X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=32701449938fef85bca8065684817671c8895df8;hb=20a4d7ddb86ee996f2b6617a0470922b83354c35;hp=954bb34bd63bc94e4eedfc845a59a073c7a0500a;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 954bb34..3270144 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,9 +20,6 @@
  */
 package jalview.bin;
 
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -64,12 +61,23 @@ 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
+ * 
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ * 
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
  * 
  * @author $author$
  * @version $Revision$
@@ -148,7 +156,6 @@ public class Jalview
           af.setProgressBar(MessageManager
                   .getString("status.das_features_being_retrived"), id);
           af.featureSettings_actionPerformed(null);
-          af.featureSettings.fetchDasFeatures(dasSources, true);
           af.setProgressBar(null, id);
           synchronized (us)
           {
@@ -188,8 +195,8 @@ 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"));
@@ -212,8 +219,8 @@ 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!
@@ -224,12 +231,12 @@ 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");
       }
     }
 
@@ -263,9 +270,8 @@ 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);
     }
 
@@ -276,20 +282,43 @@ 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());
+        }
       }
     }
 
@@ -326,8 +355,8 @@ 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
         {
@@ -339,8 +368,8 @@ 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);
           }
         }
@@ -383,8 +412,8 @@ 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.
@@ -434,8 +463,8 @@ public class Jalview
         {
           if (desktop.joinVamsasSession(vamsasSession))
           {
-            System.out.println("Successfully joined vamsas session "
-                    + vamsasSession);
+            System.out.println(
+                    "Successfully joined vamsas session " + vamsasSession);
           }
           else
           {
@@ -444,16 +473,16 @@ 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
@@ -468,8 +497,9 @@ 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!");
@@ -510,13 +540,13 @@ public class Jalview
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
-                  .getViewport().getAlignment(), data);
+          ColourSchemeI cs = ColourSchemeProperty
+                  .getColourScheme(af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {
-            System.out.println("CMD [-color " + data
-                    + "] executed successfully!");
+            System.out.println(
+                    "CMD [-color " + data + "] executed successfully!");
           }
           af.changeColour(cs);
         }
@@ -528,8 +558,8 @@ 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)
@@ -537,8 +567,8 @@ 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);
@@ -546,8 +576,8 @@ 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"))
@@ -580,12 +610,12 @@ public class Jalview
         {
           try
           {
-            System.out.println("CMD [-tree " + data
-                    + "] executed successfully!");
+            System.out.println(
+                    "CMD [-tree " + data + "] executed successfully!");
             NewickFile nf = new NewickFile(data,
                     AppletFormatAdapter.checkProtocol(data));
-            af.getViewport().setCurrentTree(
-                    af.showNewickTree(nf, data).getTree());
+            af.getViewport()
+                    .setCurrentTree(af.showNewickTree(nf, data).getTree());
           } catch (IOException ex)
           {
             System.err.println("Couldn't add tree " + data);
@@ -666,16 +696,16 @@ public class Jalview
             }
             try
             {
-              BioJsHTMLOutput
-                      .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+              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);
+            System.out
+                    .println("Creating BioJS MSA Viwer HTML file: " + file);
             continue;
           }
           else if (outputFormat.equalsIgnoreCase("imgMap"))
@@ -687,8 +717,8 @@ public class Jalview
           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;
           }
@@ -720,12 +750,12 @@ 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");
@@ -781,8 +811,8 @@ 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);
       }
     }
@@ -799,8 +829,8 @@ 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"
@@ -828,14 +858,18 @@ public class Jalview
                     + "-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");
@@ -846,10 +880,8 @@ 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)",
@@ -858,8 +890,8 @@ 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.");
               }
@@ -899,10 +931,10 @@ 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)
         {
@@ -915,8 +947,8 @@ 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;
       }
@@ -925,8 +957,8 @@ 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;
@@ -968,7 +1000,7 @@ 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)
       {
@@ -1013,9 +1045,8 @@ 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)
         {
@@ -1030,17 +1061,17 @@ 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)
     {
@@ -1053,7 +1084,7 @@ public class Jalview
       System.out.println("adding source '" + data + "'");
       if (source == null)
       {
-        source = new Vector<String>();
+        source = new Vector<>();
       }
       source.addElement(data);
     }