JAL-1503 documentation and release notes

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 49019a7..ba9dc30 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -32,7 +32,8 @@ for very large sets of sequences - usually because the JVM has run out
 of memory. A future release of Jalview will be able to avoid this by
 executing the calculation via a web service.</p>
 
 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
 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

@@ -52,26 +53,26 @@ of variation in the data set.</p>
                        href="scorematrices.html#simplenucleotide">simple single
                        nucleotide substitution matrix</a>. The options available for
                calculation are given in the
                        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>)
                        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>
        </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
        <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

diff --git a/help/html/releases.html b/help/html/releases.html
index a240a49..1eb7abf 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -34,85 +34,106 @@
                <div align="center"><em><strong>Issues Resolved</strong></em></div>
                </td>
        </tr>
                <div align="center"><em><strong>Issues Resolved</strong></em></div>
                </td>
        </tr>

-  <tr>
+               <tr>

                        <td><div align="center">
                        <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>
                                </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>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> <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>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> <em>Applet</em>

-                       <ul>
+                               <ul>

 
                                </ul> <em>Other improvements</em>
 
                                </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>
                        </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>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>
                                                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>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>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
                                                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>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>
                                </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>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> <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
                                        <li>annotation files that contain only groups imported as
                                                annotation and junk sequences</li>
                                        <li>Fasta files with sequences containing '*' incorrectly

@@ -121,15 +142,19 @@
                                                affect background (2.8.0b1)
                                        <li></li>
                                        <li>redundancy highlighting is erratic at 0% and 100%</li>
                                                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>
                                                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>
                                </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>
        <td><div align="center">
        <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
        </div>

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 639a2cf..21b67eb 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -22,30 +22,49 @@
 </head>
 <body>
        <p>
 </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>
                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 Rold&aacute;n-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 Rold&aacute;n-Martinez took on the task of

                internationalising Jalview's user interface. He also recruited Sara
                internationalising Jalview's user interface. He also recruited Sara

-               Hern&aacute;ndez D&iacute;az 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
+               Hern&aacute;ndez D&iacute;az 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
                        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>
        </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>

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