JAL-629 Add a --threads argument to allow a limited multiple number of alignframes...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 50ff7c3..33bb55e 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -12,6 +12,14 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.concurrent.ArrayBlockingQueue;
+import java.util.concurrent.BlockingQueue;
+import java.util.concurrent.Callable;
+import java.util.concurrent.RejectedExecutionException;
+import java.util.concurrent.RejectedExecutionHandler;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.bin.argparser.Arg;
@@ -63,6 +71,11 @@ public class Commands
 
   private boolean argsWereParsed = false;
 
+  private ThreadPoolExecutor executor = null;
+
+  // have we opened a file?
+  boolean opened = false;
+
   public Commands(ArgParser argparser, boolean headless)
   {
     this(Desktop.instance, argparser, headless);
@@ -74,6 +87,61 @@ public class Commands
     headless = h;
     desktop = d;
     afMap = new HashMap<String, AlignFrame>();
+
+    int threads = 3;
+    if (argParser.getBootstrapArgs().contains(Arg.THREADS))
+    {
+      String threadsString = argParser.getBootstrapArgs().get(Arg.THREADS);
+      try
+      {
+        threads = Integer.parseInt(threadsString);
+      } catch (NumberFormatException e)
+      {
+        Console.debug("Could not parse number of threads from '"
+                + Arg.THREADS.argString() + "=" + threadsString
+                + "', fallback to 1.");
+        threads = 1;
+      }
+    }
+
+    BlockingQueue<Runnable> bq = new ArrayBlockingQueue<>(1);
+    if (threads > 0)
+    {
+      // executor = Executors.newFixedThreadPool(threads);
+      executor = new ThreadPoolExecutor(threads, threads, 600,
+              TimeUnit.SECONDS, bq);
+    }
+    else
+    {
+      // executor = Executors.newCachedThreadPool();
+      executor = new ThreadPoolExecutor(threads, Integer.MAX_VALUE, 600,
+              TimeUnit.SECONDS, null);
+    }
+
+    // set a rejectedExecution to block and resubmit.
+    executor.setRejectedExecutionHandler(new RejectedExecutionHandler()
+    {
+      @Override
+      public void rejectedExecution(Runnable r, ThreadPoolExecutor tpe)
+      {
+        try
+        {
+          // block until there's room
+          tpe.getQueue().put(r);
+          // check afterwards and throw if pool shutdown
+          if (tpe.isShutdown())
+          {
+            throw new RejectedExecutionException(
+                    "Task " + r + " rejected from " + tpe);
+          }
+        } catch (InterruptedException e)
+        {
+          Thread.currentThread().interrupt();
+          throw new RejectedExecutionException("Producer interrupted", e);
+        }
+      }
+    });
+
     if (argparser != null)
     {
       processArgs(argparser, headless);
@@ -84,41 +152,76 @@ public class Commands
   {
     argParser = argparser;
     headless = h;
-    boolean theseArgsWereParsed = false;
+    AtomicBoolean theseArgsWereParsed = new AtomicBoolean(false);
 
     if (argParser != null && argParser.getLinkedIds() != null)
     {
+      long progress = -1;
+      boolean progressBarSet = false;
+      opened = false;
+      if (!headless && desktop != null)
+      {
+        desktop.setProgressBar(
+                MessageManager
+                        .getString("status.processing_commandline_args"),
+                progress = System.currentTimeMillis());
+        progressBarSet = true;
+      }
       for (String id : argParser.getLinkedIds())
       {
-        ArgValuesMap avm = argParser.getLinkedArgs(id);
-        theseArgsWereParsed = true;
-        theseArgsWereParsed &= processLinked(id);
-        processGroovyScript(id);
-        boolean processLinkedOkay = theseArgsWereParsed;
-        theseArgsWereParsed &= processImages(id);
-        if (processLinkedOkay)
-          theseArgsWereParsed &= processOutput(id);
-
-        // close ap
-        if (avm.getBoolean(Arg.CLOSE))
-        {
-          AlignFrame af = afMap.get(id);
-          if (af != null)
-          {
-            af.closeMenuItem_actionPerformed(true);
+
+        Callable<Void> process = () -> {
+          ArgValuesMap avm = argParser.getLinkedArgs(id);
+          theseArgsWereParsed.set(true);
+          theseArgsWereParsed.compareAndSet(true, processLinked(id)); // &=
+          processGroovyScript(id);
+          boolean processLinkedOkay = theseArgsWereParsed.get();
+          theseArgsWereParsed.compareAndSet(true, processImages(id)); // &=
+          if (processLinkedOkay)
+            theseArgsWereParsed.compareAndSet(true, processOutput(id)); // &=
+
+          // close ap
+          if (avm.getBoolean(Arg.CLOSE))
+          {
+            AlignFrame af = afMap.get(id);
+            if (af != null)
+            {
+              af.closeMenuItem_actionPerformed(true);
+            }
+            afMap.remove(id);
           }
-        }
+          return null;
+        };
 
+        executor.submit(process);
+        Console.debug(
+                "Running " + executor.getActiveCount() + " processes.");
+      }
+
+      if (!opened) // first=true means nothing opened
+      {
+        if (headless)
+        {
+          Jalview.exit("Did not open any files in headless mode", 1);
+        }
+        else
+        {
+          Console.warn("No more files to open");
+        }
+      }
+      if (progressBarSet && desktop != null)
+      {
+        desktop.setProgressBar(null, progress);
       }
 
     }
-    if (argParser.getBoolean(Arg.QUIT))
+    if (argParser.getBootstrapArgs().getBoolean(Arg.QUIT))
     {
       Jalview.getInstance().quit();
       return true;
     }
     // carry on with jalview.bin.Jalview
-    argsWereParsed = theseArgsWereParsed;
+    argsWereParsed |= theseArgsWereParsed.get();
     return argsWereParsed;
   }
 
@@ -132,11 +235,6 @@ public class Commands
     return argsWereParsed;
   }
 
-  protected boolean processUnlinked(String id)
-  {
-    return processLinked(id);
-  }
-
   protected boolean processLinked(String id)
   {
     boolean theseArgsWereParsed = false;
@@ -154,10 +252,6 @@ public class Commands
     if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
       commandArgsProvided = true;
-      long progress = -1;
-
-      boolean first = true;
-      boolean progressBarSet = false;
       AlignFrame af;
       // Combine the APPEND and OPEN files into one list, along with whether it
       // was APPEND or OPEN
@@ -175,18 +269,6 @@ public class Commands
           continue;
 
         theseArgsWereParsed = true;
-        if (first)
-        {
-          first = false;
-          if (!headless && desktop != null)
-          {
-            desktop.setProgressBar(
-                    MessageManager.getString(
-                            "status.processing_commandline_args"),
-                    progress = System.currentTimeMillis());
-            progressBarSet = true;
-          }
-        }
 
         if (!Platform.isJS())
         /**
@@ -221,6 +303,8 @@ public class Commands
         if (af == null || "true".equals(av.getSubVal("new"))
                 || a == Arg.OPEN || format == FileFormat.Jalview)
         {
+          opened = true;
+
           if (a == Arg.OPEN)
           {
             Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
@@ -359,19 +443,6 @@ public class Commands
         Console.debug("Command " + Arg.APPEND + " executed successfully!");
 
       }
-      if (first) // first=true means nothing opened
-      {
-        if (headless)
-        {
-          Jalview.exit("Could not open any files in headless mode", 1);
-        }
-        else
-        {
-          Console.warn("No more files to open");
-        }
-      }
-      if (progressBarSet && desktop != null)
-        desktop.setProgressBar(null, progress);
 
     }
 

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index a18057c..73dec4e 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -179,7 +179,7 @@ public enum Arg
   OPENED("Apply the following output arguments to all of the last --open'ed set of linked arguments.",
           Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
   QUIT("After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
-          Opt.UNARY),
+          Opt.UNARY, Opt.BOOTSTRAP),
 
   // secret options
   TESTOUTPUT(
@@ -198,6 +198,8 @@ public enum Arg
   UNSETARGFILE(
           "Unsets the current value of the argfilename.  Inserted after argfile contents.",
           Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION),
+  THREADS("When opening multiple alignment windows, set a limit to alignments being processed at one time.",
+          Opt.BOOTSTRAP, Opt.STRING, Opt.NODUPLICATEVALUES, Opt.NOACTION),
 
   // these last two have no purpose in the normal Jalview application but are
   // used by jalview.bin.Launcher to set memory settings. They are not used by