JAL-3220 j2sIgnore on main methods on test / utility classes

diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 9d68af1..c515e6c 100644 (file)
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -219,7 +219,7 @@ public class BlogReader extends JPanel
 
       }
     };
-  };
+  }
 
   private JLabel lblChannels = new JLabel();
 
@@ -365,7 +365,6 @@ public class BlogReader extends JPanel
     } catch (Exception x)
     {
     }
-    ;
     if (chan != null && chan.getItems() != null)
     {
       Cache.log.debug("Scanning news items: newsnew=" + newsnew
@@ -752,6 +751,10 @@ public class BlogReader extends JPanel
     }
   }
 
+  /**
+   * @j2sIgnore
+   * @param args
+   */
   public static void main(String args[])
   {
     // this tests the detection of new news based on the last read date stored
@@ -788,7 +791,6 @@ public class BlogReader extends JPanel
         } catch (InterruptedException x)
         {
         }
-        ;
       } while (me.isVisible());
 
       if (me.isNewsNew())

diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 4c019a6..2e88eeb 100644 (file)
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -497,7 +497,6 @@ public class Console extends WindowAdapter
             } catch (InterruptedException e)
             {
             }
-            ;
           }
         }
         else
@@ -633,6 +632,10 @@ public class Console extends WindowAdapter
     return input;
   }
 
+  /**
+   * @j2sIgnore
+   * @param arg
+   */
   public static void main(String[] arg)
   {
     new Console().test(); // create console with not reference

diff --git a/src/jalview/gui/RestServiceEditorPane.java b/src/jalview/gui/RestServiceEditorPane.java
index 2e2593b..cda76d9 100644 (file)
--- a/src/jalview/gui/RestServiceEditorPane.java
+++ b/src/jalview/gui/RestServiceEditorPane.java
@@ -147,9 +147,9 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
 
   }
 
-  Vector<String> _iparam = new Vector<String>();
+  Vector<String> _iparam = new Vector<>();
 
-  Vector<String> _rparam = new Vector<String>();
+  Vector<String> _rparam = new Vector<>();
 
   /**
    * generate an editable URL service string and parameter list using the
@@ -351,7 +351,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
 
   private boolean updateServiceFromGui()
   {
-    Map<String, InputType> inputTypes = new HashMap<String, InputType>();
+    Map<String, InputType> inputTypes = new HashMap<>();
     StringBuffer warnings = new StringBuffer();
     for (String its : _iparam)
     {
@@ -455,6 +455,10 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
 
   }
 
+  /**
+   * @j2sIgnore
+   * @param args
+   */
   public static void main(String[] args)
   {
     if (args.length == 0)
@@ -463,6 +467,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
       {
         boolean visible = true;
 
+        @Override
         public void run()
         {
           boolean nulserv = true;
@@ -514,7 +519,6 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
               } catch (Exception x)
               {
               }
-              ;
             }
             visible = true;
           }

diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 10798f6..976e551 100644 (file)
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -69,14 +69,13 @@ import javax.swing.border.TitledBorder;
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
 
-import net.miginfocom.swing.MigLayout;
-
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
 import compbio.metadata.Parameter;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
+import net.miginfocom.swing.MigLayout;
 
 /**
  * job parameter editing/browsing dialog box. User can browse existing settings
@@ -959,6 +958,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
    * testing method - grab a service and parameter set and show the window
    * 
    * @param args
+   * @j2sIgnore
    */
   public static void main(String[] args)
   {
@@ -967,7 +967,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     int p = 0;
     if (args.length > 0)
     {
-      Vector<String> services = new Vector<String>();
+      Vector<String> services = new Vector<>();
       services.addElement(args[p++]);
       Jws2Discoverer.getDiscoverer().setServiceUrls(services);
     }
@@ -1183,7 +1183,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
               {
                 inter = true;
               }
-              ;
             }
             jf.dispose();
           }

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 6db04a0..4916bb3 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -159,7 +159,9 @@ public class AppletFormatAdapter
 
     this.selectedFile = selectedFile;
     if (selectedFile != null)
+    {
       this.inFile = selectedFile.getPath();
+    }
     this.inFile = file;
     try
     {
@@ -435,7 +437,9 @@ public class AppletFormatAdapter
   public static DataSourceType checkProtocol(Object dataObject)
   {
     if(dataObject instanceof File)
+    {
       return DataSourceType.FILE;
+    }
     
     String data = dataObject.toString();
     DataSourceType protocol = DataSourceType.PASTE;
@@ -456,6 +460,10 @@ public class AppletFormatAdapter
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index ed67af8..b312474 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -452,6 +452,11 @@ public class IdentifyFile
     return true;
   }
 
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     for (int i = 0; args != null && i < args.length; i++)

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 517701b..1e9c5ed 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -316,8 +316,6 @@ public class NewickFile extends FileParse
 
           continue;
         }
-
-        ;
         d++;
 
         if (c.right() == null)
@@ -417,8 +415,6 @@ public class NewickFile extends FileParse
             Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
                     nf);
           }
-
-          ;
         }
         // Parse simpler field strings
         String fstring = nf.substring(ncp, fcp);
@@ -942,7 +938,11 @@ public class NewickFile extends FileParse
     }
   }
 
-  // Test
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     try

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 1635682..d40446d 100644 (file)
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -52,7 +52,7 @@ public class ParsePackedSet
   public Object[] getAlignment(JalviewDataset context,
           Iterable<DataProvider> files) throws Exception
   {
-    List<Object> rslt = new ArrayList<Object>();
+    List<Object> rslt = new ArrayList<>();
     if (context == null)
     {
       context = new JalviewDataset();
@@ -151,7 +151,7 @@ public class ParsePackedSet
         // if not, create one.
         if (context.featureColours == null)
         {
-          context.featureColours = new HashMap<String, FeatureColourI>();
+          context.featureColours = new HashMap<>();
         }
         try
         {
@@ -223,12 +223,13 @@ public class ParsePackedSet
    * would be created.
    * 
    * @param args
+   * @j2sIgnore
    */
   public static void main(String args[])
   {
     // make data providers from the set of keys/files
     int i = 0;
-    List<DataProvider> dp = new ArrayList<DataProvider>();
+    List<DataProvider> dp = new ArrayList<>();
     while ((i + 1) < args.length)
     {
       String type = args[i++];

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index d435065..5f84ca0 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -2278,6 +2278,10 @@ public class ResidueProperties
 
   // main method generates perl representation of residue property hash
   // / cut here
+  /**
+   * @j2sIgnore
+   * @param args
+   */
   public static void main(String[] args)
   {
     Hashtable<String, Vector<String>> aaProps = new Hashtable<>();

diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index a26dfbb..67309a0 100644 (file)
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -36,6 +36,7 @@ public class GroupUrlLink
 
     public int urlLength;
 
+    @Override
     public String toString()
     {
       return "Generated url is estimated to be too long (" + urlLength
@@ -317,10 +318,12 @@ public class GroupUrlLink
   private String _replaceFor(String token)
   {
     for (int i = 0; i < mtch.length; i++)
+    {
       if (segs[i] > -1 && mtch[i].equals(token))
       {
         return regexReplace[i];
       }
+    }
     return null;
   }
 
@@ -744,6 +747,7 @@ public class GroupUrlLink
     return r;
   }
 
+  @Override
   public String toString()
   {
     StringBuffer result = new StringBuffer();
@@ -812,6 +816,11 @@ public class GroupUrlLink
     }
   }
 
+  /**
+   * 
+   * @param argv
+   * @j2sIgnore
+   */
   public static void main(String argv[])
   {
     // note - JAL-1383 - these services are all dead

diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 5319eab..516a719 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -178,7 +178,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     running = true;
 
     // first set up exclusion list if needed
-    final Set<String> ignoredServices = new HashSet<String>();
+    final Set<String> ignoredServices = new HashSet<>();
     for (String ignored : Cache
             .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
     {
@@ -217,9 +217,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     {
       validServiceUrls.removeAllElements();
     }
-    ArrayList<String> svctypes = new ArrayList<String>();
+    ArrayList<String> svctypes = new ArrayList<>();
 
-    List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+    List<JabaWsServerQuery> qrys = new ArrayList<>();
     for (final String jwsserver : getServiceUrls())
     {
       JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
@@ -249,7 +249,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       } catch (Exception e)
       {
       }
-      ;
       for (JabaWsServerQuery squery : qrys)
       {
         if (squery.isRunning())
@@ -285,7 +284,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                   + svctypes.indexOf(svc.serviceType);
         }
         jalview.util.QuickSort.sort(spos, svcs);
-        services = new Vector<Jws2Instance>();
+        services = new Vector<>();
         for (Jws2Instance svc : svcs)
         {
           if (!ignoredServices.contains(svc.serviceType))
@@ -312,7 +311,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (services == null)
     {
-      services = new Vector<Jws2Instance>();
+      services = new Vector<>();
     }
     System.out.println(
             "Discovered service: " + jwsservers + " " + service.toString());
@@ -329,7 +328,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     service.hasParameters();
     if (validServiceUrls == null)
     {
-      validServiceUrls = new Vector<String>();
+      validServiceUrls = new Vector<>();
     }
     validServiceUrls.add(jwsservers);
   }
@@ -363,10 +362,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      * for moment we keep them separate.
      */
     JMenu atpoint;
-    List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+    List<Jws2Instance> enumerableServices = new ArrayList<>();
     // jws2al.removeAll();
-    Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
-    Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+    Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+    Map<String, List<Jws2Instance>> alternates = new HashMap<>();
     for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
     {
       if (!isRecalculable(service.action))
@@ -395,7 +394,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         {
           if (ph == null)
           {
-            ph = new ArrayList<Jws2Instance>();
+            ph = new ArrayList<>();
           }
           ph.add(service);
           alternates.put(service.serviceType, ph);
@@ -457,7 +456,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
                           sv.action, sv);
                   changeSupport.firePropertyChange("services",
                           new Vector<Jws2Instance>(), services);
-                };
+                }
               }).start();
 
             }
@@ -483,17 +482,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
      */
     JMenu atpoint;
 
-    List<String> hostLabels = new ArrayList<String>();
-    Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
-    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
-    ArrayList<String> hostlist = new ArrayList<String>();
+    List<String> hostLabels = new ArrayList<>();
+    Hashtable<String, String> lasthostFor = new Hashtable<>();
+    Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+    ArrayList<String> hostlist = new ArrayList<>();
     for (Jws2Instance service : enumerableServices)
     {
       ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
       if (hostservices == null)
       {
         hosts.put(service.getHost(),
-                hostservices = new ArrayList<Jws2Instance>());
+                hostservices = new ArrayList<>());
         hostlist.add(service.getHost());
       }
       hostservices.add(service);
@@ -577,16 +576,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     }
   }
 
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     if (args.length > 0)
     {
-      testUrls = new ArrayList<String>();
+      testUrls = new ArrayList<>();
       for (String url : args)
       {
         testUrls.add(url);
       }
-      ;
     }
     Thread runner = getDiscoverer()
             .startDiscoverer(new PropertyChangeListener()
@@ -618,7 +621,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       } catch (InterruptedException e)
       {
       }
-      ;
     }
     try
     {
@@ -685,7 +687,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
       // return test urls, if there are any, instead of touching cache
       return testUrls;
     }
-    List<String> urls = new ArrayList<String>();
+    List<String> urls = new ArrayList<>();
 
     if (this.preferredUrl != null)
     {
@@ -733,8 +735,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
 
   public Vector<Jws2Instance> getServices()
   {
-    return (services == null) ? new Vector<Jws2Instance>()
-            : new Vector<Jws2Instance>(services);
+    return (services == null) ? new Vector<>()
+            : new Vector<>(services);
   }
 
   /**
@@ -839,7 +841,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (urlsWithoutServices == null)
     {
-      urlsWithoutServices = new Vector<String>();
+      urlsWithoutServices = new Vector<>();
     }
 
     if ((invalidServiceUrls == null
@@ -859,7 +861,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
   {
     if (invalidServiceUrls == null)
     {
-      invalidServiceUrls = new Vector<String>();
+      invalidServiceUrls = new Vector<>();
     }
     if (!invalidServiceUrls.contains(jwsservers))
     {
@@ -947,7 +949,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
   {
-    HashSet<String> urls = new HashSet<String>();
+    HashSet<String> urls = new HashSet<>();
     urls.addAll(Arrays.asList(serviceURLs));
     Jws2Instance match = null;
     if (services != null)
@@ -974,7 +976,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return match;
   }
 
-  Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+  Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();
 
   /**
    * get current preferred service of the given type, or global default
@@ -1026,12 +1028,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
     if (preferredServiceMap == null)
     {
-      preferredServiceMap = new HashMap<String, Map<String, String>>();
+      preferredServiceMap = new HashMap<>();
     }
     Map<String, String> prefmap = preferredServiceMap.get(afid);
     if (prefmap == null)
     {
-      prefmap = new HashMap<String, String>();
+      prefmap = new HashMap<>();
       preferredServiceMap.put(afid, prefmap);
     }
     prefmap.put(serviceType, selectedServer.getHost());

diff --git a/test/jalview/gui/MouseEventDemo.java b/test/jalview/gui/MouseEventDemo.java
index 6d154de..62320c7 100644 (file)
--- a/test/jalview/gui/MouseEventDemo.java
+++ b/test/jalview/gui/MouseEventDemo.java
@@ -117,6 +117,9 @@ public class MouseEventDemo extends JPanel implements MouseListener
 
   static final String NEWLINE = System.getProperty("line.separator");
 
+  /**
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     // Schedule a job for the event dispatch thread:

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 0b501ee..6683d6c 100644 (file)
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -49,6 +49,7 @@ public class SequenceFetcherTest
    * simple run method to test dbsources.
    * 
    * @param argv
+   * @j2sIgnore
    */
   public static void main(String[] argv)
   {