JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 19ede62..7881ec9 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -201,7 +201,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
     } catch (Exception e)
     {
-      jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",
+      Cache.error("Couldn't instantiate vamsas client !",
               e);
       return false;
     }
@@ -225,12 +225,12 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       }
     } catch (Error e)
     {
-      Cache.log.warn(
+      Cache.warn(
               "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
               e);
     } catch (Exception e)
     {
-      Cache.log.warn(
+      Cache.warn(
               "Probable VAMSAS client incompatibility - carrying on regardless",
               e);
     }
@@ -244,7 +244,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   private ClientHandle getJalviewHandle()
   {
     return new ClientHandle("jalview.bin.Jalview",
-            jalview.bin.Cache.getProperty("VERSION"));
+            Cache.getProperty("VERSION"));
   }
 
   /**
@@ -271,12 +271,12 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     addStoreDocumentHandler();
     startSession();
     inInitialUpdate = true;
-    Cache.log.debug(
+    Cache.debug(
             "Jalview loading the Vamsas Session for the first time.");
     dealWithDocumentUpdate(false); // we don't push an update out to the
     inInitialUpdate = false;
     // document yet.
-    Cache.log.debug("... finished update for the first time.");
+    Cache.debug("... finished update for the first time.");
   }
 
   /**
@@ -306,7 +306,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       }
     } catch (Exception e)
     {
-      Cache.log.warn(
+      Cache.warn(
               "Exception whilst refreshing jalview windows after a vamsas document update.",
               e);
     }
@@ -320,10 +320,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       @Override
       public void run()
       {
-        Cache.log.info("Jalview updating to the Vamsas Session.");
+        Cache.info("Jalview updating to the Vamsas Session.");
 
         dealWithDocumentUpdate(true);
-        Cache.log.info("Jalview finished updating to the Vamsas Session.");
+        Cache.info("Jalview finished updating to the Vamsas Session.");
       }
 
     });
@@ -353,7 +353,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     {
       throw new Error("Jalview not connected to Vamsas session");
     }
-    Cache.log.info("Jalview disconnecting from the Vamsas Session.");
+    Cache.info("Jalview disconnecting from the Vamsas Session.");
     try
     {
       if (joinedSession)
@@ -361,12 +361,12 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         boolean ourprompt = this.promptUser;
         this.promptUser = promptUser;
         vclient.finalizeClient();
-        Cache.log.info("Jalview has left the session.");
+        Cache.info("Jalview has left the session.");
         this.promptUser = ourprompt; // restore default value
       }
       else
       {
-        Cache.log.warn(
+        Cache.warn(
                 "JV Client leaving a session that's its not joined yet.");
       }
       joinedSession = false;
@@ -377,13 +377,13 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       vobj2jv = null;
     } catch (Exception e)
     {
-      Cache.log.error("Vamsas Session finalization threw exceptions!", e);
+      Cache.error("Vamsas Session finalization threw exceptions!", e);
     }
   }
 
   public void updateJalview(IClientDocument cdoc)
   {
-    Cache.log.debug("Jalview updating from sesion document ..");
+    Cache.debug("Jalview updating from sesion document ..");
     ensureJvVamsas();
     VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
             baseProvEntry(), alRedoState);
@@ -392,7 +392,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       vds.updateToJalview();
     } catch (Exception e)
     {
-      Cache.log.error("Failed to update Jalview from vamsas document.", e);
+      Cache.error("Failed to update Jalview from vamsas document.", e);
     }
     try
     {
@@ -404,10 +404,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       }
     } catch (Exception e)
     {
-      Cache.log.error(
+      Cache.error(
               "Exception when updating Jalview settings from Appdata.", e);
     }
-    Cache.log.debug(".. finished updating from sesion document.");
+    Cache.debug(".. finished updating from sesion document.");
 
   }
 
@@ -481,7 +481,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
             } catch (Exception e)
             {
               errorsDuringUpdate = true;
-              Cache.log.error("Exception synchronizing " + af.getTitle()
+              Cache.error("Exception synchronizing " + af.getTitle()
                       + " "
                       + (af.getViewport().getViewName() == null ? ""
                               : " view " + af.getViewport().getViewName())
@@ -519,7 +519,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       }
     } catch (Exception e)
     {
-      Cache.log.error("Exception synchronizing Views to Document :", e);
+      Cache.error("Exception synchronizing Views to Document :", e);
       errorsDuringUpdate = true;
     }
 
@@ -536,7 +536,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       }
     } catch (Exception e)
     {
-      Cache.log.error("Client Appdata Write exception", e);
+      Cache.error("Client Appdata Write exception", e);
       errorsDuringAppUpdate = true;
     }
     vds.clearSkipList();
@@ -564,32 +564,32 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   {
     int storedviews = 0;
     // called by update handler for document update.
-    Cache.log.debug("Updating jalview from changed vamsas document.");
+    Cache.debug("Updating jalview from changed vamsas document.");
     disableGui(true);
     try
     {
       long time = System.currentTimeMillis();
       IClientDocument cdoc = vclient.getClientDocument();
-      if (Cache.log.isDebugEnabled())
+      if (Cache.isDebugEnabled())
       {
-        Cache.log.debug("Time taken to get ClientDocument = "
+        Cache.debug("Time taken to get ClientDocument = "
                 + (System.currentTimeMillis() - time));
         time = System.currentTimeMillis();
       }
       if (fromJalview)
       {
         storedviews += updateVamsasDocument(cdoc);
-        if (Cache.log.isDebugEnabled())
+        if (Cache.isDebugEnabled())
         {
-          Cache.log.debug(
+          Cache.debug(
                   "Time taken to update Vamsas Document from jalview\t= "
                           + (System.currentTimeMillis() - time));
           time = System.currentTimeMillis();
         }
         cdoc.setVamsasRoots(cdoc.getVamsasRoots());
-        if (Cache.log.isDebugEnabled())
+        if (Cache.isDebugEnabled())
         {
-          Cache.log.debug("Time taken to set Document Roots\t\t= "
+          Cache.debug("Time taken to set Document Roots\t\t= "
                   + (System.currentTimeMillis() - time));
           time = System.currentTimeMillis();
         }
@@ -597,9 +597,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       else
       {
         updateJalview(cdoc);
-        if (Cache.log.isDebugEnabled())
+        if (Cache.isDebugEnabled())
         {
-          Cache.log.debug(
+          Cache.debug(
                   "Time taken to update Jalview from vamsas document Roots\t= "
                           + (System.currentTimeMillis() - time));
           time = System.currentTimeMillis();
@@ -607,9 +607,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
       }
       vclient.updateDocument(cdoc);
-      if (Cache.log.isDebugEnabled())
+      if (Cache.isDebugEnabled())
       {
-        Cache.log.debug("Time taken to update Session Document\t= "
+        Cache.debug("Time taken to update Session Document\t= "
                 + (System.currentTimeMillis() - time));
         time = System.currentTimeMillis();
       }
@@ -623,7 +623,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       recover_objectMappingBackup();
       storedviews = 0;
     }
-    Cache.log.debug("Finished updating from document change.");
+    Cache.debug("Finished updating from document change.");
     disableGui(false);
     return storedviews;
   }
@@ -636,12 +636,12 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
-        Cache.log.debug("Dealing with document update event.");
+        Cache.debug("Dealing with document update event.");
         client.dealWithDocumentUpdate(false);
-        Cache.log.debug("finished dealing with event.");
+        Cache.debug("finished dealing with event.");
       }
     });
-    Cache.log.debug("Added Jalview handler for vamsas document updates.");
+    Cache.debug("Added Jalview handler for vamsas document updates.");
   }
 
   private void addStoreDocumentHandler()
@@ -656,7 +656,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               {
                 if (client.promptUser)
                 {
-                  Cache.log.debug(
+                  Cache.debug(
                           "Asking user if the vamsas session should be stored.");
                   int reply = JvOptionPane.showInternalConfirmDialog(
                           Desktop.desktop,
@@ -667,22 +667,21 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
                   if (reply == JvOptionPane.YES_OPTION)
                   {
-                    Cache.log.debug("Prompting for vamsas store filename.");
+                    Cache.debug("Prompting for vamsas store filename.");
                     Desktop.instance.vamsasSave_actionPerformed(null);
-                    Cache.log
-                            .debug("Finished attempt at storing document.");
+                    Cache.debug("Finished attempt at storing document.");
                   }
-                  Cache.log.debug(
+                  Cache.debug(
                           "finished dealing with REQUESTTOCLOSE event.");
                 }
                 else
                 {
-                  Cache.log.debug(
+                  Cache.debug(
                           "Ignoring store document request (promptUser==false)");
                 }
               }
             });
-    Cache.log.debug("Added Jalview handler for vamsas document updates.");
+    Cache.debug("Added Jalview handler for vamsas document updates.");
   }
 
   public void disableGui(boolean b)
@@ -756,7 +755,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       } catch (Exception e)
       {
         // Complain to GUI
-        Cache.log.error("Failed to join vamsas session.", e);
+        Cache.error("Failed to join vamsas session.", e);
         vclient = null;
       }
       try
@@ -785,16 +784,16 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               {
                 return;
               }
-              // if (Cache.log.isDebugEnabled())
+              // if (Cache.isDebugEnabled())
               // {
-              // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+"
+              // Cache.debug("Received MouseOverMessage "+mm.getVorbaID()+"
               // "+mm.getPosition());
               // }
               Object jvobj = vobj2jv.get(mm.getVorbaID());
               if (jvobj != null && jvobj instanceof SequenceI)
               {
                 last = mstring;
-                // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
+                // Cache.debug("Handling Mouse over "+mm.getVorbaID()+"
                 // bound to "+jvobj+" at "+mm.getPosition());
                 // position is character position in aligned sequence
                 ssm.mouseOverVamsasSequence((SequenceI) jvobj,
@@ -980,7 +979,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               if (v != null)
               {
                 // this should really be a trace message.
-                // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+                // Cache.debug("Mouse over " + v.getId() + " bound to "
                 // + seq + " at " + index);
                 last = seq;
                 i = index;
@@ -1001,7 +1000,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
           {
             if (vobj2jv == null)
             {
-              Cache.log.warn(
+              Cache.warn(
                       "Selection listener still active for dead session.");
               // not in a session.
               return;
@@ -1101,7 +1100,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               if (sm != null)
               {
                 sm.validate(); // debug
-                Cache.log.debug("Selection Message\n" + sm.getRawMessage());
+                Cache.debug("Selection Message\n" + sm.getRawMessage());
                 pm.sendMessage(sm);
               }
             }
@@ -1112,7 +1111,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         ssm.addSelectionListener(selecter);
       } catch (Exception e)
       {
-        Cache.log.error("Failed to init Vamsas Picking", e);
+        Cache.error("Failed to init Vamsas Picking", e);
       }
     }
   }