applied copyright 2008

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5d0b9d6..cf3ac30 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,26 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.bin;
 
+import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
 import java.lang.reflect.Constructor;
+import java.net.URL;
 import java.util.*;
 
 import javax.swing.*;
@@ -80,7 +85,7 @@ public class Jalview
                       + "-noquestionnaire\tTurn off questionnaire check."
                       + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
                       + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
-                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed."
+                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)"
                       + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
       System.exit(0);
     }
@@ -398,7 +403,32 @@ public class Jalview
     {
       System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
     }
-    File sfile = new File(groovyscript);
+    File sfile = null;
+    if (groovyscript.trim().equals("STDIN"))
+    {
+      // read from stdin into a tempfile and execute it
+      try {
+        sfile = File.createTempFile("jalview", "groovy");
+        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile)));
+        BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in));
+        String line=null;
+        while ((line=br.readLine())!=null)
+        {
+          outfile.write(line+"\n");
+        }
+        br.close();
+        outfile.flush();
+        outfile.close();
+        
+      } catch (Exception ex)
+      {
+        System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString()));
+        ex.printStackTrace();
+        return;
+      }
+    } else {
+      sfile = new File(groovyscript);
+    }
     if (!sfile.exists())
     {
       System.err.println("File '"+groovyscript+"' does not exist.");
@@ -414,6 +444,7 @@ public class Jalview
       System.err.println("File '"+groovyscript+"' is empty.");
       return;
     }
+    boolean success = false;
     try {
       /* The following code performs the GroovyScriptEngine invocation using reflection,
        * and is equivalent to this fragment from the embedding groovy documentation on 
@@ -436,14 +467,21 @@ public class Jalview
         java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
         setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
         Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
-        Constructor gseccons = gsec.getConstructor(new Class[] { String[].class });
-        Object gse = gseccons.newInstance(new Object[] { new String[] { groovyscript } });
+        Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class } ); // String[].class });
+        Object gse = gseccons.newInstance(new Object[] { new URL[] { sfile.toURL() } }); // .toString() } });
         java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
         run.invoke(gse, new Object[] { sfile.getName(), gbinding });
+        success = true;
     } catch (Exception e)
     {
       System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
       e.printStackTrace(System.err);
+      
+    }
+    if (success && groovyscript.equals("STDIN"))
+    {
+      // delete temp file that we made - but only if it was successfully executed
+      sfile.delete();
     }
   }
   /**