<mapID target="calcs.alconserv" url="html/calculations/conservation.html"/>
<mapID target="calcs.alstrconsensus" url="html/calculations/structureconsensus.html"/>
<mapID target="calcs.consensus" url="html/calculations/consensus.html"/>
- <mapID target="calcs.annotation" url="html/calculations/columnFilterByAnnotation.html"/>
<mapID target="nucleicAcids" url="html/na/index.html"/>
<mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
<mapID target="subtMatrices.pam250" url="html/calculations/scorematrices.html#pam250" />
+ <mapID target="biojson" url="html/features/bioJsonFormat.html" />
+ <mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+ <mapID target="pdbchooser" url="html/features/structurechooser.html" />
+ <mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
+
<mapID target="backIcon" url="icons/back.png" />
<mapID target="forwardIcon" url="icons/forward.png" />
<mapID target="homeIcon" url="icons/Home.png" />
<tocitem text="Multiple Views" target="multipleviews" />
<tocitem text="Split Frame View" target="splitframe" />
<tocitem text="Viewing Trees" target="treeviewer" expand="false" />
- <tocitem text="Fetching Sequences" target="seqfetch" />
+ <tocitem text="Fetching Sequences" target="seqfetch" />
+ <tocitem text="BioJSON v1.0" target="biojson" />
+ <tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
+ <tocitem text="PDB Structure Chooser" target="pdbchooser" />
+ <tocitem text="Select columns by annotation" target="selectcolbyannot" />
<tocitem text="Nucleic Acid Support" target="nucleicAcids" expand="false">
<tocitem text="Viewing RNA structure" target="varna" />
<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus" />
</head>
<body>
<h1>BioJSON 1.0</h1>
- BioJSON is a JavaScript Object Notation (JSON) specification for the representation and exchange of bioinformatics data.
+ BioJSON is a JavaScript Object Notation (JSON) specification for the representation and exchange of multiple sequence alignment data.
The first version of the specification was developed in 2015 and implemented in Jalview 2.9. Find out more about BioJSON
at <a href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/</a>.
selecting PDB structures to view in Jalview by querying readily
available meta-data of structures. The Interface can be invoked by selecting
the
- <strong>"View Structure"</strong> option from a sequence's
+ <strong>"3D Structure Data.."</strong> option from a sequence's
<a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
features it provides are listed below:
<ul>
<p><strong>Importing PDB Entries or files in PDB format</strong><br>
You can retrieve sequences from the PDB using the <a
- href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
+ href="pdbsequencefetcher.html">Sequence Fetcher</a>. Any sequences retrieved with
this service are automatically associated with their source database
entry. For PDB sequences, simply select PDB as the database and enter
your known PDB id (appended with ':' and a chain code, if desired).<br>
<li><strong>PileUp</strong></li>
<li><strong>AMSA</strong></li>
<li><strong>STH</strong></li>
- <li><strong>Phylip</strong></li>
+ <li><strong>PHYLIP</strong></li>
+ <li><strong>JSON</strong></li>
</ul>
</li>
<li><strong>Page Setup ...</strong><br>
Graphics</a> file from your alignment.</em></li>
<li><strong>SVG<br>
</strong><em>Create a <a href="../io/export.html">Scalable Vector Graphics</a> file from your alignment for embedding in web pages.</em></li>
+ <li><strong>BioJS<br>
+ </strong><em>Create a <a href="../io/export.html">BioJS MSA Viewer HTML </a> file from your alignment.</em></li>
</ul>
</li>
<li><strong>Export Features</strong><em><br>
<li><strong>Undefine Groups (Control U)<br>
</strong><em>The alignment will be reset with no defined groups.<br>
<strong>WARNING</strong>: This cannot be undone.</em></li>
+ <li><strong>Select/Hide Columns by Annotation...</strong> <br/><em>Select or hide columns of an alignment by filtering with properties of any annotation row added to that alignment</em></li>
</ul>
</body>
based URL links that matched the description line.
</em><strong><br> </strong></li>
</ul></li>
- <li><strong>View Structure</strong> </strong><em>This menu is only
- visible if you right-click on a sequence name. If the
- sequence has an associated PDB file(s), Jalview will open a 'Structure Chooser'
- dialogue with options to select the structure which will eventually be opened in
+ <li><strong>3D Structure Data...</strong> </strong><em>This menu is
+ visible when you right-click on a sequence name. When this option is clicked, Jalview will open a <a href="../features/structurechooser.html">'Structure Chooser' </a>
+ dialogue with options to select the structure which will eventually be opened in
a 3D interactive view.<br> These entries will only be present if the sequence
- has <a href="../features/viewingpdbs.html">associated PDB
- structures</a>.<br /> If the sequence or alignment has RNA structure,
- then <strong>2D RNA</strong> entries will also be present enabling
+ has <a href="../features/viewingpdbs.html">associated PDB structures</a>.
+ <br /> If the sequence or alignment has RNA structure,
+ then <strong>VARNA 2D Structure</strong> entries will also be present enabling
you to open a linked view of the RNA structure in <a
href="../features/varna.html">VARNA</a>.
</em>
*/
package jalview.javascript;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Propagate events involving PDB structures associated with sequences to a
* javascript function. Generally, the javascript handler is called with a
final Object source = srce;
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(jvlite);
- // if (jvlite.debug)
- // {
- // ssm.reportMapping();
- // }
+
+ if (JalviewLite.debug)
+ {
+ System.err.println(this.getClass().getName() + " modelSet[0]: "
+ + modelSet[0]);
+ ssm.reportMapping();
+ }
+
if (source instanceof jalview.api.AlignmentViewPanel)
{
SequenceI[][] sequence = new SequenceI[modelSet.length][];
git://source.jalview.org / jalview.git / commitdiff
