--- /dev/null
+/**
+ *
+ */
+package uk.ac.vamsas.test.simpleclient.simpleapp;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+
+import org.vamsas.test.simpleclient.ArchiveClient;
+import org.vamsas.test.simpleclient.ClientDoc;
+
+import uk.ac.vamsas.client.UserHandle;
+import uk.ac.vamsas.client.simpleclient.FileWatcher;
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.VamsasDocument;
+
+/**
+ * @author jimp
+ *
+ */
+public class VamsasClient extends ArchiveClient {
+ org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasClient.class);
+ /**
+ * create a new vamsas client session from the archive at sessionPath.
+ * @param sessionPath
+ */
+ public VamsasClient(File sessionPath) {
+ super(System.getProperty("user.name"),System.getProperty("host.name"), "SimpleVamsasClientApp","0.1",
+ sessionPath);
+ }
+ /**
+ * Called by gui to read anything from the vamsas session into the apps datamodel
+ * after it has started up.
+ *
+ */
+ public void initial_update() {
+ log.info("Jalview loading the Vamsas Session.");
+ // load in the vamsas archive for the first time
+ ClientDoc cdoc = this.getUpdateable();
+ updateJalview(cdoc);
+ // TODO: flush any new VorbaIds to the document : updateVamsasClient may actually generate new Vamsas Document data in the form of vamsas element ids - these should be written back to the document.
+ //doUpdate(cdoc); // JBPNote: this should flush new VorbaIds but I've not tested it yet.
+ cdoc.closeDoc();
+ // then tell app to update its display based on the datamodel changes.
+ }
+ VamsasClientWatcher watcher=null;
+ /**
+ * Called by app when internal datamodel should exported (syncrhonised outwards) to vamsas document
+ *
+ */
+ public void push_update() {
+
+ watchForChange=false; // this makes any watch(long) loops return.
+ // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
+ try {
+ Thread.sleep(WATCH_SLEEP);
+ } catch (Exception e) {
+
+ };
+
+ ClientDoc cdoc = getUpdateable();
+ updateVamsasDocument(cdoc);
+ doUpdate(cdoc);
+ cdoc.closeDoc();
+ cdoc=null;
+ watchForChange=true;
+ startWatcher();
+ }
+ public void end_session() {
+ watchForChange=false; // this makes any watch(long) loops return.
+ // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
+ try {
+ Thread.sleep(WATCH_SLEEP);
+ } catch (Exception e) {
+
+ };
+
+ // stop any update/watcher thread.
+ log.info("VamsasClientApplication disconnecting from the Vamsas Session.");
+ }
+ public void updateJalview(ClientDoc cdoc) {
+ ensureVamsasBindings();
+ VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry());
+ vds.updateToJalview();
+ }
+ private void ensureVamsasBindings() {
+ if (jv2vobj==null) {
+ jv2vobj = new IdentityHashMap();
+ vobj2jv = new Hashtable();
+ }
+ }
+ /**
+ * App's object binding to VorbaIds
+ */
+ IdentityHashMap jv2vobj = null;
+ Hashtable vobj2jv = null;
+ /**
+ * called with a vamsas document which will be updated with new data from the app
+ * @param doc
+ */
+ public void updateVamsasDocument(ClientDoc doc) {
+ ensureVamsasBindings();
+ VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, baseProvEntry());
+ // wander through frames
+ vds.storeVAMSAS(new Object()); // Object is the apps datamodel ;)
+ }
+ /**
+ *
+ * @return a base provenance entry used by the VamsasDatastore object to get attributes from. this isn't particularly elegant either.
+ */
+ private Entry baseProvEntry() {
+ uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry();
+ pentry.setUser(this.getProvenanceUser());
+ pentry.setApp(this.getClientHandle().getClientName());
+ pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
+ pentry.setAction("created");
+ return pentry;
+ }
+ protected class VamsasClientWatcher extends Thread implements Runnable {
+ /* (non-Javadoc)
+ * @see java.lang.Thread#run()
+ */
+ VamsasClient client=null;
+ VamsasClientWatcher(VamsasClient client) {
+ this.client = client;
+ }
+ boolean running=false;
+ public void run() {
+ running=true;
+ while (client.watchForChange) {
+ ClientDoc docio = client.watch(0);
+ if (docio!=null) {
+ // VamsasClient GUI bits should be disabled whilst an update is in progress so the user doesn't screw anything up.
+ client.disableGui(true);
+ log.debug("Updating VamsasClient app from changed vamsas document.");
+ client.updateJalview(docio);
+ log.debug("Finished updating from document change.");
+ docio.closeDoc();
+ docio=null;
+ client.disableGui(false);
+ }
+ }
+ running=false;
+
+ }
+
+ }
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ // TODO Auto-generated method stub
+
+ }
+ /**
+ * disable (if b is true) or enable (if b is true) the VamsasClient's vamsas session gui bits whilst a document change is being updated to the app.
+ * @param b
+ */
+ public void disableGui(boolean b) {
+ // in jalview, we turn off the VAMSAS Session menu : Desktop.instance.setVamsasUpdate(b);
+ }
+ /**
+ * spawn a new thread to start the VamsasClientWatcher.
+ *
+ */
+ public void startWatcher() {
+ if (watcher==null)
+ watcher=new VamsasClientWatcher(this);
+ Thread thr = new Thread() {
+ public void run() {
+ watcher.start();
+ }
+ };
+ thr.start();
+ }
+
+}
git://source.jalview.org / vamsas.git / blobdiff