X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0b1cf6039385cd125076aae18cd83143fbbfa3fd;hb=4865a4110b7725acefd5b166f9b7c482ac01ce15;hp=764c92c1fe2fc0c8ce079dd6e2db32f048a5ee89;hpb=50973d198edf5874fc8c41275e30a698dd51c2e9;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 764c92c..0b1cf60 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,22 +20,23 @@
  */
 package jalview.bin;
 
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
+import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -49,6 +50,7 @@ import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.MalformedURLException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.security.AllPermission;
 import java.security.CodeSource;
@@ -59,12 +61,17 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
 
+import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
 /**
  * Main class for Jalview Application <br>
  * <br>
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * start with java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$"
+ * jalview.bin.Jalview
  * 
  * @author $author$
  * @version $Revision$
@@ -183,8 +190,8 @@ public class Jalview
   void doMain(String[] args)
   {
     System.setSecurityManager(null);
-    System.out.println("Java version: "
-            + System.getProperty("java.version"));
+    System.out
+            .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
@@ -207,8 +214,8 @@ public class Jalview
     Cache.loadProperties(usrPropsFile); // must do this before
     if (usrPropsFile != null)
     {
-      System.out.println("CMD [-props " + usrPropsFile
-              + "] executed successfully!");
+      System.out.println(
+              "CMD [-props " + usrPropsFile + "] executed successfully!");
     }
 
     // anything else!
@@ -219,12 +226,12 @@ public class Jalview
       try
       {
         Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-        System.out.println("CMD [-jabaws " + jabawsUrl
-                + "] executed successfully!");
+        System.out.println(
+                "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
       } catch (MalformedURLException e)
       {
-        System.err.println("Invalid jabaws parameter: " + jabawsUrl
-                + " ignored");
+        System.err.println(
+                "Invalid jabaws parameter: " + jabawsUrl + " ignored");
       }
     }
 
@@ -258,9 +265,8 @@ public class Jalview
     } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
-      System.out
-              .println("\nEssential logging libraries not found."
-                      + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+      System.out.println("\nEssential logging libraries not found."
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
       System.exit(0);
     }
 
@@ -271,23 +277,55 @@ public class Jalview
       UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
     } catch (Exception ex)
     {
+      System.err.println("Unexpected Look and Feel Exception");
+      ex.printStackTrace();
     }
     if (Platform.isAMac())
     {
+
+      LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
+              .getLookAndFeel();
       System.setProperty("com.apple.mrj.application.apple.menu.about.name",
               "Jalview");
       System.setProperty("apple.laf.useScreenMenuBar", "true");
-      try
+      if (lookAndFeel != null)
       {
-        UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
-                .getLookAndFeel());
-      } catch (Throwable e)
+        try
+        {
+          UIManager.setLookAndFeel(lookAndFeel);
+        } catch (Throwable e)
+        {
+          System.err.println(
+                  "Failed to set QuaQua look and feel: " + e.toString());
+        }
+      }
+      if (lookAndFeel == null || !(lookAndFeel.getClass()
+              .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+              || !UIManager.getLookAndFeel().getClass().toString()
+                      .toLowerCase().contains("quaqua"))
       {
-        System.err.println("Failed to set QuaQua look and feel: "
-                + e.toString());
+        try
+        {
+          System.err.println(
+                  "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+          UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+        } catch (Throwable e)
+        {
+          System.err.println(
+                  "Failed to reset look and feel: " + e.toString());
+        }
       }
     }
 
+    /*
+     * configure 'full' SO model if preferences say to, 
+     * else use the default (SO Lite)
+     */
+    if (Cache.getDefault("USE_FULL_SO", false))
+    {
+      SequenceOntologyFactory.setInstance(new SequenceOntology());
+    }
+
     if (!headless)
     {
       desktop = new Desktop();
@@ -312,8 +350,8 @@ public class Jalview
           // questionnaire
           Cache.log.debug("Starting questionnaire url at " + url);
           desktop.checkForQuestionnaire(url);
-          System.out.println("CMD questionnaire[-" + url
-                  + "] executed successfully!");
+          System.out.println(
+                  "CMD questionnaire[-" + url + "] executed successfully!");
         }
         else
         {
@@ -325,10 +363,9 @@ public class Jalview
             // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
             // //
             String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
-            Cache.log.debug("Starting questionnaire with default url: "
-                    + defurl);
+            Cache.log.debug(
+                    "Starting questionnaire with default url: " + defurl);
             desktop.checkForQuestionnaire(defurl);
-
           }
         }
       }
@@ -336,18 +373,18 @@ public class Jalview
       {
         System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
+
       if (!aparser.contains("nonews"))
       {
         desktop.checkForNews();
       }
-    }
 
-    if (!isHeadlessMode())
-    {
       BioJsHTMLOutput.updateBioJS();
     }
 
-    String file = null, protocol = null, format = null, data = null;
+    String file = null, data = null;
+    FileFormatI format = null;
+    DataSourceType protocol = null;
     FileLoader fileLoader = new FileLoader(!headless);
     Vector<String> getFeatures = null; // vector of das source nicknames to
                                        // fetch
@@ -370,8 +407,8 @@ public class Jalview
     {
       if (desktop == null || headless)
       {
-        System.out
-                .println("Headless vamsas sessions not yet supported. Sorry.");
+        System.out.println(
+                "Headless vamsas sessions not yet supported. Sorry.");
         System.exit(1);
       }
       // if we have a file, start a new session and import it.
@@ -380,13 +417,13 @@ public class Jalview
       {
         try
         {
-          String viprotocol = AppletFormatAdapter
+          DataSourceType viprotocol = AppletFormatAdapter
                   .checkProtocol(vamsasImport);
-          if (viprotocol == jalview.io.FormatAdapter.FILE)
+          if (viprotocol == DataSourceType.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
           }
-          else if (viprotocol == FormatAdapter.URL)
+          else if (viprotocol == DataSourceType.URL)
           {
             inSession = desktop.vamsasImport(new URL(vamsasImport));
           }
@@ -421,8 +458,8 @@ public class Jalview
         {
           if (desktop.joinVamsasSession(vamsasSession))
           {
-            System.out.println("Successfully joined vamsas session "
-                    + vamsasSession);
+            System.out.println(
+                    "Successfully joined vamsas session " + vamsasSession);
           }
           else
           {
@@ -431,16 +468,16 @@ public class Jalview
           }
         } catch (Exception e)
         {
-          System.err.println("ERROR: Failed to join vamsas session "
-                  + vamsasSession);
+          System.err.println(
+                  "ERROR: Failed to join vamsas session " + vamsasSession);
           e.printStackTrace();
         }
         if (vamsasImport != null)
         {
           // the Jalview specific remnants can now be imported into the new
           // session at the user's leisure.
-          Cache.log
-                  .info("Skipping Push for import of data into existing vamsas session."); // TODO:
+          Cache.log.info(
+                  "Skipping Push for import of data into existing vamsas session."); // TODO:
           // enable
           // this
           // when
@@ -455,8 +492,9 @@ public class Jalview
     {
       if (!headless)
       {
-        desktop.setProgressBar(MessageManager
-                .getString("status.processing_commandline_args"),
+        desktop.setProgressBar(
+                MessageManager
+                        .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
@@ -475,7 +513,13 @@ public class Jalview
 
       protocol = AppletFormatAdapter.checkProtocol(file);
 
-      format = new IdentifyFile().identify(file, protocol);
+      try
+      {
+        format = new IdentifyFile().identify(file, protocol);
+      } catch (FileFormatException e1)
+      {
+        // TODO ?
+      }
 
       AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
@@ -491,19 +535,13 @@ public class Jalview
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(af
-                  .getViewport().getAlignment(), data);
+          ColourSchemeI cs = ColourSchemeProperty
+                  .getColourScheme(af.getViewport().getAlignment(), data);
 
-          if (cs == null)
-          {
-            UserColourScheme ucs = new UserColourScheme("white");
-            ucs.parseAppletParameter(data);
-            cs = ucs;
-          }
-          else
+          if (cs != null)
           {
-            System.out.println("CMD [-color " + data
-                    + "] executed successfully!");
+            System.out.println(
+                    "CMD [-color " + data + "] executed successfully!");
           }
           af.changeColour(cs);
         }
@@ -515,8 +553,8 @@ public class Jalview
           af.parseFeaturesFile(data,
                   AppletFormatAdapter.checkProtocol(data));
           // System.out.println("Added " + data);
-          System.out.println("CMD groups[-" + data
-                  + "]  executed successfully!");
+          System.out.println(
+                  "CMD groups[-" + data + "]  executed successfully!");
         }
         data = aparser.getValue("features", true);
         if (data != null)
@@ -524,8 +562,8 @@ public class Jalview
           af.parseFeaturesFile(data,
                   AppletFormatAdapter.checkProtocol(data));
           // System.out.println("Added " + data);
-          System.out.println("CMD [-features " + data
-                  + "]  executed successfully!");
+          System.out.println(
+                  "CMD [-features " + data + "]  executed successfully!");
         }
 
         data = aparser.getValue("annotations", true);
@@ -533,8 +571,8 @@ public class Jalview
         {
           af.loadJalviewDataFile(data, null, null, null);
           // System.out.println("Added " + data);
-          System.out.println("CMD [-annotations " + data
-                  + "] executed successfully!");
+          System.out.println(
+                  "CMD [-annotations " + data + "] executed successfully!");
         }
         // set or clear the sortbytree flag.
         if (aparser.contains("sortbytree"))
@@ -565,18 +603,14 @@ public class Jalview
         data = aparser.getValue("tree", true);
         if (data != null)
         {
-          jalview.io.NewickFile fin = null;
           try
           {
-            System.out.println("CMD [-tree " + data
-                    + "] executed successfully!");
-            fin = new NewickFile(data,
+            System.out.println(
+                    "CMD [-tree " + data + "] executed successfully!");
+            NewickFile nf = new NewickFile(data,
                     AppletFormatAdapter.checkProtocol(data));
-            if (fin != null)
-            {
-              af.getViewport().setCurrentTree(
-                      af.ShowNewickTree(fin, data).getTree());
-            }
+            af.getViewport()
+                    .setCurrentTree(af.showNewickTree(nf, data).getTree());
           } catch (IOException ex)
           {
             System.err.println("Couldn't add tree " + data);
@@ -620,17 +654,17 @@ public class Jalview
         String imageName = "unnamed.png";
         while (aparser.getSize() > 1)
         {
-          format = aparser.nextValue();
+          String outputFormat = aparser.nextValue();
           file = aparser.nextValue();
 
-          if (format.equalsIgnoreCase("png"))
+          if (outputFormat.equalsIgnoreCase("png"))
           {
             af.createPNG(new File(file));
             imageName = (new File(file)).getName();
             System.out.println("Creating PNG image: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("svg"))
+          else if (outputFormat.equalsIgnoreCase("svg"))
           {
             File imageFile = new File(file);
             imageName = imageFile.getName();
@@ -638,25 +672,48 @@ public class Jalview
             System.out.println("Creating SVG image: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("html"))
+          else if (outputFormat.equalsIgnoreCase("html"))
           {
             File imageFile = new File(file);
             imageName = imageFile.getName();
-            new HtmlSvgOutput(new File(file), af.alignPanel);
+            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+            htmlSVG.exportHTML(file);
+
             System.out.println("Creating HTML image: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("imgMap"))
+          else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+          {
+            if (file == null)
+            {
+              System.err.println("The output html file must not be null");
+              return;
+            }
+            try
+            {
+              BioJsHTMLOutput.refreshVersionInfo(
+                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+            } catch (URISyntaxException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+            bjs.exportHTML(file);
+            System.out
+                    .println("Creating BioJS MSA Viwer HTML file: " + file);
+            continue;
+          }
+          else if (outputFormat.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new File(file), imageName);
             System.out.println("Creating image map: " + file);
             continue;
           }
-          else if (format.equalsIgnoreCase("eps"))
+          else if (outputFormat.equalsIgnoreCase("eps"))
           {
             File outputFile = new File(file);
-            System.out.println("Creating EPS file: "
-                    + outputFile.getAbsolutePath());
+            System.out.println(
+                    "Creating EPS file: " + outputFile.getAbsolutePath());
             af.createEPS(outputFile);
             continue;
           }
@@ -688,12 +745,12 @@ public class Jalview
     if (!headless && file == null && vamsasImport == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
-      file = jalview.bin.Cache.getDefault(
-              "STARTUP_FILE",
+      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
               jalview.bin.Cache.getDefault("www.jalview.org",
                       "http://www.jalview.org")
                       + "/examples/exampleFile_2_7.jar");
-      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+      if (file.equals(
+              "http://www.jalview.org/examples/exampleFile_2_3.jar"))
       {
         // hardwire upgrade of the startup file
         file.replace("_2_3.jar", "_2_7.jar");
@@ -701,20 +758,26 @@ public class Jalview
         jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
 
-      protocol = "File";
+      protocol = DataSourceType.FILE;
 
       if (file.indexOf("http:") > -1)
       {
-        protocol = "URL";
+        protocol = DataSourceType.URL;
       }
 
       if (file.endsWith(".jar"))
       {
-        format = "Jalview";
+        format = FileFormat.Jalview;
       }
       else
       {
-        format = new IdentifyFile().identify(file, protocol);
+        try
+        {
+          format = new IdentifyFile().identify(file, protocol);
+        } catch (FileFormatException e)
+        {
+          // TODO what?
+        }
       }
 
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@ -743,8 +806,8 @@ public class Jalview
       }
       else
       {
-        System.err
-                .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+        System.err.println(
+                "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
                         + groovyscript);
       }
     }
@@ -761,8 +824,8 @@ public class Jalview
 
   private static void showUsage()
   {
-    System.out
-            .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+    System.out.println(
+            "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                     + "-nodisplay\tRun Jalview without User Interface.\n"
                     + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
                     + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
@@ -781,21 +844,27 @@ public class Jalview
                     + "-png FILE\tCreate PNG image FILE from alignment.\n"
                     + "-svg FILE\tCreate SVG image FILE from alignment.\n"
                     + "-html FILE\tCreate HTML file from alignment.\n"
+                    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
                     + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
                     + "-eps FILE\tCreate EPS file FILE from alignment.\n"
                     + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                     + "-noquestionnaire\tTurn off questionnaire check.\n"
+                    + "-nonews\tTurn off check for Jalview news.\n"
                     + "-nousagestats\tTurn off google analytics tracking for this session.\n"
                     + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
                     // +
-                    // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
+                    // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
+                    // after all other properties files have been read\n\t
+                    // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
+                    // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                     + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
                     + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
                     + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     // +
-                    // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
+                    // "-vdoc vamsas-document\tImport vamsas document into new
+                    // session or join existing session with same URN\n"
                     // + "-vses vamsas-session\tJoin session with given URN\n"
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                     + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
@@ -806,10 +875,8 @@ public class Jalview
     /**
      * start a User Config prompt asking if we can log usage statistics.
      */
-    PromptUserConfig prompter = new PromptUserConfig(
-            Desktop.desktop,
-            "USAGESTATS",
-            "Jalview Usage Statistics",
+    PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
+            "USAGESTATS", "Jalview Usage Statistics",
             "Do you want to help make Jalview better by enabling "
                     + "the collection of usage statistics with Google Analytics ?"
                     + "\n\n(you can enable or disable usage tracking in the preferences)",
@@ -818,8 +885,8 @@ public class Jalview
               @Override
               public void run()
               {
-                Cache.log
-                        .debug("Initialising googletracker for usage stats.");
+                Cache.log.debug(
+                        "Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
                 Cache.log.debug("Tracking enabled.");
               }
@@ -859,10 +926,10 @@ public class Jalview
       try
       {
         tfile = File.createTempFile("jalview", "groovy");
-        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
-                new FileOutputStream(tfile)));
-        BufferedReader br = new BufferedReader(new InputStreamReader(
-                System.in));
+        PrintWriter outfile = new PrintWriter(
+                new OutputStreamWriter(new FileOutputStream(tfile)));
+        BufferedReader br = new BufferedReader(
+                new InputStreamReader(System.in));
         String line = null;
         while ((line = br.readLine()) != null)
         {
@@ -875,8 +942,8 @@ public class Jalview
       } catch (Exception ex)
       {
         System.err.println("Failed to read from STDIN into tempfile "
-                + ((tfile == null) ? "(tempfile wasn't created)" : tfile
-                        .toString()));
+                + ((tfile == null) ? "(tempfile wasn't created)"
+                        : tfile.toString()));
         ex.printStackTrace();
         return;
       }
@@ -885,8 +952,8 @@ public class Jalview
         sfile = tfile.toURI().toURL();
       } catch (Exception x)
       {
-        System.err
-                .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+        System.err.println(
+                "Unexpected Malformed URL Exception for temporary file created from STDIN: "
                         + tfile.toURI());
         x.printStackTrace();
         return;
@@ -928,7 +995,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<String, Object>();
+      Map<String, Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {
@@ -973,9 +1040,8 @@ public class Jalview
         nickname = data.substring(0, pos);
       }
       url = data.substring(pos + 1);
-      if (url != null
-              && (url.startsWith("http:") || url
-                      .startsWith("sequence:http:")))
+      if (url != null && (url.startsWith("http:")
+              || url.startsWith("sequence:http:")))
       {
         if (nickname == null)
         {
@@ -990,17 +1056,17 @@ public class Jalview
           locsources += "\t";
         }
         locsources = locsources + nickname + "|" + url;
-        System.err
-                .println("NOTE! dasserver parameter not yet really supported (got args of "
+        System.err.println(
+                "NOTE! dasserver parameter not yet really supported (got args of "
                         + nickname + "|" + url);
         if (source == null)
         {
-          source = new Vector<String>();
+          source = new Vector<>();
         }
         source.addElement(nickname);
       }
-      System.out.println("CMD [-dasserver " + data
-              + "] executed successfully!");
+      System.out.println(
+              "CMD [-dasserver " + data + "] executed successfully!");
     } // loop until no more server entries are found.
     if (locsources != null && locsources.indexOf('|') > -1)
     {
@@ -1013,7 +1079,7 @@ public class Jalview
       System.out.println("adding source '" + data + "'");
       if (source == null)
       {
-        source = new Vector<String>();
+        source = new Vector<>();
       }
       source.addElement(data);
     }