\r
/**\r
* DOCUMENT ME!\r
- *\r
+ * \r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class SeqSearchWSClient\r
- extends WSClient\r
+public class SeqSearchWSClient extends WSClient\r
{\r
/**\r
* server is a WSDL2Java generated stub for an archetypal MsaWSI service.\r
*/\r
ext.vamsas.SeqSearchI server;\r
+\r
AlignFrame alignFrame;\r
\r
/**\r
- * Creates a new MsaWSClient object that uses a service\r
- * given by an externally retrieved ServiceHandle\r
- *\r
- * @param sh service handle of type AbstractName(MsaWS)\r
- * @param altitle DOCUMENT ME!\r
- * @param msa DOCUMENT ME!\r
- * @param submitGaps DOCUMENT ME!\r
- * @param preserveOrder DOCUMENT ME!\r
+ * Creates a new MsaWSClient object that uses a service given by an externally\r
+ * retrieved ServiceHandle\r
+ * \r
+ * @param sh\r
+ * service handle of type AbstractName(MsaWS)\r
+ * @param altitle\r
+ * DOCUMENT ME!\r
+ * @param msa\r
+ * DOCUMENT ME!\r
+ * @param submitGaps\r
+ * DOCUMENT ME!\r
+ * @param preserveOrder\r
+ * DOCUMENT ME!\r
*/\r
\r
public SeqSearchWSClient(ext.vamsas.ServiceHandle sh, String altitle,\r
- jalview.datamodel.AlignmentView msa, String db,\r
- Alignment seqdataset,\r
- AlignFrame _alignFrame)\r
+ jalview.datamodel.AlignmentView msa, String db,\r
+ Alignment seqdataset, AlignFrame _alignFrame)\r
{\r
super();\r
alignFrame = _alignFrame;\r
- // can generalise the two errors below for metadata mapping from interface name to service client name\r
+ // can generalise the two errors below for metadata mapping from interface\r
+ // name to service client name\r
if (!sh.getAbstractName().equals(this.getServiceActionKey()))\r
{\r
JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Service called \n" + sh.getName() +\r
- "\nis not a \nSequence Search Service !",\r
- "Internal Jalview Error",\r
- JOptionPane.WARNING_MESSAGE);\r
+ "The Service called \n" + sh.getName()\r
+ + "\nis not a \nSequence Search Service !",\r
+ "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
\r
return;\r
}\r
\r
- if ( (wsInfo = setWebService(sh)) == null)\r
+ if ((wsInfo = setWebService(sh)) == null)\r
{\r
JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Sequence Search Service named " +\r
- sh.getName() +\r
- " is unknown", "Internal Jalview Error",\r
- JOptionPane.WARNING_MESSAGE);\r
+ "The Sequence Search Service named " + sh.getName()\r
+ + " is unknown", "Internal Jalview Error",\r
+ JOptionPane.WARNING_MESSAGE);\r
\r
return;\r
}\r
startSeqSearchClient(altitle, msa, db, seqdataset);\r
\r
}\r
+\r
/**\r
- * non-process web service interaction - use this for calling HEADLESS synchronous service methods\r
- * @param sh\r
- */\r
+ * non-process web service interaction - use this for calling HEADLESS\r
+ * synchronous service methods\r
+ * \r
+ * @param sh\r
+ */\r
public SeqSearchWSClient(ServiceHandle sh)\r
{\r
setWebService(sh, true);\r
super();\r
// add a class reference to the list\r
}\r
+\r
private void startSeqSearchClient(String altitle, AlignmentView msa,\r
- String db,\r
- Alignment seqdataset)\r
+ String db, Alignment seqdataset)\r
{\r
if (!locateWebService())\r
{\r
return;\r
}\r
- String visdb = (db==null || db == "") ? "default" : db; // need a visible name for a sequence db\r
- boolean profileSearch = msa.getSequences().length>2 ? true : false;\r
+ String visdb = (db == null || db == "") ? "default" : db; // need a visible\r
+ // name for a\r
+ // sequence db\r
+ boolean profileSearch = msa.getSequences().length > 2 ? true : false;\r
// single sequence or profile from alignment view\r
- wsInfo.setProgressText( "Searching "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()\r
- : " with profile") +\r
- " from " + altitle + "\nJob details\n");\r
- \r
- String jobtitle = WebServiceName+((WebServiceName.indexOf("earch")>-1) ? " " : " search ")+" of "+visdb+(!profileSearch ? " with sequence "+msa.getSequences()[0].getRefSeq().getName()\r
- : " with profile") +\r
- " from " + altitle;\r
- SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL, wsInfo, alignFrame,\r
- WebServiceName,\r
- jobtitle,\r
- msa,\r
- db,\r
- seqdataset);\r
+ wsInfo.setProgressText("Searching "\r
+ + visdb\r
+ + (!profileSearch ? " with sequence "\r
+ + msa.getSequences()[0].getRefSeq().getName()\r
+ : " with profile") + " from " + altitle\r
+ + "\nJob details\n");\r
+\r
+ String jobtitle = WebServiceName\r
+ + ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")\r
+ + " of "\r
+ + visdb\r
+ + (!profileSearch ? " with sequence "\r
+ + msa.getSequences()[0].getRefSeq().getName()\r
+ : " with profile") + " from " + altitle;\r
+ SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,\r
+ wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,\r
+ seqdataset);\r
wsInfo.setthisService(ssthread);\r
ssthread.start();\r
}\r
\r
/**\r
* Initializes the server field with a valid service implementation.\r
- *\r
+ * \r
* @return true if service was located.\r
*/\r
private boolean locateWebService()\r
\r
try\r
{\r
- this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(WsURL));\r
- ( (SeqSearchServiceSoapBindingStub)this.server).setTimeout(60000); // One minute timeout\r
- }\r
- catch (Exception ex)\r
+ this.server = (SeqSearchI) loc.getSeqSearchService(new java.net.URL(\r
+ WsURL));\r
+ ((SeqSearchServiceSoapBindingStub) this.server).setTimeout(60000); // One\r
+ // minute\r
+ // timeout\r
+ } catch (Exception ex)\r
{\r
- wsInfo.setProgressText("Serious! " + WebServiceName +\r
- " Service location failed\nfor URL :" + WsURL +\r
- "\n" +\r
- ex.getMessage());\r
+ wsInfo.setProgressText("Serious! " + WebServiceName\r
+ + " Service location failed\nfor URL :" + WsURL + "\n"\r
+ + ex.getMessage());\r
wsInfo.setStatus(WebserviceInfo.ERROR);\r
ex.printStackTrace();\r
\r
{\r
return "Sequence Database Search";\r
}\r
+\r
// simple caching of db parameters for each service endpoint\r
private static Hashtable dbParamsForEndpoint;\r
- static { \r
+ static\r
+ {\r
dbParamsForEndpoint = new Hashtable();\r
}\r
+\r
public String[] getSupportedDatabases() throws Exception\r
{\r
- \r
+\r
// check that we haven't already been to this service endpoint\r
if (dbParamsForEndpoint.containsKey(WsURL))\r
{\r
}\r
if (!locateWebService())\r
{\r
- throw new Exception("Cannot contact service endpoint at "+WsURL); \r
+ throw new Exception("Cannot contact service endpoint at " + WsURL);\r
}\r
String database = server.getDatabase();\r
- if (database==null)\r
+ if (database == null)\r
{\r
- dbParamsForEndpoint.put(WsURL, new String[] {});\r
+ dbParamsForEndpoint.put(WsURL, new String[]\r
+ {});\r
return null;\r
}\r
StringTokenizer en = new StringTokenizer(database.trim(), ",| ");\r
String[] dbs = new String[en.countTokens()];\r
- for (int i=0; i<dbs.length; i++)\r
+ for (int i = 0; i < dbs.length; i++)\r
{\r
dbs[i++] = en.nextToken().trim();\r
}\r
dbParamsForEndpoint.put(WsURL, dbs);\r
return dbs;\r
}\r
+\r
public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,\r
final AlignFrame af)\r
{\r
// look for existing database service submenus on wsmenu\r
Hashtable dbsrchs = new Hashtable();\r
Vector newdbsrch = new Vector();\r
- Component entries[] = wsmenu.getComponents();\r
- for (int i = 0; entries!=null && i<entries.length; i++)\r
+ Component entries[] = wsmenu.getComponents();\r
+ for (int i = 0; entries != null && i < entries.length; i++)\r
{\r
if (entries[i] instanceof JMenu)\r
{\r
dbsrchs.put(entries[i].getName(), entries[i]);\r
}\r
}\r
- JMenu defmenu=(JMenu) dbsrchs.get("Default Database");\r
- if (defmenu==null)\r
+ JMenu defmenu = (JMenu) dbsrchs.get("Default Database");\r
+ if (defmenu == null)\r
{\r
- dbsrchs.put("Default Database", defmenu = new JMenu("Default Database"));\r
+ dbsrchs.put("Default Database", defmenu = new JMenu(\r
+ "Default Database"));\r
newdbsrch.addElement(defmenu);\r
}\r
- \r
- String dbs[] = null;\r
- try {\r
- dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();\r
- } catch (Exception e)\r
+\r
+ String dbs[] = null;\r
+ try\r
+ {\r
+ dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();\r
+ } catch (Exception e)\r
+ {\r
+ jalview.bin.Cache.log.warn(\r
+ "Database list request failed, so disabling SeqSearch Service client "\r
+ + sh.getName() + " at " + sh.getEndpointURL(), e);\r
+ return;\r
+ }\r
+ JMenuItem method;\r
+ // do default entry\r
+ defmenu.add(method = new JMenuItem(sh.getName()));\r
+ method.setToolTipText(sh.getEndpointURL());\r
+ method.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
{\r
- jalview.bin.Cache.log.warn("Database list request failed, so disabling SeqSearch Service client "+sh.getName()+" at "+sh.getEndpointURL(), e);\r
- return;\r
+ // use same input gatherer as for secondary structure prediction\r
+ // we could actually parameterise the gatherer method here...\r
+ AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();\r
+ new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, null, af\r
+ .getViewport().getAlignment().getDataset(), af);\r
}\r
- JMenuItem method;\r
- // do default entry\r
- defmenu.add(method = new JMenuItem(sh.getName()));\r
+ });\r
+ // add entry for each database the service supports\r
+ for (int db = 0; dbs != null && db < dbs.length; db++)\r
+ {\r
+ JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);\r
+ if (dbmenu == null)\r
+ {\r
+ dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));\r
+ newdbsrch.addElement(dbmenu);\r
+ }\r
+ // add the client handler code for this service\r
+ dbmenu.add(method = new JMenuItem(sh.getName()));\r
method.setToolTipText(sh.getEndpointURL());\r
+ final String searchdb = dbs[db];\r
method.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- // use same input gatherer as for secondary structure prediction\r
- // we could actually parameterise the gatherer method here...\r
AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();\r
- new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, null, \r
- af.getViewport().getAlignment().getDataset(),\r
+ new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa,\r
+ searchdb, af.getViewport().getAlignment().getDataset(),\r
af);\r
- }\r
- }\r
- );\r
- // add entry for each database the service supports\r
- for (int db=0; dbs!=null && db<dbs.length; db++)\r
- {\r
- JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);\r
- if (dbmenu==null)\r
- {\r
- dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));\r
- newdbsrch.addElement(dbmenu);\r
}\r
- // add the client handler code for this service\r
- dbmenu.add(method = new JMenuItem(sh.getName()));\r
- method.setToolTipText(sh.getEndpointURL());\r
- final String searchdb = dbs[db];\r
- method.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();\r
- new jalview.ws.SeqSearchWSClient(sh, af.getTitle(), msa, searchdb, \r
- af.getViewport().getAlignment().getDataset(),\r
- af);\r
- }\r
- });\r
- }\r
+ });\r
+ }\r
// add the databases onto the seqsearch menu\r
Enumeration e = newdbsrch.elements();\r
while (e.hasMoreElements())\r
if (el instanceof JMenu)\r
{\r
wsmenu.add((JMenu) el);\r
- } else {\r
+ }\r
+ else\r
+ {\r
wsmenu.add((JMenuItem) el);\r
}\r
}\r
- \r
+\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff