JAL-629 Commands more objecty, less classy. FileLoader with sync option (or rather...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3cc71af..a728bc8 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -26,7 +26,9 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.OutputStream;
 import java.io.OutputStreamWriter;
+import java.io.PrintStream;
 import java.io.PrintWriter;
 import java.net.MalformedURLException;
 import java.net.URI;
@@ -63,6 +65,7 @@ import com.threerings.getdown.util.LaunchUtil;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.bin.ArgParser.Arg;
+import jalview.bin.ArgParser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -123,6 +126,8 @@ public class Jalview
 
   private Desktop desktop;
 
+  protected Commands cmds;
+
   public static AlignFrame currentAlignFrame;
 
   static
@@ -282,7 +287,29 @@ public class Jalview
     }
 
     // get args needed before proper ArgParser
-    Map<String, String> bootstrapArgs = ArgParser.bootstrapArgs(args);
+    BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+
+    if (!Platform.isJS())
+    {
+      // are we being --quiet ?
+      if (bootstrapArgs.contains(Arg.QUIET))
+      {
+        OutputStream devNull = new OutputStream()
+        {
+          @Override
+          public void write(int b)
+          {
+            // DO NOTHING
+          }
+        };
+        System.setOut(new PrintStream(devNull));
+        // redirecting stderr not working
+        if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
+        {
+          System.setErr(new PrintStream(devNull));
+        }
+      }
+    }
 
     System.out
             .println("Java version: " + System.getProperty("java.version"));
@@ -314,7 +341,7 @@ public class Jalview
 
     // get bootstrap properties (mainly for the logger level)
     Properties bootstrapProperties = Cache
-            .bootstrapProperties(bootstrapArgs.get("props"));
+            .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
 
     // report Jalview version
     Cache.loadBuildProperties(true);
@@ -322,11 +349,14 @@ public class Jalview
     // old ArgsParser
     ArgsParser aparser = new ArgsParser(args);
 
+    // old
     boolean headless = false;
+    // new
+    boolean headlessArg = false;
 
     try
     {
-      String logLevel = bootstrapArgs.containsKey("debug") ? "DEBUG" : null;
+      String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
       if (logLevel == null && !(bootstrapProperties == null))
       {
         logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
@@ -363,8 +393,8 @@ public class Jalview
       }
     });
 
-    String usrPropsFile = bootstrapArgs.containsKey("props")
-            ? bootstrapArgs.get("props")
+    String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
+            ? bootstrapArgs.get(Arg.PROPS)
             : aparser.getValue("props");
     Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
@@ -374,10 +404,17 @@ public class Jalview
     }
 
     // new ArgParser
-    ArgParser argparser = new ArgParser(args);
-
-    if (argparser.isSet(Arg.HEADLESS))
-      headless = argparser.getBool(Arg.HEADLESS);
+    ArgParser argparser;
+    // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
+    if (bootstrapArgs.contains(Arg.ARGFILE))
+    {
+      argparser = ArgParser
+              .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
+    }
+    else
+    {
+      argparser = new ArgParser(args);
+    }
 
     if (!Platform.isJS())
     /**
@@ -386,20 +423,24 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      if (argparser.isSet(Arg.HEADLESS))
+      if (aparser.contains("help") || aparser.contains("h")
+              || argparser.getBool(Arg.HELP))
       {
-        headless = argparser.getBool(Arg.HEADLESS);
+        showUsage();
+        System.exit(0);
       }
 
-      if (aparser.contains("help") || aparser.contains("h"))
+      if (bootstrapArgs.contains(Arg.HEADLESS))
       {
-        showUsage();
-        System.exit(0);
+        System.setProperty("java.awt.headless", "true");
+        // new
+        headlessArg = argparser.getBool(Arg.HEADLESS);
       }
-      if (headless || aparser.contains("nodisplay")
-              || aparser.contains("nogui") || aparser.contains("headless"))
+      if (aparser.contains("nodisplay") || aparser.contains("nogui")
+              || aparser.contains("headless"))
       {
         System.setProperty("java.awt.headless", "true");
+        // old
         headless = true;
       }
       // anything else!
@@ -466,7 +507,8 @@ public class Jalview
     }
     desktop = null;
 
-    setLookAndFeel();
+    if (!(headless || headlessArg))
+      setLookAndFeel();
 
     /*
      * configure 'full' SO model if preferences say to, else use the default (full SO)
@@ -478,7 +520,7 @@ public class Jalview
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
 
-    if (!headless)
+    if (!(headless || headlessArg))
     {
       Desktop.nosplash = aparser.contains("nosplash");
       desktop = new Desktop();
@@ -601,17 +643,21 @@ public class Jalview
       }
     }
     // Run Commands from cli
-    boolean commandsSuccess = Commands.processArgs(argparser, headless);
+    cmds = new Commands(argparser, headlessArg);
+    boolean commandsSuccess = cmds.argsWereParsed();
     if (commandsSuccess)
     {
       Console.info("Successfully completed commands");
-      if (headless)
+      if (headlessArg)
+      {
+        System.out.println("#### EXITING");
         System.exit(0);
+      }
     }
     else
     {
       Console.warn("Error when running commands");
-      if (headless)
+      if (headlessArg)
         System.exit(1);
     }
 
@@ -727,7 +773,7 @@ public class Jalview
           if (cs != null)
           {
             System.out.println(
-                    "CMD [-color " + data + "] executed successfully!");
+                    "CMD [-colour " + data + "] executed successfully!");
           }
           af.changeColour(cs);
         }
@@ -930,7 +976,10 @@ public class Jalview
     // ////////////////////
 
     if (!Platform.isJS() && !headless && file == null
-            && Cache.getDefault("SHOW_STARTUP_FILE", true))
+            && Cache.getDefault("SHOW_STARTUP_FILE", true)
+            && !cmds.commandArgsProvided())
+    // don't open the startup file if command line args have been processed
+    // (&& !Commands.commandArgsProvided())
     /**
      * Java only
      * 
@@ -1529,6 +1578,7 @@ public class Jalview
   public void quit()
   {
     // System.exit will run the shutdownHook first
+    System.out.println("Quitting now. Bye!");
     System.exit(0);
   }
 
@@ -1541,4 +1591,9 @@ public class Jalview
   {
     Jalview.currentAlignFrame = currentAlignFrame;
   }
+
+  protected Commands getCommands()
+  {
+    return cmds;
+  }
 }