installed the chosen viewer in a non-standard location, you can specify it
here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
<p>
+ <em>Sequence <-> Structure Mapping Method</em> - This setting controls whether
+ Jalview attempts to retrieve mappings between Uniprot protein
+ sequences and 3D structures in the PDBe with SIFTS, or constructs a
+ mapping by conservative alignment between the sequences and chains
+ in the 3D structure data using the Needleman and Wunsch algorithm.
+ SIFTS is enabled by default.
+ <p>
<em>PDB Fields shown in Search and Structure Summaries</em> - ticks
in this table indicate fields shown by default when browsing results
of a free text search via the PDB sequence fetcher, or 3D structures
than anonymous 'Java' icons
</li>
<li>
- <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel used by Jalview
+ <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel (LaF) used by Jalview
+ </li>
+ <li>
+ <!-- JAL-3552, JAL-3609 -->Metal LaF used to improved operation on Linux Ubuntu with
+ HiDPI display in Java 11 (still known issues with HiDPI screens in java
+ 8 and 11. see <a
+ href="https://issues.jalview.org/browse/JAL-3137">JAL-3137</a>)
</li>
<li>
<!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
* <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
* </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</li>
* <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
* <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* warning dialog box is displayed.</li>
* <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
* <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
* </li>
- *
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
* </ul>
* Deprecated settings:
* <ul>
.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains("nonews"))
+ if (!aparser.contains("nonews")
+ || Cache.getProperty("NONEWS") == null)
{
desktop.checkForNews();
}
- BioJsHTMLOutput.updateBioJS();
+ if (!aparser.contains("nohtmltemplates")
+ || Cache.getProperty("NOHTMLTEMPLATES") == null)
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
}
}
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- boolean new_sspred = false;
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
+ // logic for 2.11.1.4 is
+ // always look to see if there is a discover. if there isn't
+ // we can't show any Jws2 services
+ // if there are services available, show them - regardless of
+ // the 'show JWS2 preference'
+ // if the discoverer is running then say so
+ // otherwise offer to trigger discovery if 'show JWS2' is not
+ // enabled
Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
{
}
}
}
-
}
+
if (jws2servs.isRunning())
{
JMenuItem tm = new JMenuItem(
tm.setEnabled(false);
webService.add(tm);
}
+ else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ JMenuItem enableJws2 = new JMenuItem(
+ "Discover Web Services");
+ enableJws2.setToolTipText(
+ "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
+ enableJws2.setEnabled(true);
+ enableJws2.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // start service discoverer, but ignore preference
+ Desktop.instance.startServiceDiscovery(false,
+ true);
+ }
+ });
+ webService.add(enableJws2);
+ }
}
}
build_urlServiceMenu(me.webService);
initItems(chan);
updating = false;
- boolean setvisible = checkForNew(chan, true);
-
- if (setvisible)
+ if (!Cache.getDefault("NONEWS", false))
{
+ boolean setvisible = checkForNew(chan, true);
+
+ if (setvisible)
+ {
- Console.debug("Will show jalview news automatically");
- showNews();
+ Console.debug("Will show jalview news automatically");
+ showNews();
+ }
}
Console.debug("Completed construction of reader.");
}).start();
}
- public void getIdentifiersOrgData() {
- if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {
- // Thread off the identifiers fetcher
- new Thread(new Runnable() {
+ public void getIdentifiersOrgData()
+ {
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+ {// Thread off the identifiers fetcher
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
jalview.bin.Console.debug("Downloading data from identifiers.org");
- try {
- UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation());
- } catch (IOException e) {
- jalview.bin.Console.debug("Exception downloading identifiers.org data" + e.getMessage());
+ try
+ {
+ UrlDownloadClient.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ jalview.bin.Console.debug("Exception downloading identifiers.org data"
+ + e.getMessage());
}
}
}).start();
+ ;
}
}
/**
* start service discovery and wait till it is done
*/
- public void startServiceDiscovery() {
+ public void startServiceDiscovery()
+ {
startServiceDiscovery(false);
}
*
* @param blocking
*/
- public void startServiceDiscovery(boolean blocking) {
- startServiceDiscovery(blocking, false);
+ public void startServiceDiscovery(boolean blocking)
+ {
+ startServiceDiscovery(blocking,false);
}
/**
public class UrlDownloadClient
{
- public UrlDownloadClient()
- {
-
- }
-
/**
* Download and save a file from a URL
*
git://source.jalview.org / jalview.git / commitdiff