JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[jalview.git] / src / jalview / ws / jws2 / jabaws2 / Jws2Instance.java

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index 509b96f..9e49ce7 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -1,24 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws2.jabaws2;
 
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.util.MessageManager;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.MsaWSClient;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
@@ -34,7 +38,7 @@ import compbio.data.msa.SequenceAnnotation;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-public class Jws2Instance
+public class Jws2Instance implements AutoCloseable
 {
   public String hosturl;
 
@@ -50,11 +54,17 @@ public class Jws2Instance
 
   /**
    * 
-   * @param hosturl Service endpoint
-   * @param serviceType Category for this service's analysis
-   * @param action text describing their action that service performs (eg 'aligning', 'analysing')
-   * @param description Description from JABAWS registry
-   * @param service JABAWS registry ID for service
+   * @param hosturl
+   *          Service endpoint
+   * @param serviceType
+   *          Category for this service's analysis
+   * @param action
+   *          text describing their action that service performs (eg 'aligning',
+   *          'analysing')
+   * @param description
+   *          Description from JABAWS registry
+   * @param service
+   *          JABAWS registry ID for service
    */
   public Jws2Instance(String hosturl, String serviceType, String action,
           String description, JABAService service)
@@ -104,7 +114,7 @@ public class Jws2Instance
         }
       } catch (Exception ex)
       {
-        System.err.println("Exception when retrieving presets for service "
+        jalview.bin.Console.errPrintln("Exception when retrieving presets for service "
                 + serviceType + " at " + hosturl);
       }
     }
@@ -118,7 +128,7 @@ public class Jws2Instance
      * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80) {
      * return serviceurl.getHost()+":"+serviceurl.getPort(); } return
      * serviceurl.getHost(); } catch (Exception e) {
-     * System.err.println("Failed to parse service URL '" + hosturl +
+     * jalview.bin.Console.errPrintln("Failed to parse service URL '" + hosturl +
      * "' as a valid URL!"); } return null;
      */
   }
@@ -147,27 +157,26 @@ public class Jws2Instance
     {
       return ((SequenceAnnotation) service).getRunnerOptions();
     }
-    throw new Error(
-            "Implementation Error: Runner Config not available for a JABAWS service of type "
-                    + serviceType + " (" + service.getClass() + ")");
+    throw new Error(MessageManager.formatMessage(
+            "error.implementation_error_runner_config_not_available",
+            new String[]
+            { serviceType, service.getClass().toString() }));
   }
 
   @Override
-  protected void finalize() throws Throwable
+  public void close()
   {
     if (service != null)
     {
       try
       {
-        Closeable svc = (Closeable) service;
-        service = null;
-        svc.close();
-      } catch (Exception e)
+        ((Closeable) service).close();
+      } catch (Throwable t)
       {
+        // ignore
       }
-      ;
     }
-    super.finalize();
+    // super.finalize();
   }
 
   public ParamDatastoreI getParamStore()
@@ -181,7 +190,7 @@ public class Jws2Instance
                         : null));
       } catch (Exception ex)
       {
-        System.err.println("Unexpected exception creating JabaParamStore.");
+        jalview.bin.Console.errPrintln("Unexpected exception creating JabaParamStore.");
         ex.printStackTrace();
       }
 
@@ -194,7 +203,8 @@ public class Jws2Instance
     // this is only valid for Jaba 1.0 - this formula might have to change!
     return hosturl
             + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
-                    : "/") + serviceType;
+                    : "/")
+            + serviceType;
   }
 
   private boolean hasParams = false, lookedForParams = false;
@@ -232,7 +242,9 @@ public class Jws2Instance
   {
     return "java:" + serviceType;
   }
+
   jalview.ws.uimodel.AlignAnalysisUIText aaui;
+
   public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()
   {
     return aaui;