+/*
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
+ */
package uk.ac.vamsas.test;
import uk.ac.vamsas.client.*;
}
public String Usage = "ExampleApplication :/n [-arena <vamsasFileDirectory>][-session <vamsasSessionURN>] <action> [+<arguments>]\n"
- + "<action> is one of :\n\tsave,new,watch\n"+
- "-arena and -session are not yet supported"; // TODO for release
+ + "<action> is one of :\n\tsave,new,watch\n"
+ + "-arena and -session are not yet supported"; // TODO for release
String sess = null;
String importFile = null;
String outputFile = null;
- boolean newSession=false;
- boolean imported=false;
+
+ boolean newSession = false;
+
+ boolean imported = false;
+
private boolean parseArgs(String args[]) {
if (args.length == 0) {
return false;
boolean parsed = false;
while (!parsed && cpos < args.length) {
// TODO: note importDocument not yet supported.
- //if (args[cpos].toLowerCase().equals("load") && cpos + 1 < args.length) {
- // importFile = args[cpos + 1];
- // cpos += 2;
- // continue;
- //}
+ // if (args[cpos].toLowerCase().equals("load") && cpos + 1 < args.length)
+ // {
+ // importFile = args[cpos + 1];
+ // cpos += 2;
+ // continue;
+ // }
if (args[cpos].toLowerCase().equals("new") && cpos + 1 < args.length) {
importFile = args[cpos + 1];
- newSession=true;
+ newSession = true;
cpos += 2;
continue;
}
// get an Iclient with session data
app = new ClientHandle("uk.ac.vamsas.test.ExampleApplication", "0.1");
user = new UserHandle("arnolduser", "deathsdoor");
- if (sess!=null && importFile!=null)
- {
- System.err.println("Import of an existing document into an existing session is not fully supported yet.");
+ if (sess != null && importFile != null) {
+ System.err
+ .println("Import of an existing document into an existing session is not fully supported yet.");
System.exit(3);
}
try {
System.out.println("Connecting to " + sess);
vorbaclient = clientfactory.getIClient(app, user, sess);
} else {
- if (newSession)
- {
- if (importFile==null)
- {
+ if (newSession) {
+ if (importFile == null) {
System.out.println("Connecting to a new VAMSAS Session.");
vorbaclient = clientfactory.getNewSessionIClient(app, user);
} else {
- System.out.println("Connecting to a new VAMSAS Session to share data in existing document:"+importFile);
+ System.out
+ .println("Connecting to a new VAMSAS Session to share data in existing document:"
+ + importFile);
File vfile = new File(importFile);
- vorbaclient = clientfactory.openAsNewSessionIClient(app, user, vfile);
- System.out.println("Succesfully imported document into new session.");
+ vorbaclient = clientfactory.openAsNewSessionIClient(app, user,
+ vfile);
+ System.out
+ .println("Succesfully imported document into new session.");
imported = true;
- importFile=null;
+ importFile = null;
}
} else {
- vorbaclient = clientfactory.getIClient(app, user);
+ vorbaclient = clientfactory.getIClient(app, user);
}
}
- }
- catch (InvalidSessionDocumentException e) {
- System.err.println("Failed to create a session to share "+importFile);
+ } catch (InvalidSessionDocumentException e) {
+ System.err.println("Failed to create a session to share " + importFile);
System.err.println("Sorry it didn't work out. This is what went wrong:");
e.printStackTrace(System.err);
System.exit(3);
- }
- catch (NoDefaultSessionException e) {
+ } catch (NoDefaultSessionException e) {
System.err
.println("There appear to be several sessions to choose from :");
String[] sessions = clientfactory.getCurrentSessions();
File vfile = new File(importFile);
try {
vorbaclient.importDocument(vfile);
- imported=true;
+ imported = true;
} catch (Exception e) {
System.err.println("Failed to import file " + importFile);
System.err.println("Exception received was " + e);
// get document data
try {
IClientDocument cdoc = vorbaclient.getClientDocument();
- if (imported)
- {
- if (cdoc.getVamsasRoots()==null || cdoc.getVamsasRoots()[0].getDataSetCount()<1)
- {
- System.err.println("Imported an Empty vamsas document. Is this correct ?");
+ if (imported) {
+ if (cdoc.getVamsasRoots() == null
+ || cdoc.getVamsasRoots()[0].getDataSetCount() < 1) {
+ System.err
+ .println("Imported an Empty vamsas document. Is this correct ?");
}
}
processVamsasDocument(cdoc);
}
try {
Thread.sleep(200);
- } catch (Exception e){}
+ } catch (Exception e) {
+ }
}
} else {
if (System.currentTimeMillis() > shutdown) {
git://source.jalview.org / vamsas.git / blobdiff