<td>file2</td>
<td>fileName</td>
<td>A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
- is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (<em>since 2.9</em>).</td>
+ matches the translation of one of the nucleotide sequences, then alignments will be displayed linked in a Split Frame. Parameter is ignored if enableSplitFrame is set to false (<em>since 2.9</em>).</td>
+ </tr>
+ <tr>
+ <td>enableSplitFrame</td>
+ <td>true or false (default true)</td>
+ <td>Enable or disable the display of linked cDNA and Protein alignments in a split frame (<em>since 2.9</em>).</td>
</tr>
<tr>
<td>sequence1,<br>
<param name="embedded"
value="true"> </li>
</ul>
+
+ <p><strong>**NEW FEATURES** in Jalview 2.9</strong></p>
+ <ul>
+ <li>Split Views for cDNA and Protein alignments<br/>Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
+ </li>
+ </ul>
+ </p>
<p><strong>**NEW FEATURES** in Jalview 2.8</strong></p>
<ul>
<li>Normalised sequence logo display
</table>
<p><strong><a name="pam250">PAM250</a></strong><br/>
<em><strong>P</strong>ercentage <strong>A</strong>ccepted <strong>M</strong>utation matrix. PAM250 estimates substitutions after 250% of sites have changed (each site can be mutated multple times).<br/>
-Jalview 2.8.1 introduced support for PAM250 based <a href="../calculations/pca.html">PCA</a> and <a href="../calculations/trees.html">tree</a> calculations.</em>
+Jalview 2.8.1 introduced support for PAM250 based <a href="../calculations/pca.html">PCA</a> and <a href="../calculations/tree.html">tree</a> calculations.</em>
<table border="1">
<tr><td></td><td> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </td></tr>
<tr><td>A</td><td>2</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>0</td><td>1</td><td>0</td><td>-2</td><td>1</td><td>1</td><td>0</td><td>0</td><td>-6</td><td>0</td><td>-3</td><td>0</td></tr>
On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.</p>
<p><strong><em>Realign a Split View</em></strong></p>
-<p>If you invoke a web service to realign either half of a Split Frame, then the resulting realignment is displayed in a new
-Split Frame.</p>
-<ul>
-<li>the alignment you chose to realign (for example, peptide) is displayed as aligned by the external web service</li>
-<li>Jalview 'aligns' its complement (in this case, cDNA) similarly, by inserting corresponding gaps
- <ul>
- <li>NB this is <em>not</em> the same as aligning the complement using the external service, which may give different results</li>
- </ul>
-</li>
-</ul>
-
-<p><strong><em>Applet</em></strong></p>
-<p>To see a split frame view in the Jalview applet, provide these applet parameters:
-<table border="1">
-<tr><th>Parameter</th><th>Value</th><th>Description</th>
-<tr><td>file</td><td>path to an alignment file</td><td>a cDNA (or protein) alignment</td>
-<tr><td>file</td><td>path to an alignment file</td><td>a protein (or cDNA) alignment</td>
-<tr><td>enableSplitFrame</td><td>true</td><td>to enable the Split Frame feature</td>
-</table>
-<p/>If compatible sequences are present in the input alignments, Jalview will open a Split Frame view.<br/>
-If not, only the first alignment will be opened (an error message is written to the Java console).
-
- <p>
+ <p>If you invoke a web service to realign either half of a Split
+ Frame, then the resulting realignment is displayed in a new Split
+ Frame.
+ </p>
+ <ul>
+ <li>the alignment you chose to realign (for example, peptide)
+ is displayed as aligned by the external web service</li>
+ <li>Jalview reconstructs the alignment of its complement (in
+ this case, cDNA) by inserting gaps in the corresponding positions</li>
+ </ul>
+ <p><strong>Reconstructed Alignments</strong>
+ Reconstructed alignments are typically <em>not</em>
+ the same as the alignment produced by aligning the complement
+ sequence set directly with the external service. However, in the
+ case of protein alignments, a reconstructed cDNA alignment is often
+ more reliable than one calculated without coding information.
+ Reconstructed cDNA alignments are also more informative than the
+ original protein alignment when calculating phylogenetic trees or
+ performing other kinds of molecular evolution analysis.
+ </p>
+ <p>
<em>Split Frame Views were introduced in Jalview 2.9</em>
</p>
- <p>
- Example files for cDNA/Protein: <a
- href="http://www.jalview.org/builds/nextrel/examples/estrogenReceptorProtein.fa">estrogenReceptorProtein.fa</a>
- and <a
- href="http://www.jalview.org/builds/nextrel/examples/estrogenReceptorCdna.fa">estrogenReceptorCdna.fa</a>
- taken from xxx.
- </p>
</body>
</html>
</div>
</td>
</tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview.2.9">2.9</a><br /> <em>1/9/2015</em></strong>
- </div></td>
- <td><em>General</em>
- <ul>
- </ul> <em>Application</em>
- <ul>
- </ul>
- <em>Applet</em>
- <ul>
- </ul>
- </td>
- <td>
- <em>General</em>
- <ul>
- <li>Make selection for columns now works on marked columns
- rather than columns in rubber-band selection region.</li>
- </ul>
- <!-- issues resolved -->
- <em>Application</em>
- <ul>
- </ul>
- <!-- <em>Applet</em>
- <ul>
- </ul> <em>General</em>
- <ul>
- </ul>--> <em>Deployment and Documentation</em>
- <ul>
- </ul> <em>Application Known issues</em>
- <ul>
- </ul> <em>Applet Known Issues</em>
- <ul>
- </ul>
- </td>
- </tr>
- <tr>
+ <tr>
+ <td><div align="center">
+ <strong><a name="Jalview.2.9">2.9</a><br /> <em>9/9/2015</em></strong>
+ </div></td>
+ <td><em>General</em>
+ <ul>
+ <li>Linked visualisation and analysis of DNA and Protein
+ alignments:
+ <ul>
+ <li>Translated cDNA alignments shown as split protein
+ and DNA alignment views</li>
+ <li>Codon consensus annotation for linked protein and
+ cDNA alignment views</li>
+ <li>Link cDNA or Protein product sequences by loading
+ them onto Protein or cDNA alignments</li>
+ <li>Reconstruct linked cDNA alignment from aligned
+ protein sequences</li>
+ </ul>
+ </li>
+ <li>Jmol integration updated to Jmol v14.2.14</li>
+ <li>Import and export of Jalview alignment views as <a href="">BioJSON</a></li>
+ <li>New alignment annotation file statements for
+ reference sequences and marking hidden columns</li>
+ <li>Assign an alignment reference sequence to highlight
+ variation</li>
+ <li>Select or hide columns according to alignment
+ annotation</li>
+ <li>Find option for locating sequences by
+ description</li>
+ <li>Conserved physicochemical properties shown in amino
+ acid conservation row</li>
+ <li>Alignments can be sorted by number of RNA helices</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Optional embedding of BioJSON data when exporting
+ alignment figures to HTML</li>
+ <li>New Export Settings dialog to control hidden region
+ export in flat file generation</li>
+ <li>New cDNA/Protein analysis capabilities
+ <ul>
+ <li>Get Cross-References should open a Split Frame
+ view with cDNA/Protein</li>
+ <li>Detect when nucleotide sequences and protein
+ sequences are placed in the same alignment</li>
+ <li>Split cDNA/Protein views are saved in Jalview
+ projects</li>
+ </ul>
+ </li>
+
+ <li>Use REST API to talk to Chimera</li>
+ <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
+
+ <li>Calculate UPGMA and NJ trees using sequence feature
+ similarity</li>
+
+ <li>VARNA RNA viewer updated to v3.93</li>
+ <li>VARNA views are saved in Jalview
+ Projects</li>
+ <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
+
+ <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
+ <li>change "View protein structure" menu option to "3D Structure ..."</li>
+
+ <li>Make groups for selection uses marked columns as well
+ as the active selected region</li>
+
+ <li>allow different similarity matrix calculations for
+ tree building and PCA</li>
+
+ <li>Export alignment views for display with the <a
+ href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+
+ <li>Export scrollable SVG in HTML page</li>
+
+ <li>Interactive free text and structured queries with the
+ PDBe Search API for PDB data retrieval</li>
+ <li>PDBe Search API based discovery and selection of PDB structures to
+ view for a sequence set</li>
+
+ <li>JPred4 employed for protein secondary structure
+ predictions</li>
+ <li>Hide Insertions menu option to hide unaligned columns
+ for one or a group of sequences</li>
+ <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
+ <li>(Nearly) Native 'Quaqua' dialogs for browsing file
+ system on OSX<br />LGPL libraries courtesy of <a
+ href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
+ </li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
+ <li>New example demonstrating linked viewing of cDNA and
+ Protein alignments</li>
+ <li>New layout for applet example pages</li>
+ </ul>
+ <em>Development and deployment</em>
+ <li>Java 1.7 minimum requirement for Jalview 2.9</li>
+ <li>Include installation type and git revision in build
+ properties and console log output</li>
+ <li>Github project and web URL for storing BioJsMSA
+ Templates</li>
+ <li>Jalview's unit tests now managed with TestNG</li></td>
+ <td>
+ <!-- <em>General</em>
+ <ul>
+ </ul> -->
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+ <li>Escape should close any open find dialogs</li>
+ <li>Typo in select-by-features status report</li>
+ <li>Consensus RNA secondary secondary structure
+ predictions are not highlighted in amber</li>
+ <li>Missing gap character in v2.7 example file means
+ alignment appears unaligned when pad-gaps is not enabled</li>
+ <li>First switch to RNA Helices colouring doesn't colour
+ associated structure views</li>
+ <li>ID width preference option is greyed out when auto
+ width checkbox not enabled</li>
+ <li>Stopped a warning dialog from being shown when
+ creating user defined colours</li>
+ <li>'View Mapping' in structure viewer shows sequence
+ mappings for just that viewer's sequences</li>
+ <li>Workaround for superposing PDB files containing
+ multiple models in Chimera</li>
+ <li>Report sequence position in status bar when hovering
+ over Jmol structure</li>
+ <li>Cannot output gaps as '.' symbols with Selection ->
+ output to text box</li>
+ <li>Flat file exports of alignments with hidden columns
+ have incorrect sequence start/end</li>
+ <li>'Aligning' a second chain to a Chimera structure from
+ Jalview fails</li>
+ <li>Colour schemes applied to structure viewers don't
+ work for nucleotide</li>
+ <li>Loading/cut'n'pasting an empty or invalid file leads
+ to a grey/invisible alignment window</li>
+ <li>Exported Jpred annotation from a sequence region
+ imports to different position</li>
+ <li>Space at beginning of sequence feature tooltips shown
+ on some platforms</li>
+ <li>Chimera viewer 'View | Show Chain' menu is not
+ populated</li>
+ <li>'New View' fails with a Null Pointer Exception in
+ console if Chimera has been opened</li>
+ <li>Mouseover to Chimera not working</li>
+ <li>Miscellaneous ENA XML feature qualifiers not
+ retrieved</li>
+ <li>NPE in annotation renderer after 'Extract Scores'</li>
+ <li>If two structures in one Chimera window, mouseover of
+ either sequence shows on first structure</li>
+ <li>'Show annotations' options should not make
+ non-positional annotations visible</li>
+ <li>Subsequence secondary structure annotation not shown
+ in right place after 'view flanking regions'</li>
+ <li>File Save As type unset when current file format is
+ unknown</li>
+ <li>Save as '.jar' option removed for saving Jalview
+ projects</li>
+ <li>Colour by Sequence colouring in Chimera more
+ responsive</li>
+ <li>Cannot 'add reference annotation' for a sequence in
+ several views on same alignment</li>
+ <li>Cannot show linked products for EMBL / ENA records</li>
+ <li>Jalview's tooltip wraps long texts containing no
+ spaces</li>
+ </ul> <em>Applet</em>
+ <li>Jmol to JalviewLite mouseover/link not working</li>
+ <li>JalviewLite can't import sequences with ID descriptions
+ containing angle brackets</li>
+ <ul>
+ </ul> <em>General</em>
+ <ul>
+ <li>Cannot export and reimport RNA secondary structure
+ via jalview annotation file</li>
+ <li>Random helix colour palette for colour by annotation
+ with RNA secondary structure</li>
+ <li>Mouseover to cDNA from STOP residue in protein
+ translation doesn't work.</li>
+ <li>hints when using the select by annotation dialog box</li>
+ <li>Jmol alignment incorrect if PDB file has alternate CA
+ positions</li>
+ <li>FontChooser message dialog appears to hang after
+ choosing 1pt font</li>
+ <li>Peptide secondary structure incorrectly imported from
+ annotation file when annotation display text includes 'e' or
+ 'h'</li>
+ <li>Cannot set colour of new feature type whilst creating
+ new feature</li>
+ <li>cDNA translation alignment should not be sequence
+ order dependent</li>
+ <li>'Show unconserved' doesn't work for lower case
+ sequences</li>
+ <li>Nucleotide ambiguity codes involving R not recognised</li>
+ </ul> <em>Deployment and Documentation</em>
+ <ul>
+ <li>Applet example pages appear different to the rest of
+ www.jalview.org</li>
+ </ul> <em>Application Known issues</em>
+ <ul>
+ <li>Incomplete sequence extracted from PDB entry 3a6s</li>
+ <li>Misleading message appears after trying to delete
+ solid column.</li>
+ <li>Jalview icon not shown in dock after InstallAnywhere
+ version launches</li>
+ <li>Fetching EMBL reference for an RNA sequence results
+ fails with a sequence mismatch</li>
+ <li>Corrupted or unreadable alignment display when
+ scrolling alignment to right</li>
+ <li>ArrayIndexOutOfBoundsException thrown when remove
+ empty columns called on alignment with ragged gapped ends</li>
+ <li>auto calculated alignment annotation rows do not get
+ placed above or below non-autocalculated rows</li>
+ <li>Jalview dekstop becomes sluggish at full screen in
+ ultra-high resolution</li>
+ <li>Cannot disable consensus calculation independently of
+ quality and conservation</li>
+ <li>Mouseover highlighting between cDNA and protein can
+ become sluggish with more than one splitframe shown</li>
+ </ul> <em>Applet Known Issues</em>
+ <ul>
+ <li>Core PDB parsing code requires Jmol</li>
+ <li>Sequence canvas panel goes white when alignment
+ window is being resized
+ <li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
<li>RNA pseudoknot annotation can be
imported/exported/displayed</li>
<li>'colour by annotation' can colour by RNA and
- protein secondary structure</li>
+ protein secondary structure</li>
+ <li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
+
</ul> <em>Application</em>
<ul>
<li>Extract and display secondary structure for sequences with
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong>
- </p>
- <p>
- Jalview 2.8.2 is the first release produced by our new core
- development team.<br /> It incorporates many minor improvements and
- bug-fixes, and new features for working with 3D structure data,
- shading alignments by secondary structure and generation of alignment
- figures as Scalable Vector Graphics. <br />The majority of
- improvements in this version of Jalview concern the desktop
- application. As ever, the highlights are detailed below,
- and the full list is given in the <a
- href="releases.html#Jalview.2.8.2">Jalview 2.8.2 Release Notes</a>.
- </p>
- <p>
- <strong>Annotation visualisation</strong> <br /> The alignment window
- includes a new <em>Annotations</em> menu which provides controls for
- the layout and display of sequence, group and alignment associated
- annotation rows. It also now includes the <em>Autocalculated
- Annotation</em> submenu (formerly located in the View menu), which
- includes settings for the calculation and display of sequence
- consensus, logos, and amino acid conservation for the alignment and
- subgroups.
- </p>
- <p>
- <strong>Sequence associated annotation</strong><br /> New controls
- have also been added to the Sequence ID popup menu for the propagation
- and display of sequence associated annotation such as secondary
- structure assignments and disorder predictions. Annotation associated
- with one or a group of sequence already shown on the alignment may be
- shown or hidden, and any available annotation from 3D structure or
- calculations performed in other Jalview windows can be copied to the
- alignment
- <em>via</em> the <strong>Add Reference Annotation</strong> option.<br />
- The <strong>Colour by annotation</strong> function has also been
- improved, allowing secondary structure annotation to be used to shade
- sequences and alignment columns. Protein sequences can be coloured
- according to the presence of a helix or sheet at each position, and
- RNA sequences can be shaded according to each structure's stem/helix
- pattern - which enables different RNA folding topologies to be quickly
- identified.
- </p>
- <p>
- <strong>3D Structural data analysis and display</strong><br />
- Jalview now employs Jmol's PDB data API to retrieve secondary
- structure assignments made by the DSSP algorithm. It can also employ
- web services to obtain secondary structure assignments from RNA
- structures. These assignments are shown as sequence associated
- annotation for sequences which have cross-references to the PDB, or
- have had PDB files associated with them via the <em>Structures</em>
- submenu of the sequence ID popup menu. The extraction and display of
- secondary structure and B-factor column annotation is controlled <em>via</em>
- a new <strong>Structure</strong> tab in the Jalview Desktop's
- Preferences dialog box.
- </p>
- <p>
- <Strong>Interoperation with UCSF Chimera</Strong><br /> The desktop
- application can now be configured to employ UCSF Chimera for the
- display of 3D structure data. UCSF Chimera is a python-based
- high-performance molecular graphics and animation system developed by
- the Resource for Biocomputing, Visualisation, and Informatics at the
- University of California.<br />Jalview employs the 'StructureViz'
- communication mechanism developed for Cytoscape by Morris et al.
- (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
- allows Jalview to send commands to Chimera, enabling structures to be
- superimposed and shaded according to associated multiple aligmment
- views. <br />Support for Chimera in Jalview 2.8.2 is experimental, and we
- would appreciate feedback ! Please send your comments to
- jalview-discuss@jalview.org, and keep up to date with this feature's
- development via http://issues.jalview.org/browse/JAL-1333.
- </p>
- <p>
- <strong>Export of alignment figures as Scalable Vector
- Graphics</strong> <br />Scalable Vector Graphics (SVG) files are now widely
- supported by web browsers and graphics design programs, and allow
- high-quality graphics for interactive exploration and publication.
- Jalview now supports the generation of SVGs interactively (via the
- Export) menu, and from the command line for server-side figure
- generation.
- </p>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>
+ Jalview 2.9 has been in development since December 2014. In addition
+ to a multitude of bug fixes and minor improvements (both small, and
+ rather big!), it also brings major new capabilities for codon-level
+ analysis of protein alignments and the manipulation of structural
+ data.<br />For the full list of changes, see the <a
+ href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview 2.9</strong>
+
+ <ul>
+ <li><strong>Visualisation, editing and analysis of
+ cDNA and Protein alignments</strong><br />A new <a
+ href="features/splitView.html">Split View</a> window allows linked
+ protein and nucleotide sequence alignments to be viewed, edited,
+ and analysed as one. <br />cDNA alignments can also be
+ reconstructed from protein alignments calculated by Jalview's web
+ services, and update in response to edits in the amino acid view.<br />To
+ start experimenting with cDNA/Protein analysis, jut drop a file
+ containing cDNA sequences which code for, and have IDs matching
+ proteins in an existing alignment, and Jalview will do the rest.</li>
+ <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
+ 2.9 provides full support for the use of Chimera to view 3D
+ structures linked to alignment views in the Jalview Desktop. We've
+ also included support for saving Chimera sessions in Jalview
+ project files.<br />Jalview and Chimera communicate using local
+ web server connections, which may cause firewall alerts on some
+ systems, but has the advantage of allowing bidirectional
+ communication. Communication between Jalview and Chimera is now
+ much more responsive, and selected regions in Chimera are now
+ shown as highlighted regions in the Jalview desktop.</li>
+ <li><strong>Interactive querying of the PDBe</strong><br />Jalview
+ users can now browse and retrieve 3D structure data from the PDB
+ via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
+ Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
+ et al 2014</a>). Developed in collaboration with the PDBe group at
+ EMBL-EBI, the interface allows both structured and free-text
+ queries to be performed, and allows automatic selection of the
+ most relevant structures for an alignment acording to a variety of
+ criteria.</li>
+ <li><strong>Improved support for RNA visualisation</strong><br />Jalview
+ 2.9 integrates the latest version of the <a
+ href="http://varna.lri.fr">VARNA RNA Viewer</a>, and VARNA views
+ can also now be stored in Jalview projects. We've also dealt with
+ a number of lingering bugs in the VARNA/Jalview interface,
+ including the loss of pseudoknots when RNA secondary structure is
+ shown VARNA.</li>
+ <li><strong>Protein Secondary Structure predictions
+ with JPred4</strong>Jalview includes a number of new features for working
+ with secondary structure predictions from the JPred4 server. These
+ include the ability to automatically hide insertions and highlight
+ mutations in an alignment with respect to a reference sequence.
+ Jalview 2.9's new scrollable SVG HTML export mode was also
+ developed specifically for the JPred4 server.</li>
+ </ul>
</body>
</html>
file = data.toString();
}
}
- if (TRUE.equalsIgnoreCase(getParameter("enableSplitFrame")))
+ if (getDefaultParameter("enableSplitFrame", true))
{
file2 = getParameter("file2");
}
{
return def;
}
- if (stn.toLowerCase().equals(TRUE))
+ if (TRUE.equalsIgnoreCase(stn))
{
return true;
}
git://source.jalview.org / jalview.git / commitdiff