X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=26ce8c32c1709ebfa7d81a923b8d4271947392a0;hb=a5928e2c1b9e2cea8d9c43f3d03f9cce2604f3b2;hp=b42f08e6db95ec65461eb7739a1850b372be7eaf;hpb=1f41372a2bda3efcc27abaed092495548135b6b4;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index b42f08e..26ce8c3 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -50,46 +50,65 @@ public class Commands
 {
   Desktop desktop;
 
-  private static boolean headless;
+  private boolean headless;
 
-  private static ArgParser argParser;
+  private ArgParser argParser;
 
   private Map<String, AlignFrame> afMap;
 
-  private static boolean commandArgsProvided = false;
+  private boolean commandArgsProvided = false;
 
-  public static boolean commandArgsProvided()
+  private boolean argsWereParsed = false;
+
+  public Commands(ArgParser argparser, boolean headless)
   {
-    return commandArgsProvided;
+    this(Desktop.instance, argparser, headless);
   }
 
-  public static boolean processArgs(ArgParser ap, boolean h)
+  public Commands(Desktop d, ArgParser argparser, boolean h)
   {
-    argParser = ap;
+    argParser = argparser;
     headless = h;
-    boolean argsWereParsed = true;
-    if (headless)
+    desktop = d;
+    afMap = new HashMap<String, AlignFrame>();
+    if (argparser != null)
     {
-      System.setProperty("java.awt.headless", "true");
+      processArgs(argparser, headless);
     }
+  }
+
+  private boolean processArgs(ArgParser argparser, boolean h)
+  {
+    argParser = argparser;
+    headless = h;
+    boolean theseArgsWereParsed = false;
 
     if (argParser != null && argParser.linkedIds() != null)
     {
       for (String id : argParser.linkedIds())
       {
-        Commands cmds = new Commands();
+        ArgValuesMap avm = argParser.linkedArgs(id);
+        theseArgsWereParsed = true;
         if (id == null)
         {
-          cmds.processUnlinked(id);
-          argsWereParsed &= cmds.wereParsed();
+          theseArgsWereParsed &= processUnlinked(id);
         }
         else
         {
-          cmds.processLinked(id);
-          argsWereParsed &= cmds.wereParsed();
+          theseArgsWereParsed &= processLinked(id);
+        }
+        theseArgsWereParsed &= processImages(id);
+
+        // close ap
+        if (avm.getBoolean(Arg.CLOSE))
+        {
+          AlignFrame af = afMap.get(id);
+          if (af != null)
+          {
+            af.closeMenuItem_actionPerformed(true);
+          }
         }
-        cmds.processImages(id);
-        argsWereParsed &= cmds.wereParsed();
+
       }
 
     }
@@ -99,39 +118,31 @@ public class Commands
       return true;
     }
     // carry on with jalview.bin.Jalview
+    argsWereParsed = theseArgsWereParsed;
     return argsWereParsed;
   }
 
-  boolean argsWereParsed = true; // set false as soon as an arg is found
-
-  private boolean wereParsed()
-  {
-    return argsWereParsed;
-  }
-
-  public Commands()
+  public boolean commandArgsProvided()
   {
-    this(Desktop.instance);
+    return commandArgsProvided;
   }
 
-  public Commands(Desktop d)
+  public boolean argsWereParsed()
   {
-    this.desktop = d;
-    afMap = new HashMap<String, AlignFrame>();
+    return argsWereParsed;
   }
 
-  protected void processUnlinked(String id)
+  protected boolean processUnlinked(String id)
   {
-    processLinked(id);
+    return processLinked(id);
   }
 
-  protected void processLinked(String id)
+  protected boolean processLinked(String id)
   {
+    boolean theseArgsWereParsed = false;
     ArgValuesMap avm = argParser.linkedArgs(id);
     if (avm == null)
-      return;
-    else
-      argsWereParsed = false;
+      return true;
 
     /*
     // script to execute after all loading is completed one way or another
@@ -157,7 +168,7 @@ public class Commands
         if (openFile == null)
           continue;
 
-        argsWereParsed = true;
+        theseArgsWereParsed = true;
         if (first)
         {
           first = false;
@@ -353,7 +364,7 @@ public class Commands
         {
           Console.debug(
                   "Opening '" + openFile + "' in existing alignment frame");
-          af.getCurrentView().addFile(new File(openFile), format);
+          af.getCurrentView().addFile(new File(openFile), format, false);
         }
 
         Console.debug("Command " + Arg.OPEN + " executed successfully!");
@@ -541,9 +552,11 @@ public class Commands
         Console.info("Changed colour " + acg.toString());
       }
     }
+
+    return theseArgsWereParsed;
   }
 
-  protected void processImages(String id)
+  protected boolean processImages(String id)
   {
     ArgValuesMap avm = argParser.linkedArgs(id);
     AlignFrame af = afMap.get(id);
@@ -551,7 +564,7 @@ public class Commands
     if (af == null)
     {
       Console.warn("Did not have an alignment window for id=" + id);
-      return;
+      return false;
     }
 
     if (avm.containsArg(Arg.IMAGE))
@@ -602,6 +615,7 @@ public class Commands
         }
       }
     }
+    return true;
   }
 
   private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)