-/**
- *
- */
-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 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;
-import uk.ac.vamsas.test.simpleclient.ArchiveClient;
-import uk.ac.vamsas.test.simpleclient.ClientDoc;
-
-/**
- * @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 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();
- }
-
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.test.simpleclient.simpleapp;\r
+\r
+import java.io.File;\r
+import java.io.FileOutputStream;\r
+import java.io.OutputStreamWriter;\r
+import java.io.PrintWriter;\r
+import java.util.Hashtable;\r
+import java.util.IdentityHashMap;\r
+import java.util.Vector;\r
+import java.util.jar.JarOutputStream;\r
+\r
+import javax.swing.JInternalFrame;\r
+\r
+import uk.ac.vamsas.client.UserHandle;\r
+import uk.ac.vamsas.client.simpleclient.FileWatcher;\r
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;\r
+import uk.ac.vamsas.client.simpleclient.VamsasFile;\r
+import uk.ac.vamsas.objects.core.Entry;\r
+import uk.ac.vamsas.objects.core.VamsasDocument;\r
+import uk.ac.vamsas.test.simpleclient.ArchiveClient;\r
+import uk.ac.vamsas.test.simpleclient.ClientDoc;\r
+\r
+/**\r
+ * @author jimp\r
+ * \r
+ */\r
+public class VamsasClient extends ArchiveClient {\r
+ org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory\r
+ .getLog(VamsasClient.class);\r
+\r
+ /**\r
+ * create a new vamsas client session from the archive at sessionPath.\r
+ * \r
+ * @param sessionPath\r
+ */\r
+ public VamsasClient(File sessionPath) {\r
+ super(System.getProperty("user.name"), System.getProperty("host.name"),\r
+ "SimpleVamsasClientApp", "0.1", sessionPath);\r
+ }\r
+\r
+ /**\r
+ * Called by gui to read anything from the vamsas session into the apps\r
+ * datamodel after it has started up.\r
+ * \r
+ */\r
+ public void initial_update() {\r
+ log.info("Jalview loading the Vamsas Session.");\r
+ // load in the vamsas archive for the first time\r
+ ClientDoc cdoc = this.getUpdateable();\r
+ updateJalview(cdoc);\r
+ // TODO: flush any new VorbaIds to the document : updateVamsasClient may\r
+ // actually generate new Vamsas Document data in the form of vamsas element\r
+ // ids - these should be written back to the document.\r
+ // doUpdate(cdoc); // JBPNote: this should flush new VorbaIds but I've not\r
+ // tested it yet.\r
+ cdoc.closeDoc();\r
+ // then tell app to update its display based on the datamodel changes.\r
+ }\r
+\r
+ VamsasClientWatcher watcher = null;\r
+\r
+ /**\r
+ * Called by app when internal datamodel should exported (syncrhonised\r
+ * outwards) to vamsas document\r
+ * \r
+ */\r
+ public void push_update() {\r
+\r
+ watchForChange = false; // this makes any watch(long) loops return.\r
+ // we should also wait arount for this.WATCH_SLEEP to really make sure the\r
+ // watcher thread has stopped.\r
+ try {\r
+ Thread.sleep(WATCH_SLEEP);\r
+ } catch (Exception e) {\r
+\r
+ }\r
+ ;\r
+\r
+ ClientDoc cdoc = getUpdateable();\r
+ updateVamsasDocument(cdoc);\r
+ doUpdate(cdoc);\r
+ cdoc.closeDoc();\r
+ cdoc = null;\r
+ watchForChange = true;\r
+ startWatcher();\r
+ }\r
+\r
+ public void end_session() {\r
+ watchForChange = false; // this makes any watch(long) loops return.\r
+ // we should also wait arount for this.WATCH_SLEEP to really make sure the\r
+ // watcher thread has stopped.\r
+ try {\r
+ Thread.sleep(WATCH_SLEEP);\r
+ } catch (Exception e) {\r
+\r
+ }\r
+ ;\r
+\r
+ // stop any update/watcher thread.\r
+ log.info("VamsasClientApplication disconnecting from the Vamsas Session.");\r
+ }\r
+\r
+ public void updateJalview(ClientDoc cdoc) {\r
+ ensureVamsasBindings();\r
+ VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj,\r
+ baseProvEntry());\r
+ vds.updateToJalview();\r
+ }\r
+\r
+ private void ensureVamsasBindings() {\r
+ if (jv2vobj == null) {\r
+ jv2vobj = new IdentityHashMap();\r
+ vobj2jv = new Hashtable();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * App's object binding to VorbaIds\r
+ */\r
+ IdentityHashMap jv2vobj = null;\r
+\r
+ Hashtable vobj2jv = null;\r
+\r
+ /**\r
+ * called with a vamsas document which will be updated with new data from the\r
+ * app\r
+ * \r
+ * @param doc\r
+ */\r
+ public void updateVamsasDocument(ClientDoc doc) {\r
+ ensureVamsasBindings();\r
+ VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj,\r
+ baseProvEntry());\r
+ // wander through frames\r
+ vds.storeVAMSAS(new Object()); // Object is the apps datamodel ;)\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return a base provenance entry used by the VamsasDatastore object to get\r
+ * attributes from. this isn't particularly elegant either.\r
+ */\r
+ private Entry baseProvEntry() {\r
+ uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry();\r
+ pentry.setUser(this.getProvenanceUser());\r
+ pentry.setApp(this.getClientHandle().getClientName());\r
+ pentry.setDate(new java.util.Date());\r
+ pentry.setAction("created");\r
+ return pentry;\r
+ }\r
+\r
+ protected class VamsasClientWatcher extends Thread implements Runnable {\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see java.lang.Thread#run()\r
+ */\r
+ VamsasClient client = null;\r
+\r
+ VamsasClientWatcher(VamsasClient client) {\r
+ this.client = client;\r
+ }\r
+\r
+ boolean running = false;\r
+\r
+ public void run() {\r
+ running = true;\r
+ while (client.watchForChange) {\r
+ ClientDoc docio = client.watch(0);\r
+ if (docio != null) {\r
+ // VamsasClient GUI bits should be disabled whilst an update is in\r
+ // progress so the user doesn't screw anything up.\r
+ client.disableGui(true);\r
+ log.debug("Updating VamsasClient app from changed vamsas document.");\r
+ client.updateJalview(docio);\r
+ log.debug("Finished updating from document change.");\r
+ docio.closeDoc();\r
+ docio = null;\r
+ client.disableGui(false);\r
+ }\r
+ }\r
+ running = false;\r
+\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * @param args\r
+ */\r
+ public static void main(String[] args) {\r
+ // TODO Auto-generated method stub\r
+\r
+ }\r
+\r
+ /**\r
+ * disable (if b is true) or enable (if b is true) the VamsasClient's vamsas\r
+ * session gui bits whilst a document change is being updated to the app.\r
+ * \r
+ * @param b\r
+ */\r
+ public void disableGui(boolean b) {\r
+ // in jalview, we turn off the VAMSAS Session menu :\r
+ // Desktop.instance.setVamsasUpdate(b);\r
+ }\r
+\r
+ /**\r
+ * spawn a new thread to start the VamsasClientWatcher.\r
+ * \r
+ */\r
+ public void startWatcher() {\r
+ if (watcher == null)\r
+ watcher = new VamsasClientWatcher(this);\r
+ Thread thr = new Thread() {\r
+ public void run() {\r
+ watcher.start();\r
+ }\r
+ };\r
+ thr.start();\r
+ }\r
+\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff