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

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index a98069a..26ce8c3 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -50,39 +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;
 
-  public static boolean processArgs(ArgParser ap, boolean h)
+  private boolean commandArgsProvided = false;
+
+  private boolean argsWereParsed = false;
+
+  public Commands(ArgParser argparser, boolean headless)
   {
-    argParser = ap;
+    this(Desktop.instance, argparser, headless);
+  }
+
+  public Commands(Desktop d, ArgParser argparser, boolean h)
+  {
+    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();
+
       }
 
     }
@@ -92,39 +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)
   {
-    ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(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
@@ -136,11 +154,13 @@ public class Commands
     FileFormatI format = null;
     DataSourceType protocol = null;
     */
-    if (avm.hasValue(Arg.OPEN))
+    if (avm.containsArg(Arg.OPEN))
     {
+      commandArgsProvided = true;
       long progress = -1;
 
       boolean first = true;
+      boolean progressBarSet = false;
       AlignFrame af;
       for (ArgValue av : avm.getArgValueList(Arg.OPEN))
       {
@@ -148,7 +168,7 @@ public class Commands
         if (openFile == null)
           continue;
 
-        argsWereParsed = true;
+        theseArgsWereParsed = true;
         if (first)
         {
           first = false;
@@ -158,6 +178,7 @@ public class Commands
                     MessageManager.getString(
                             "status.processing_commandline_args"),
                     progress = System.currentTimeMillis());
+            progressBarSet = true;
           }
         }
 
@@ -224,7 +245,8 @@ public class Commands
 
           // get kind of temperature factor annotation
           StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
-          if ((!avm.getBoolean(Arg.NOTEMPFAC)) && avm.hasValue(Arg.TEMPFAC))
+          if ((!avm.getBoolean(Arg.NOTEMPFAC))
+                  && avm.containsArg(Arg.TEMPFAC))
           {
             try
             {
@@ -269,13 +291,13 @@ public class Commands
           }
 
           // colour aligment?
-          if (avm.hasValue(Arg.COLOUR))
+          if (avm.containsArg(Arg.COLOUR))
           {
             af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
           }
 
           // change alignment frame title
-          if (avm.hasValue(Arg.TITLE))
+          if (avm.containsArg(Arg.TITLE))
             af.setTitle(avm.getValue(Arg.TITLE));
 
           /* hacky approach to hiding the annotations */
@@ -305,7 +327,7 @@ public class Commands
            if (showTemperatureFactor)
              */
           {
-            if (avm.hasValue(Arg.TEMPFAC_LABEL))
+            if (avm.containsArg(Arg.TEMPFAC_LABEL))
             {
               AlignmentAnnotation aa = AlignmentUtils
                       .getFirstSequenceAnnotationOfType(
@@ -342,7 +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!");
@@ -358,10 +380,10 @@ public class Commands
         else
         {
           Console.warn("No more files to open");
-          if (desktop != null)
-            desktop.setProgressBar(null, progress);
         }
       }
+      if (progressBarSet && desktop != null)
+        desktop.setProgressBar(null, progress);
 
     }
 
@@ -369,8 +391,9 @@ public class Commands
     if (!avm.getBoolean(Arg.NOSTRUCTURE))
     {
       AlignFrame af = afMap.get(id);
-      if (avm.hasValue(Arg.STRUCTURE))
+      if (avm.containsArg(Arg.STRUCTURE))
       {
+        commandArgsProvided = true;
         for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
           String val = av.getValue();
@@ -443,14 +466,21 @@ public class Commands
             Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
                     StructureViewer.ViewerType.JMOL.toString());
           }
-          StructureChooser.openStructureFileForSequence(ap, seq,
-                  structureFile);
+
+          // get tft, paeFilename, label?
+          /*
+          ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
+                  Arg.TEMPFAC);
+           */
+          StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+                  false, structureFile.getAbsolutePath(), null, null); // tft,
+                                                                       // paeFilename);
         }
       }
     }
 
     // load a pAE file if given
-    if (avm.hasValue(Arg.PAEMATRIX))
+    if (avm.containsArg(Arg.PAEMATRIX))
     {
       AlignFrame af = afMap.get(id);
       if (af != null)
@@ -522,20 +552,22 @@ public class Commands
         Console.info("Changed colour " + acg.toString());
       }
     }
+
+    return theseArgsWereParsed;
   }
 
-  protected void processImages(String id)
+  protected boolean processImages(String id)
   {
-    ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
+    ArgValuesMap avm = argParser.linkedArgs(id);
     AlignFrame af = afMap.get(id);
 
     if (af == null)
     {
       Console.warn("Did not have an alignment window for id=" + id);
-      return;
+      return false;
     }
 
-    if (avm.hasValue(Arg.IMAGE))
+    if (avm.containsArg(Arg.IMAGE))
     {
       for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
       {
@@ -583,6 +615,7 @@ public class Commands
         }
       }
     }
+    return true;
   }
 
   private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)