}
final AlignFrame me = this;
buildingMenu = true;
- new Thread(new Runnable() {
- public void run() {
- try
+ new Thread(new Runnable()
{
- System.err
- .println("Building ws menu again " + Thread.currentThread());
- // TODO: add support for context dependent disabling of services based on
- // alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract
- // handler
- // class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or introduce
- // object broker mechanism.
- final Vector wsmenu = new Vector();
- final IProgressIndicator af = me;
- if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
- && Discoverer.services != null
- && (Discoverer.services.size() > 0))
+ public void run()
{
- // TODO: refactor to allow list of AbstractName/Handler bindings to be
- // stored or retrieved from elsewhere
- Vector msaws = (Vector) Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
- Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
- // TODO: move GUI generation code onto service implementation - so a
- // client instance attaches itself to the GUI with method call like
- // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
- // alignframe)
- if (msaws != null)
+ try
{
- // Add any Multiple Sequence Alignment Services
- final JMenu msawsmenu = new JMenu("Alignment");
- for (int i = 0, j = msaws.size(); i < j; i++)
+ System.err.println("Building ws menu again "
+ + Thread.currentThread());
+ // TODO: add support for context dependent disabling of services based
+ // on
+ // alignment and current selection
+ // TODO: add additional serviceHandle parameter to specify abstract
+ // handler
+ // class independently of AbstractName
+ // TODO: add in rediscovery GUI function to restart discoverer
+ // TODO: group services by location as well as function and/or
+ // introduce
+ // object broker mechanism.
+ final Vector wsmenu = new Vector();
+ final IProgressIndicator af = me;
+ if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
+ && Discoverer.services != null
+ && (Discoverer.services.size() > 0))
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, me);
+ // TODO: refactor to allow list of AbstractName/Handler bindings to
+ // be
+ // stored or retrieved from elsewhere
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services
+ .get("SecStrPred");
+ Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
+ // TODO: move GUI generation code onto service implementation - so a
+ // client instance attaches itself to the GUI with method call like
+ // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
+ // alignframe)
+ if (msaws != null)
+ {
+ // Add any Multiple Sequence Alignment Services
+ final JMenu msawsmenu = new JMenu("Alignment");
+ for (int i = 0, j = msaws.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(msawsmenu, me);
+ }
+ wsmenu.add(msawsmenu);
+ }
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(secstrmenu, me);
+ }
+ wsmenu.add(secstrmenu);
+ }
+ if (seqsrch != null)
+ {
+ // Add any sequence search services
+ final JMenu seqsrchmenu = new JMenu(
+ "Sequence Database Search");
+ for (int i = 0, j = seqsrch.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
+ .elementAt(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(seqsrchmenu, me);
+ }
+ wsmenu.add(seqsrchmenu);
+ }
}
- wsmenu.add(msawsmenu);
- }
- if (secstrpr != null)
- {
- // Add any secondary structure prediction services
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
- for (int i = 0, j = secstrpr.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(secstrmenu, me);
- }
- wsmenu.add(secstrmenu);
- }
- if (seqsrch != null)
- {
- // Add any sequence search services
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- for (int i = 0, j = seqsrch.size(); i < j; i++)
+
+ // TODO: move into separate menu builder class.
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, me);
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+ if (jws2servs.hasServices())
+ {
+ JMenu jws2men = new JMenu("Jalview 2 Services");
+ jws2servs.attachWSMenuEntry(jws2men, me);
+ for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
+ {
+ wsmenu.add(jws2men.getMenuComponent(i));
+ }
+ }
+ }
}
- wsmenu.add(seqsrchmenu);
- }
- }
- // TODO: move into separate menu builder class.
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- JMenu jws2men = new JMenu("Jalview 2 Services");
- jws2servs.attachWSMenuEntry(jws2men, me);
- for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
+ public void run()
{
- wsmenu.add(jws2men.getMenuComponent(i));
+ try
+ {
+
+ resetWebServiceMenu();
+ // finally, add the whole shebang onto the webservices menu
+ if (wsmenu.size() > 0)
+ {
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add((JMenu) wsmenu.get(i));
+ }
+ }
+ else
+ {
+ me.webService.add(me.webServiceNoServices);
+ }
+ } catch (Exception e)
+ {
+ }
+ ;
}
- }
- }
- }
-
- javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() {
- try {
-
- resetWebServiceMenu();
- // finally, add the whole shebang onto the webservices menu
- if (wsmenu.size() > 0)
- {
- for (int i = 0, j = wsmenu.size(); i < j; i++)
+ });
+ } catch (Exception e)
{
- webService.add((JMenu) wsmenu.get(i));
}
+ ;
+
+ buildingMenu = false;
}
- else
- {
- me.webService.add(me.webServiceNoServices);
- }
- } catch (Exception e)
- {
- }
- ;
- }
- });
- } catch (Exception e)
- {
- }
- ;
-
- buildingMenu = false;
- }}).start();
-
+ }).start();
+
}
/**
// TODO We probably want to store a sequence database checklist in
// preferences and have checkboxes.. rather than individual sources selected
// here
- JMenu rfetch = new JMenu("Fetch DB References");
+ final JMenu rfetch = new JMenu("Fetch DB References");
rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
webService.add(rfetch);
});
rfetch.add(fetchr);
- JMenu dfetch = new JMenu();
- rfetch.add(dfetch);
- jalview.ws.SequenceFetcher sf = SequenceFetcher
- .getSequenceFetcherSingleton(this);
- String[] otherdb = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
- int comp = 0, mcomp = 15;
- String mname = null;
- if (otherdb != null && otherdb.length > 0)
- {
- for (int i = 0; i < otherdb.length; i++)
+ final AlignFrame me=this;
+ new Thread(new Runnable()
+ {
+ public void run()
{
- String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
- if (mname == null)
+ final jalview.ws.SequenceFetcher sf = SequenceFetcher
+ .getSequenceFetcherSingleton(me);
+ final String[] otherdb = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- mname = "from '" + dbname + "'";
- }
- fetchr = new JMenuItem(otherdb[i]);
- final String[] dassource = new String[]
- { otherdb[i] };
- fetchr.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
+ public void run()
{
- new Thread(new Runnable()
- {
- public void run()
+ JMenu dfetch = new JMenu();
+ JMenuItem fetchr;
+ rfetch.add(dfetch);
+ int comp = 0, mcomp = 15;
+ String mname = null;
+ if (otherdb != null && otherdb.length > 0)
+ {
+ for (int i = 0; i < otherdb.length; i++)
{
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame,
- dassource).fetchDBRefs(false);
+ String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
+ if (mname == null)
+ {
+ mname = "from '" + dbname + "'";
+ }
+ fetchr = new JMenuItem(otherdb[i]);
+ final String[] dassource = new String[]
+ { otherdb[i] };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("Retrieve from " + dbname);
+ dfetch.add(fetchr);
+ if (comp++ == mcomp || i == (otherdb.length - 1))
+ {
+ dfetch.setText(mname + " to '" + dbname + "'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
}
- }).start();
+ }
}
-
});
- fetchr.setToolTipText("Retrieve from " + dbname);
- dfetch.add(fetchr);
- if (comp++ == mcomp || i == (otherdb.length - 1))
- {
- dfetch.setText(mname + " to '" + dbname + "'");
- rfetch.add(dfetch);
- dfetch = new JMenu();
- mname = null;
- comp = 0;
- }
}
- }
+ }).start();
+
}
/**
git://source.jalview.org / jalview.git / commitdiff