in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 1913555..551c07c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -677,6 +677,7 @@ public final class MainFrameApplication extends MainFrame {
     }
 
     void buildPhylogeneticInferenceMenu() {
+        final InferenceManager inference_manager = InferenceManager.getInstance();
         _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
         _inference_menu
                 .add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java b/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java
new file mode 100644 (file)
index 0000000..0c4ed99
--- /dev/null
+++ b/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java
@@ -0,0 +1,82 @@
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2012 Christian M. Zmasek\r
+// Copyright (C) 2008-2012 Sanford Burnham Medical Research Institute\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: www.phylosoft.org/forester\r
+\r
+package org.forester.archaeopteryx.tools;\r
+\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+\r
+public class ProcessPool {\r
+\r
+    final static private ArrayList<ProcessRunning> _processes = new ArrayList<ProcessRunning>();\r
+\r
+    public synchronized ProcessRunning getProcessByIndex( final int i ) {\r
+        return getProcesses().get( i );\r
+    }\r
+\r
+    public synchronized int size() {\r
+        return getProcesses().size();\r
+    }\r
+\r
+    public synchronized ProcessRunning getProcessById( final int id ) {\r
+        for( final ProcessRunning p : getProcesses() ) {\r
+            if ( p.getId() == id ) {\r
+                return p;\r
+            }\r
+        }\r
+        return null;\r
+    }\r
+\r
+    public synchronized int addProcess( final String name ) {\r
+        final ProcessRunning p = ProcessRunning.createInstance( name );\r
+        final int id = p.getId();\r
+        if ( getProcessById( id ) != null ) {\r
+            throw new IllegalStateException( "process with id " + id + "already exists" );\r
+        }\r
+        getProcesses().add( p );\r
+        return id;\r
+    }\r
+\r
+    public synchronized boolean removeProcess( final int id ) {\r
+        final int i = getProcessIndexById( id );\r
+        if ( i >= 0 ) {\r
+            getProcesses().remove( i );\r
+            return true;\r
+        }\r
+        return false;\r
+    }\r
+\r
+    private synchronized int getProcessIndexById( final int id ) {\r
+        final ProcessRunning p = getProcessById( id );\r
+        if ( p != null ) {\r
+            return p.getId();\r
+        }\r
+        return -1;\r
+    }\r
+\r
+    private synchronized List<ProcessRunning> getProcesses() {\r
+        return _processes;\r
+    }\r
+}\r

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ProcessRunning.java b/forester/java/src/org/forester/archaeopteryx/tools/ProcessRunning.java
new file mode 100644 (file)
index 0000000..4630f28
--- /dev/null
+++ b/forester/java/src/org/forester/archaeopteryx/tools/ProcessRunning.java
@@ -0,0 +1,66 @@
+// $Id:\r
+// FORESTER -- software libraries and applications\r
+// for evolutionary biology research and applications.\r
+//\r
+// Copyright (C) 2008-2012 Christian M. Zmasek\r
+// Copyright (C) 2008-2012 Sanford Burnham Medical Research Institute\r
+// All rights reserved\r
+//\r
+// This library is free software; you can redistribute it and/or\r
+// modify it under the terms of the GNU Lesser General Public\r
+// License as published by the Free Software Foundation; either\r
+// version 2.1 of the License, or (at your option) any later version.\r
+//\r
+// This library is distributed in the hope that it will be useful,\r
+// but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
+// Lesser General Public License for more details.\r
+//\r
+// You should have received a copy of the GNU Lesser General Public\r
+// License along with this library; if not, write to the Free Software\r
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+//\r
+// Contact: phylosoft @ gmail . com\r
+// WWW: www.phylosoft.org/forester\r
+\r
+package org.forester.archaeopteryx.tools;\r
+\r
+import java.text.SimpleDateFormat;\r
+import java.util.Calendar;\r
+\r
+final class ProcessRunning {\r
+\r
+    private static int   count = 0;\r
+    final private int    _id;\r
+    final private String _name;\r
+    final private String _start;\r
+\r
+    int getId() {\r
+        return _id;\r
+    }\r
+    \r
+     String getName() {\r
+        return _name;\r
+    }\r
+    \r
+     String getStart() {\r
+        return _start;\r
+    }\r
+    \r
+    public String toString() {\r
+        return getName() + " [id=" + getId() + "] [start=" + getStart() + "]";\r
+    }\r
+    \r
+    synchronized static ProcessRunning createInstance( final String name ) {\r
+        final Calendar cal = Calendar.getInstance();\r
+        final SimpleDateFormat sdf = new SimpleDateFormat( "HH:mm:ss" );\r
+        return new ProcessRunning( count++, name, sdf.format( cal.getTime() ) );\r
+    }\r
+    \r
+    private ProcessRunning( final int id, final String name, final String start ) {\r
+        _id = id;\r
+        _name = name;\r
+        _start = start;  \r
+    }\r
+\r
+}\r