JAL-3048 refactored export settings to bean+dialog with callbacks - basically works...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2007814..e890cb8 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -160,7 +160,6 @@ 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)
           {
@@ -214,17 +213,6 @@ public class Jalview
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
 
-    if (aparser.contains("help") || aparser.contains("h"))
-    {
-      showUsage();
-      System.exit(0);
-    }
-    if (aparser.contains("nodisplay") || aparser.contains("nogui")
-            || aparser.contains("headless"))
-    {
-      System.setProperty("java.awt.headless", "true");
-      headless = true;
-    }
     String usrPropsFile = aparser.getValue("props");
     Cache.loadProperties(usrPropsFile); // must do this before
     if (usrPropsFile != null)
@@ -233,23 +221,41 @@ public class Jalview
               "CMD [-props " + usrPropsFile + "] executed successfully!");
     }
 
-    // anything else!
-
-    final String jabawsUrl = aparser.getValue("jabaws");
-    if (jabawsUrl != null)
+    /**
+     * BH 2018 ignoring this section for JS
+     * 
+     * @j2sNative
+     */
     {
-      try
+      if (aparser.contains("help") || aparser.contains("h"))
       {
-        Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-        System.out.println(
-                "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
-      } catch (MalformedURLException e)
+        showUsage();
+        System.exit(0);
+      }
+      if (aparser.contains("nodisplay") || aparser.contains("nogui")
+              || aparser.contains("headless"))
       {
-        System.err.println(
-                "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        System.setProperty("java.awt.headless", "true");
+        headless = true;
+      }
+      // anything else!
+
+      final String jabawsUrl = aparser.getValue("jabaws");
+      if (jabawsUrl != null)
+      {
+        try
+        {
+          Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+          System.out.println(
+                  "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+        } catch (MalformedURLException e)
+        {
+          System.err.println(
+                  "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        }
       }
-    }
 
+    }
     String defs = aparser.getValue("setprop");
     while (defs != null)
     {
@@ -346,55 +352,65 @@ public class Jalview
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
-      desktop.startServiceDiscovery();
-      if (!aparser.contains("nousagestats"))
-      {
-        startUsageStats(desktop);
-      }
-      else
-      {
-        System.err.println("CMD [-nousagestats] executed successfully!");
-      }
 
-      if (!aparser.contains("noquestionnaire"))
+      /**
+       * BH 2018 JS bypass this section
+       * 
+       * @j2sNative
+       * 
+       */
       {
-        String url = aparser.getValue("questionnaire");
-        if (url != null)
+        desktop.startServiceDiscovery();
+        if (!aparser.contains("nousagestats"))
         {
-          // Start the desktop questionnaire prompter with the specified
-          // questionnaire
-          Cache.log.debug("Starting questionnaire url at " + url);
-          desktop.checkForQuestionnaire(url);
-          System.out.println(
-                  "CMD questionnaire[-" + url + "] executed successfully!");
+          startUsageStats(desktop);
         }
         else
         {
-          if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+          System.err.println("CMD [-nousagestats] executed successfully!");
+        }
+
+        if (!aparser.contains("noquestionnaire"))
+        {
+          String url = aparser.getValue("questionnaire");
+          if (url != null)
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            // String defurl =
-            // "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);
-            desktop.checkForQuestionnaire(defurl);
+            Cache.log.debug("Starting questionnaire url at " + url);
+            desktop.checkForQuestionnaire(url);
+            System.out.println("CMD questionnaire[-" + url
+                    + "] executed successfully!");
+          }
+          else
+          {
+            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            {
+              // Start the desktop questionnaire prompter with the specified
+              // questionnaire
+              // String defurl =
+              // "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);
+              desktop.checkForQuestionnaire(defurl);
+            }
           }
         }
-      }
-      else
-      {
-        System.err.println("CMD [-noquestionnaire] executed successfully!");
-      }
+        else
+        {
+          System.err
+                  .println("CMD [-noquestionnaire] executed successfully!");
+        }
 
-      if (!aparser.contains("nonews"))
-      {
-        desktop.checkForNews();
-      }
+        if (!aparser.contains("nonews"))
+        {
+          desktop.checkForNews();
+        }
 
-      BioJsHTMLOutput.updateBioJS();
+        BioJsHTMLOutput.updateBioJS();
+      }
     }
 
     String file = null, data = null;
@@ -514,7 +530,7 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!file.startsWith("http://"))
+      if (!isJS && !file.startsWith("http://"))
       {
         if (!(new File(file)).exists())
         {
@@ -526,7 +542,7 @@ public class Jalview
         }
       }
 
-      protocol = AppletFormatAdapter.checkProtocol(file);
+        protocol = AppletFormatAdapter.checkProtocol(file);
 
       try
       {
@@ -733,7 +749,8 @@ public class Jalview
             continue;
           }
 
-          if (af.saveAlignment(file, format))
+          af.saveAlignment(file, format);
+          if (af.isSaveAlignmentSuccessful())
           {
             System.out.println("Written alignment in " + format
                     + " format to " + file);
@@ -757,7 +774,8 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!headless && file == null && vamsasImport == null
+    if (/** @j2sNative false && */ // BH 2018
+    !headless && file == null && vamsasImport == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",