 months. <br /> As usual you can find the
highlights below, and the comprehensive list is given in the <a
href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
</p>
- <strong>Internationalisation</strong>
- <p>
- In August 2013, David Roldán-Martinez took on the task of
+ <p>The Desktop and web based applet include new keystrokes for
+ defining and undefining groups, and PAM250 has been added to the range
+ of score models available for use by the tree and PCA calculations.
+ The Jalview project file format has also been extended for handling
+ RNA and protein secondary structure annotation, in anticipation for
+ new structure based secondary structure support in Jalview 2.8.2.</p>
+ <p><strong>Internationalisation</strong></p>
+ <p>Jalview 2.8.1 is the first release to include support for
+ displaying Jalview's user interface in different languages. In August
+ 2013, David Roldán-Martinez took on the task of
internationalising Jalview's user interface. He also recruited Sara
- Hernández Díaz and Laura Ferrandis Martinez who created Jalview's
- first spanish user interface translation.</p><p>If you notice any
- problems, or would like to help translate Jalview's user interface
- into other languages, head over to <a href="http://issues.jalview.org">issues.jalview.org</a>
- and put in a feature request describing the translations you can
- provide to the <a
+ Hernández Díaz and Laura Ferrandis Martinez who created
+ Jalview's first spanish user interface translation.</p>
+ <p>
+ If you notice any problems, or would like to help translate Jalview's
+ user interface into other languages, head over to <a
+ href="http://issues.jalview.org">issues.jalview.org</a> and put in a
+ feature request describing the translations you can provide to the <a
href="http://issues.jalview.org/browse/JAL/component/10682">i18n
- component</a>. David has also <a href="https://wiki.jalview.org/index.php/Development:i18n">documented the process of creating i18n translations</a> to help you get started.
+ component</a>. David has also <a
+ href="https://wiki.jalview.org/index.php/Development:i18n">documented
+ the process of creating i18n translations</a> to help you get started.
+ </p>
+ <p><strong>RNA Secondary Structure Prediction with JABA 2.1</strong></p>
+ <p>
+ This version of Jalview includes a client to access the new services available in <a
+ href="http://www.compbio.dundee.ac.uk/jaba">JABA v2.1</a> , which
+ provides services for RNA consensus secondary structure prediction and
+ two new alignment programs (<a
+ href="http://sourceforge.net/projects/glprobs/">GLProbs</a> and <a
+ href="http://sourceforge.net/projects/msaprobs/">MSAProbs</a>).</p>
+ <p>
+ To see how to perform RNA secondary structure predictions like the one below, take a look at the <a href="webServices/RNAalifold.html">RNAAliFold
+ client documentation</a>.
</p>
- <strong>Enhancements and new features</strong>
- <ul>
- <li>
- <li>Extended the feature settings dialog to <a href="features/featuresettings.html#selectbyfeature">select columns containing particular sequence features.</a></li>
- </ul>
- <strong>Bug fixes</strong>
- <ul>
- </ul>
+ <div align="center">
+ <img src="webServices/RNAalifoldAnnotationRows.png" width="500" height="216"> <br> <em>The RNAalifold client was implemented by Jalview's 2013
+ summer student, Dan Barton.</em>
+ </div>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff