src/jalview/gui/VamsasClient.java

   1 /**
   2  *
   3  */
   4 package jalview.gui;
   5
   6 import java.io.File;
   7 import java.io.FileOutputStream;
   8 import java.io.OutputStreamWriter;
   9 import java.io.PrintWriter;
  10 import java.util.Hashtable;
  11 import java.util.Vector;
  12 import java.util.jar.JarOutputStream;
  13
  14 import javax.swing.JInternalFrame;
  15
  16 import jalview.bin.Cache;
  17
  18 import org.vamsas.client.UserHandle;
  19 import org.vamsas.client.simpleclient.FileWatcher;
  20 import org.vamsas.client.simpleclient.VamsasArchive;
  21 import org.vamsas.client.simpleclient.VamsasFile;
  22 import org.vamsas.objects.core.VamsasDocument;
  23 import org.vamsas.test.simpleclient.ArchiveClient;
  24 import org.vamsas.test.simpleclient.ClientDoc;
  25
  26 /**
  27  * @author jimp
  28  *
  29  */
  30 public class VamsasClient extends ArchiveClient {
  31         Desktop us;
  32         // Cache.preferences for vamsas client session arena
  33         // preferences for check for default session at startup.
  34         // user and organisation stuff.
  35         public VamsasClient(Desktop jdesktop,
  36                         File sessionPath) {
  37                 super(System.getProperty("user.name"),System.getProperty("host.name"), "jalview","2.7",
  38                                 sessionPath);
  39                 us=jdesktop;
  40         }
  41         public void initial_update() {
  42                 Cache.log.info("Jalview loading the Vamsas Session.");
  43                 // load in the vamsas archive for the first time
  44                 ClientDoc cdoc = this.getUpdateable();
  45
  46         }
  47         public void get_update(VamsasArchive doc) {
  48                 Cache.log.info("Jalview updating from Vamsas Session.");
  49         }
  50         public void push_update() {
  51                 // collect all uncached alignments and put them into the vamsas dataset.
  52                 // store them.
  53                 Cache.log.info("Jalview updating the Vamsas Session.");
  54         }
  55         public void end_session() {
  56                 // stop any update/watcher thread.
  57                 Cache.log.info("Jalview disconnecting from the Vamsas Session.");
  58         }
  59         java.util.Hashtable jv2vobj = null;
  60         public void updateVamsasDocument(ClientDoc doc) {
  61                 if (jv2vobj==null)
  62                         jv2vobj = new Hashtable();
  63                 // wander through frames
  64                 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
  65
  66         if (frames == null)
  67         {
  68             return;
  69         }
  70
  71         try
  72         {
  73                 // Mapping
  74                 // Alignframe.alignment (non-null dataset)==alignment
  75                 // alignframe .alignment (dataset==null) = VAMAS[]
  76                 // Tree.alignment = vamsas[].tree (vamsas[] given by dataset, alignment given by local ref]
  77
  78                 Vector shortNames = new Vector();
  79
  80                 //REVERSE ORDER
  81             for (int i = frames.length - 1; i > -1; i--)
  82             {
  83                 if (frames[i] instanceof AlignFrame)
  84                 {
  85                         AlignFrame af = (AlignFrame) frames[i];
  86                         // check if this frame has an associated alignment object ?
  87                         // update alignment and root from frame.
  88
  89                 }
  90             }
  91         }
  92         catch (Exception e) {
  93                 Cache.log.error("Vamsas Document store exception",e);
  94         }
  95         }
  96         protected class VamsasClientWatcher extends Thread implements Runnable {
  97                 /* (non-Javadoc)
  98                  * @see java.lang.Thread#run()
  99                  */
 100                 VamsasClient client=null;
 101                 VamsasClientWatcher(VamsasClient client) {
 102                         this.client = client;
 103                 }
 104                 public void run() {
 105                         ClientDoc docio = client.watch(0);
 106
 107                 }
 108
 109         }
 110         /**
 111          * @param args
 112          */
 113         public static void main(String[] args) {
 114                 // TODO Auto-generated method stub
 115
 116         }
 117
 118 }