X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fsimpleclient%2FClientsFile.java;h=f83324aa6f6ad51e3a347e479d30dcac93594f73;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=e700ee44abe27fdf3196f97523aa6c413577c08f;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/client/simpleclient/ClientsFile.java b/src/uk/ac/vamsas/client/simpleclient/ClientsFile.java
index e700ee4..f83324a 100644
--- a/src/uk/ac/vamsas/client/simpleclient/ClientsFile.java
+++ b/src/uk/ac/vamsas/client/simpleclient/ClientsFile.java
@@ -1,298 +1,355 @@
-package uk.ac.vamsas.client.simpleclient;
-
-import uk.ac.vamsas.client.*;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutput;
-import java.io.ObjectOutputStream;
-import java.io.OutputStream;
-import java.util.Vector;
-
-/**
- * Handler for the clientsFile within a vamsas session thread.
- * @author jim 
- */
-public class ClientsFile extends ListFile {
-  private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog(ClientsFile.class);
-  /**
-   * number of my client in list - passed back when a client 
-   * is added to list, and used (if valid) for quickly 
-   * looking up presence of client handle in the list.
-   */
-  private int syncnum = 1;
-
-  public ClientsFile(File filelist) throws IOException {
-    super(filelist);
-  }
-
-  /**
-   * internal method for getting clientList - ensures a lock has been made but
-   * does not release it.
-   * 
-   * @return list of clients
-   */
-  private ClientHandle[] retrieveClientHandles() {
-    if (lockFile()) {
-      try {
-        ClientHandle[] clients=null;
-        if (fileLock.length()>0) {
-          
-          ObjectInputStream is = new ObjectInputStream(fileLock.getBufferedInputStream(true));
-          Object o;
-          o=is.readObject();
-          if (o!=null) {
-            try {
-              clients = (ClientHandle[]) o;
-            }
-            catch (Exception e) {
-              System.err.println("Garbage in the clientHandle list "+this.sessionFile);
-            }
-          }
-        }
-        return clients;
-      } catch (FileNotFoundException e) {
-        // TODO Auto-generated catch block
-        e.printStackTrace(System.err);
-      } catch (Exception e) {
-        e.printStackTrace(System.err);
-      }
-    }
-    return null;
-  }
-  /**
-   * get the clientList from the file. May return null if lock failed!
-   * @return clientList
-   */
-  public ClientHandle[] retrieveClientList() {
-    if (lockFile()) {
-      ClientHandle[] clients = retrieveClientHandles();
-      unlockFile();
-      return clients;
-    }
-    return null;
-  }
-  /**
-   * get list from the locked ClientList.
-   * @param extantlock
-   * @return clientList or null if lock failed (or file was empty)
-   */
-  public ClientHandle[] retrieveClientList(Lock extantlock) {
-    if (lockFile(extantlock)) {
-      ClientHandle[] clients = retrieveClientHandles();
-      unlockFile();
-      return clients;
-    }
-    return null;
-  }
-  /**
-   * adds clientHandle me to the clientList under an existing lock extantLock.
-   * @param me
-   * @param extantLock
-   * @return client index in list or 0 if lock was invalid or addClient operation failed.
-   */
-  public int addClient(ClientHandle me, Lock extantLock) {
-    return addClient(me, true, extantLock);
-  }
-  
-  /**
-   * adds clientHandle me to the clientList under an existing lock.
-   * @param me - clientHandle
-   * @param disambig - if true then add will fail if an identical clientHandle already exists
-   * @param extantLock - existing lock
-   * @return client index in list or 0 if addClient (or the lock) failed.
-   */
-  
-  public int addClient(ClientHandle me, boolean disambig, Lock extantLock) {
-    if (lockFile(extantLock)) {
-      syncnum = addClient(me, disambig);
-      unlockFile();
-      return syncnum;
-    }
-    return 0;
-  }
-  
-  /**
-   * adds the ClientHandle to the list - if it is not unique, then the
-   * ClientHandle object is modified to make it unique in the list. returns the
-   * clientNumber for the client in the session.
-   * 
-   * @param me
-   * @return
-   */
-
-  public int addClient(ClientHandle me) {
-    syncnum = addClient(me, true);
-    unlockFile();
-    return syncnum;
-  }
-
-  /**
-   * removes 'me' from the session ClientList without complaint if 'me' isn't in the clientList already.
-   * @param me client handle to be removed
-   * @param clientlock existing lock passed from watcher.
-   */
-  public void removeClient(ClientHandle me, Lock clientlock) {
-    int mynum=-1;
-    if (lockFile(clientlock)) {
-      ClientHandle[] clients = retrieveClientHandles();
-      if (clients != null) {
-        if ((syncnum<=0 || syncnum>clients.length) || clients[syncnum-1]!=me) {
-          for (int i = 0, j = clients.length; i < j; i++) 
-            if (clients[i].equals(me)) {
-              mynum=i;
-              break;
-            }
-        } else {
-          mynum=syncnum-1;
-        }
-        if (mynum>-1) {
-          ClientHandle[] newlist = new ClientHandle[clients.length - 1];
-          for (int k=0,i = 0, j = clients.length; i < j; i++)
-            if (i!=mynum)
-              newlist[k++] = clients[i];
-          if (!putClientList(newlist))
-            throw new Error("Failed to write new clientList!"); // failed to put the clientList to disk.
-        }
-      }
-      unlockFile();
-    } else {
-      throw new Error("Couldn't get lock for "+((sessionFile==null) ? "Unitialised sessionFile in ClientsFile" : sessionFile.getAbsolutePath()));
-    }
-  }
-  /**
-   * Adds a ClientHandle to the ClientList file - optionally disambiguating 
-   * the ClientHandle (modifes the URN). 
-   * Note: Caller is left to release the lock on the ClientList.
-   * @param me
-   * @param disambiguate -
-   *          flag indicating if the URN for me should be disambiguated to
-   *          differentiate between sessions.
-   * @return index of clientHandle in new list, or -1-position of existing
-   *         clientHandle (if disambiguate is true)
-   */
-  protected int addClient(ClientHandle me, boolean disambiguate) {
-    int newclient = 0;
-    int tries=5;
-    while (tries-->0 && !lockFile())
-      try { Thread.sleep(1); } catch (Exception e){};
-    if (lockFile()) {
-      ClientHandle[] clients = retrieveClientHandles();
-      if (me.getClientUrn()==null) {
-        // TODO: move this into ClientUrn as a standard form method.
-        me.setClientUrn("vamsas://"+me.getClientName()+":"+me.getVersion()+"/");
-      }
-      if (clients == null) {
-        clients = new ClientHandle[1];
-        clients[0] = me;
-        newclient = 1;
-      } else {
-        int k = 0;
-        for (int i = 0, j = clients.length; i < j; i++) {
-          if (clients[i].equals(me)) {
-            if (disambiguate) {
-              while (clients[i].equals(me)) {
-                me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better
-                                                          // disambiguation of
-                                                          // urn.
-              }
-            } else {
-              // will not write the ambiguous clientHandle to disk, just return
-              // its index.
-              return -1 - i;
-            }
-          }
-        }
-        int i, j;
-        ClientHandle[] newlist = new ClientHandle[clients.length + 1];
-        for (i = 0, j = clients.length; i < j; i++)
-          newlist[i] = clients[i];
-        newlist[j] = me;
-        clients = newlist;
-        newclient = j+1;
-      }
-      if (!putClientList(clients))
-        return 0; // failed to put the clientList to disk.
-    }
-    return newclient;
-  }
-  /**
-   * when set true - get FileNotFoundExceptions on WinXP when writing to locked stream after the backup has been made (via the backupFile method)
-   */
-  boolean backup=false;
-  /**
-   * safely writes clients array to the file referred to by sessionFile.
-   * 
-   * @param clients
-   * @return true if successful write. Throws Errors otherwise.
-   */
-  protected boolean putClientList(ClientHandle[] clients) {
-    if (lockFile()) {
-      File templist=null;
-      if (backup) {
-        templist = backupSessionFile();
-      }
-      if (!backup || (templist != null)) {
-        int retries=3;
-        while (retries-->0) {
-          try {
-            ObjectOutputStream os = 
-              new ObjectOutputStream(fileLock.getBufferedOutputStream(true));
-            log.debug("About to write "+clients.length+" clientHandles to output stream.");
-            os.writeObject(clients);
-            os.close();
-          // All done - remove the backup.
-          if (backup)
-            templist.delete();
-          templist = null;
-          retries=-1;
-          } catch (Exception e) {
-            System.err
-            .println("Serious - problems writing to sessionFile.");
-            if (retries>0 && templist != null) {
-              System.err.println("Recovering from Backup in "
-                      + templist.getAbsolutePath());
-              templist.renameTo(fileLock.target);
-            }
-            e.printStackTrace(System.err);
-          }
-        }
-        if (retries>-2) {
-          System.err
-          .println("Serious - problems writing to sessionFile. Giving Up.");
-          return false;
-        }
-      } else {
-        throw new Error(
-            "Couldn't create backup of the clientList before writing to it!");
-      }
-    } else {
-      throw new Error("Could not lock the clientList: "
-          + ((sessionFile == null) ? "Unitialized ClientsFile"
-              : " failed to get lock on " + sessionFile.getAbsolutePath()));
-    }
-    // successful!
-    return true;
-  }
-
-  public void clearList() {
-    if (lockFile()) {
-      try {
-        FileOutputStream fout = fileLock.getFileOutputStream(true);
-        fout.flush();
-        fout.close();
-      } catch (Exception e) {
-        throw new Error("Problems trying to clear clientlist!",e);
-        
-      }
-    }
-    
-  }
-}
+/*
+ * 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.client.simpleclient;
+
+import uk.ac.vamsas.client.*;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutput;
+import java.io.ObjectOutputStream;
+import java.io.OutputStream;
+import java.util.Vector;
+
+/**
+ * Handler for the clientsFile within a vamsas session thread.
+ * 
+ * @author jim
+ */
+public class ClientsFile extends ListFile {
+  private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory
+      .getLog(ClientsFile.class);
+
+  /**
+   * number of my client in list - passed back when a client is added to list,
+   * and used (if valid) for quickly looking up presence of client handle in the
+   * list.
+   */
+  private int syncnum = 1;
+
+  public ClientsFile(File filelist) throws IOException {
+    super(filelist);
+  }
+
+  /**
+   * internal method for getting clientList - ensures a lock has been made but
+   * does not release it.
+   * 
+   * @return list of clients
+   */
+  private ClientHandle[] retrieveClientHandles() {
+    if (lockFile()) {
+      try {
+        ClientHandle[] clients = null;
+        if (fileLock.length() > 0) {
+
+          ObjectInputStream is = new ObjectInputStream(fileLock
+              .getBufferedInputStream(true));
+          Object o;
+          o = is.readObject();
+          if (o != null) {
+            try {
+              clients = (ClientHandle[]) o;
+            } catch (Exception e) {
+              System.err.println("Garbage in the clientHandle list "
+                  + this.sessionFile);
+            }
+          }
+        }
+        return clients;
+      } catch (FileNotFoundException e) {
+        // TODO Auto-generated catch block
+        e.printStackTrace(System.err);
+      } catch (Exception e) {
+        e.printStackTrace(System.err);
+      }
+    }
+    return null;
+  }
+
+  /**
+   * get the clientList from the file. May return null if lock failed!
+   * 
+   * @return clientList
+   */
+  public ClientHandle[] retrieveClientList() {
+    if (lockFile()) {
+      ClientHandle[] clients = retrieveClientHandles();
+      unlockFile();
+      return clients;
+    }
+    return null;
+  }
+
+  /**
+   * get list from the locked ClientList.
+   * 
+   * @param extantlock
+   * @return clientList or null if lock failed (or file was empty)
+   */
+  public ClientHandle[] retrieveClientList(Lock extantlock) {
+    if (lockFile(extantlock)) {
+      ClientHandle[] clients = retrieveClientHandles();
+      unlockFile();
+      return clients;
+    }
+    return null;
+  }
+
+  /**
+   * adds clientHandle me to the clientList under an existing lock extantLock.
+   * 
+   * @param me
+   * @param extantLock
+   * @return client index in list or 0 if lock was invalid or addClient
+   *         operation failed.
+   */
+  public int addClient(ClientHandle me, Lock extantLock) {
+    return addClient(me, true, extantLock);
+  }
+
+  /**
+   * adds clientHandle me to the clientList under an existing lock.
+   * 
+   * @param me
+   *          - clientHandle
+   * @param disambig
+   *          - if true then add will fail if an identical clientHandle already
+   *          exists
+   * @param extantLock
+   *          - existing lock
+   * @return client index in list or 0 if addClient (or the lock) failed.
+   */
+
+  public int addClient(ClientHandle me, boolean disambig, Lock extantLock) {
+    if (lockFile(extantLock)) {
+      syncnum = addClient(me, disambig);
+      unlockFile();
+      return syncnum;
+    }
+    return 0;
+  }
+
+  /**
+   * adds the ClientHandle to the list - if it is not unique, then the
+   * ClientHandle object is modified to make it unique in the list. returns the
+   * clientNumber for the client in the session.
+   * 
+   * @param me
+   * @return
+   */
+
+  public int addClient(ClientHandle me) {
+    syncnum = addClient(me, true);
+    unlockFile();
+    return syncnum;
+  }
+
+  /**
+   * removes 'me' from the session ClientList without complaint if 'me' isn't in
+   * the clientList already.
+   * 
+   * @param me
+   *          client handle to be removed
+   * @param clientlock
+   *          existing lock passed from watcher.
+   */
+  public void removeClient(ClientHandle me, Lock clientlock) {
+    int mynum = -1;
+    if (lockFile(clientlock)) {
+      ClientHandle[] clients = retrieveClientHandles();
+      if (clients != null) {
+        if ((syncnum <= 0 || syncnum > clients.length)
+            || clients[syncnum - 1] != me) {
+          for (int i = 0, j = clients.length; i < j; i++)
+            if (clients[i].equals(me)) {
+              mynum = i;
+              break;
+            }
+        } else {
+          mynum = syncnum - 1;
+        }
+        if (mynum > -1) {
+          ClientHandle[] newlist = new ClientHandle[clients.length - 1];
+          for (int k = 0, i = 0, j = clients.length; i < j; i++)
+            if (i != mynum)
+              newlist[k++] = clients[i];
+          if (!putClientList(newlist))
+            throw new Error("Failed to write new clientList!"); // failed to put
+                                                                // the
+                                                                // clientList to
+                                                                // disk.
+        }
+      }
+      unlockFile();
+    } else {
+      throw new Error("Couldn't get lock for "
+          + ((sessionFile == null) ? "Unitialised sessionFile in ClientsFile"
+              : sessionFile.getAbsolutePath()));
+    }
+  }
+
+  /**
+   * Adds a ClientHandle to the ClientList file - optionally disambiguating the
+   * ClientHandle (modifes the URN). Note: Caller is left to release the lock on
+   * the ClientList.
+   * 
+   * @param me
+   * @param disambiguate
+   *          - flag indicating if the URN for me should be disambiguated to
+   *          differentiate between sessions.
+   * @return index of clientHandle in new list, or -1-position of existing
+   *         clientHandle (if disambiguate is true)
+   */
+  protected int addClient(ClientHandle me, boolean disambiguate) {
+    int newclient = 0;
+    int tries = 5;
+    while (tries-- > 0 && !lockFile())
+      try {
+        Thread.sleep(1);
+      } catch (Exception e) {
+      }
+    ;
+    if (lockFile()) {
+      ClientHandle[] clients = retrieveClientHandles();
+      if (me.getClientUrn() == null) {
+        // TODO: move this into ClientUrn as a standard form method.
+        me.setClientUrn("vamsas://" + me.getClientName() + ":"
+            + me.getVersion() + "/");
+      }
+      if (clients == null) {
+        clients = new ClientHandle[1];
+        clients[0] = me;
+        newclient = 1;
+      } else {
+        int k = 0;
+        for (int i = 0, j = clients.length; i < j; i++) {
+          if (clients[i].equals(me)) {
+            if (disambiguate) {
+              while (clients[i].equals(me)) {
+                me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better
+                // disambiguation of
+                // urn.
+              }
+            } else {
+              // will not write the ambiguous clientHandle to disk, just return
+              // its index.
+              return -1 - i;
+            }
+          }
+        }
+        int i, j;
+        ClientHandle[] newlist = new ClientHandle[clients.length + 1];
+        for (i = 0, j = clients.length; i < j; i++)
+          newlist[i] = clients[i];
+        newlist[j] = me;
+        clients = newlist;
+        newclient = j + 1;
+      }
+      if (!putClientList(clients))
+        return 0; // failed to put the clientList to disk.
+    }
+    return newclient;
+  }
+
+  /**
+   * when set true - get FileNotFoundExceptions on WinXP when writing to locked
+   * stream after the backup has been made (via the backupFile method)
+   */
+  boolean backup = false;
+
+  /**
+   * safely writes clients array to the file referred to by sessionFile.
+   * 
+   * @param clients
+   * @return true if successful write. Throws Errors otherwise.
+   */
+  protected boolean putClientList(ClientHandle[] clients) {
+    if (lockFile()) {
+      File templist = null;
+      if (backup) {
+        templist = backupSessionFile();
+      }
+      if (!backup || (templist != null)) {
+        int retries = 3;
+        while (retries-- > 0) {
+          try {
+            ObjectOutputStream os = new ObjectOutputStream(fileLock
+                .getBufferedOutputStream(true));
+            log.debug("About to write " + clients.length
+                + " clientHandles to output stream.");
+            os.writeObject(clients);
+            os.close();
+            // All done - remove the backup.
+            if (backup)
+              templist.delete();
+            templist = null;
+            retries = -1;
+          } catch (Exception e) {
+            System.err.println("Serious - problems writing to sessionFile.");
+            if (retries > 0 && templist != null) {
+              System.err.println("Recovering from Backup in "
+                  + templist.getAbsolutePath());
+              templist.renameTo(fileLock.target);
+            }
+            e.printStackTrace(System.err);
+          }
+        }
+        if (retries > -2) {
+          System.err
+              .println("Serious - problems writing to sessionFile. Giving Up.");
+          return false;
+        }
+      } else {
+        throw new Error(
+            "Couldn't create backup of the clientList before writing to it!");
+      }
+    } else {
+      throw new Error("Could not lock the clientList: "
+          + ((sessionFile == null) ? "Unitialized ClientsFile"
+              : " failed to get lock on " + sessionFile.getAbsolutePath()));
+    }
+    // successful!
+    return true;
+  }
+
+  public void clearList() {
+    if (lockFile()) {
+      try {
+        FileOutputStream fout = fileLock.getFileOutputStream(true);
+        fout.flush();
+        fout.close();
+      } catch (Exception e) {
+        throw new Error("Problems trying to clear clientlist!", e);
+
+      }
+    }
+
+  }
+}