pick manager and simulation of alignment modification within existing document.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@385 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/test/ExampleApplication.java b/src/uk/ac/vamsas/test/ExampleApplication.java
index 3722109..18b6cac 100644 (file)
--- a/src/uk/ac/vamsas/test/ExampleApplication.java
+++ b/src/uk/ac/vamsas/test/ExampleApplication.java
@@ -1,9 +1,3 @@
-/**
- * Created on 14-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
 package uk.ac.vamsas.test;
 
 import uk.ac.vamsas.client.*;
@@ -20,46 +14,82 @@ import java.io.IOException;
 import java.util.Vector;
 
 /**
- * Toy vamsas command line client application demonstrating the API. TODO: test
- * appData get/set methods TODO: verify and test pickManager and interaction
- * between it and other session events TODO: add more session interaction events
- * (currently: modifies document on start up, then modifies every 2 updates
- * before finalizing after 5 updates.
+ * Toy vamsas command line client application demonstrating the API. 
+ * Currently runs with one argument: ExampleApplication.main(new String("watch"))
+ * Test: Start up at least two of these processes independently and they will 
+ * successively modify and handle update events from the document model.
+ * 
+ * Behaviour of each client:
+ * Event handlers are registered for documentUpdate.
+ * - every document update:
+ *   * the vamsas document will be dumped to standard out using uk.ac.vamsas.test.simpleclient.ArchiveReports
+ *   * if there are more than 4 vamsas roots, the first sequence in the first alignment of the first dataset of the second vamsas root will be appended with a single gap character and then written back to the session document. 
+ * A pick thread is started, which sends random CUSTOM pick events every so often (tuning: flooding the pick channel seems to affect the behaviour of other vamsasClient threads, suggesting some object lock contention).
+ * A new vamsas root generated from uk.ac.vamsas.test.objects.Core.getDemoVamsas is added to the document.
+ * Then a while loop waits around for events until shutdown:
+ *  - currently it will shutdown after 9 updates (totalUpdates)
+ *  - an update will be made after every other update that is detected.
+ *  
+ * Status: PickManager now shuts down correctly. Serial updates for two instances work correctly and are detected under j1.4 (need to test in 1.5 and 1.6).
+ * 
+ * TODO: test
+ * appData get/set methods 
+ * 
+ * TODO: verify and test pickManager and interaction
+ * between it and other session events 
+ * 
+ * TODO: add more session interaction events
+ * 
+ * TODO: test client add/leave events - currently library generates exceptions for sessionlist and clientlist modifications.
  * 
  * @author jimp
  */
 
 public class ExampleApplication
 {
-  private static ClientHandle app;
+  private ClientHandle app;
 
-  private static UserHandle user; // TODO: make this something defined by the
+  private UserHandle user; // TODO: make this something defined by the
   // api
 
-  private static IClientFactory clientfactory;
-
-  private static IClient vorbaclient;
+  private IClientFactory clientfactory;
 
-  private static byte[] mydata;
+  private IClient vorbaclient;
 
-  private static Vector vamsasObjects;
+  private byte[] mydata;
 
-  private static boolean isUpdated = false;
+  private Vector vamsasObjects;
 
-  private static boolean isShuttingdown = false;
+  private boolean isUpdated = false;
 
-  private static boolean isFinalizing = false;
+  private boolean isShuttingdown = false;
 
-  private static void processVamsasDocument(IClientDocument doc)
+  private boolean isFinalizing = false;
+  private int totalUpdates = 9;
+  private void processVamsasDocument(IClientDocument doc)
   {
+    if (doc.getVamsasRoots().length<4) {
     doc.addVamsasRoot(Core.getDemoVamsas());
+    } else {
+      try {
+        uk.ac.vamsas.objects.core.DataSet ds = doc.getVamsasRoots()[1].getDataSet(0);
+        uk.ac.vamsas.objects.core.AlignmentSequence alsq = ds.getAlignment(0).getAlignmentSequence(0);
+        System.out.println("Modifying Sequence:\n"+alsq.hashCode());
+        alsq.setSequence(alsq.getSequence()+ds.getAlignment(0).getGapChar());
+        System.out.println("Modifying Sequence:\n"+alsq.hashCode());
+        System.out.println("Modified Sequence:\n"+alsq.getSequence());
+        doc.setVamsasRoots(doc.getVamsasRoots());
+      } catch (Exception ee) {
+      
+      }
+    }
     vorbaclient.updateDocument(doc);
     // merge vamsasObjects with vamsas objects in document
     // get this apps 'mydata' if it hasn't got it already.
     // .. access this application's 'public' mydata' if there is any.
   }
 
-  private static void addHandlers(IClient avorbaclient)
+  private void addHandlers(IClient avorbaclient)
   {
     // make a non-volatile reference to the client instance.
     final IClient vorbaclient = avorbaclient;
@@ -77,6 +107,21 @@ public class ExampleApplication
           IClientDocument cdoc = vorbaclient.getClientDocument();
           uk.ac.vamsas.test.simpleclient.ArchiveReports.rootReport(
               cdoc.getVamsasRoots(), true, System.out);
+          // Simple update
+          try {
+            if (cdoc.getVamsasRoots().length>2) {
+              uk.ac.vamsas.objects.core.DataSet ds = cdoc.getVamsasRoots()[1].getDataSet(0);
+              uk.ac.vamsas.objects.core.AlignmentSequence alsq = ds.getAlignment(0).getAlignmentSequence(0);
+              if (alsq.isUpdated())
+                System.out.println("Seqeuence was updated since last time.");
+              alsq.setSequence(alsq.getSequence()+ds.getAlignment(0).getGapChar());
+              System.out.println("Newly Modified Sequence:\n"+alsq.getSequence());
+              cdoc.setVamsasRoots(cdoc.getVamsasRoots());
+            }
+          } catch (Exception ee) {
+            System.err.println("Exception whilst updating :");
+            ee.printStackTrace(System.err);
+          }
           vorbaclient.updateDocument(cdoc);
         }
         catch (Exception e)
@@ -150,12 +195,12 @@ public class ExampleApplication
 
   }
 
-  public static String Usage = "ExampleApplication [session urn] watch/n( future usage is :/n <vamsasFileDirectory> <vamsasSessionURN> <action> [+<arguments>]\n"
+  public String Usage = "ExampleApplication [session urn] watch/n( future usage is :/n <vamsasFileDirectory> <vamsasSessionURN> <action> [+<arguments>]\n"
     + "<action> is one of :\n\tsave,update,close,watch";
 
-  static String sess = null;
+  String sess = null;
 
-  private static boolean parseArgs(String args[])
+  private boolean parseArgs(String args[])
   {
     if (args.length == 0)
     {
@@ -168,37 +213,37 @@ public class ExampleApplication
     return true;
   }
 
-  public static void main(String[] args)
+  class ExamplePicker extends Thread
   {
-    class ExamplePicker extends Thread
-    {
-      String me = null;
+    String me = null;
 
-      public IPickManager pm = null;
+    public IPickManager pm = null;
 
-      ExamplePicker(String me, IPickManager pm)
-      {
-        this.me = me;
-        this.pm = pm;
-      }
+    ExamplePicker(String me, IPickManager pm)
+    {
+      this.me = me;
+      this.pm = pm;
+    }
 
-      public void run()
+    public void run()
+    {
+      int mcount = 1;
+      while (pm != null)
       {
-        int mcount = 1;
-        while (pm != null)
-        {
-          try { Thread.sleep(1000 + (long) Math.random() * 10000); }
-          catch (Exception e) {}
+        try { Thread.sleep(1000 + (long) Math.random() * 10000); }
+        catch (Exception e) {}
 
-          if (pm != null)
-          {
-            pm.sendMessage(new uk.ac.vamsas.client.picking.CustomMessage("Message " + mcount++ + " from " + me));
-          }
+        if (pm != null)
+        {
+          pm.sendMessage(new uk.ac.vamsas.client.picking.CustomMessage("Message " + mcount++ + " from " + me));
         }
       }
-
     }
 
+  }
+
+  public void runMe(String[] args)
+  {
     if (!parseArgs(args))
     {
       System.err.print(Usage);
@@ -271,7 +316,7 @@ public class ExampleApplication
 
       });
     }
-    while (!isShuttingdown && update < 5)
+    while (!isShuttingdown && update < totalUpdates)
     {
       // do something with data
       // , update document, or something.
@@ -327,5 +372,9 @@ public class ExampleApplication
     // finish
     System.out.println("Byee!");
   }
-
+  public static void main(String[] args)
+  {
+    ExampleApplication example = new ExampleApplication();
+    example.runMe(args);
+  }
 }