Beefed up command-line usage string.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@629 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java

@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.utils.cmdLine;
 
 import org.apache.log4j.*;
+import org.broadinstitute.sting.utils.JVMUtils;
+import org.broadinstitute.sting.utils.StingException;
 
 import java.io.IOException;
 import java.text.DateFormat;
@@ -73,12 +75,43 @@ public abstract class CommandLineProgram {
               required=false)    
     protected Boolean debugMode = false;
 
+    /**
+     * this is used to indicate if they've asked for help
+     */
+    @Argument(fullName="help",shortName="h",doc="Generate this help message",required=false)
+    public Boolean help = false;    
+
     /**
      * our logging output patterns
      */
     private static String patternString = "%p %m %n";
     private static String debugPatternString = "%n[level] %p%n[date]\t\t %d{dd MMM yyyy HH:mm:ss,SSS} %n[class]\t\t %C %n[location]\t %l %n[line number]\t %L %n[message]\t %m %n";
 
+    /**
+     * Retrieves text from the application regarding what parameters to put on the
+     * JVM command line to run this application.
+     * @return helpful instructions on the class / jar to run.
+     */
+    protected String getRunningInstructions() {
+        // Default implementation to find a command line that makes sense.
+        // If the user is running from a jar, return '-jar <jarname>'; otherwise
+        // return the full class name.
+        String runningInstructions = null;
+        try {
+            runningInstructions = JVMUtils.getLocationFor( getClass() ).getName();
+        }
+        catch( IOException ex ) {
+            throw new StingException("Unable to determine running instructions", ex);
+        }
+
+        if( runningInstructions.endsWith(".jar") )
+            runningInstructions = String.format("-jar %s", runningInstructions);
+        else
+            runningInstructions = getClass().getName();
+
+        return runningInstructions;
+    }
+
     /**
      * Will this application want to vary its argument list dynamically?
      * If so, parse the command-line options and then prompt the subclass to return
@@ -109,12 +142,6 @@ public abstract class CommandLineProgram {
     protected abstract int execute();
 
 
-    /**
-     * this is used to indicate if they've asked for help
-     */
-    @Argument(fullName="help",shortName="h",doc="Generate this help message",required=false)    
-    public Boolean help = false;
-
     /**
      * This function is called to start processing the command line, and kick
      * off the execute message of the program.
@@ -177,7 +204,7 @@ public abstract class CommandLineProgram {
 
             // they asked for help, give it to them
             if (clp.help) {
-                parser.printHelp();
+                parser.printHelp( clp.getRunningInstructions() );
                 System.exit(1);
             }
 
@@ -206,7 +233,7 @@ public abstract class CommandLineProgram {
         }
         catch (ParseException e) {
             logger.fatal("Unable to pass command line arguments: " + e.getMessage() );
-            clp.parser.printHelp();
+            clp.parser.printHelp( clp.getRunningInstructions() );
         }
         catch (Exception e) {
             // we catch all exceptions here. if it makes it to this level, we're in trouble.  Let's bail!

java/src/org/broadinstitute/sting/utils/cmdLine/HelpFormatter.java

@@ -42,12 +42,12 @@ public class HelpFormatter {
      * Prints the help, given a collection of argument definitions.
      * @param argumentDefinitions Argument definitions for which help should be printed.
      */
-    public void printHelp( ArgumentDefinitions argumentDefinitions ) {
+    public void printHelp( String runningInstructions, ArgumentDefinitions argumentDefinitions ) {
         SortedSet<ArgumentDefinition> mainArguments = getMainArguments( argumentDefinitions );
         Map<String,SortedSet<ArgumentDefinition>> pluginsByGroup = getPluginArguments( argumentDefinitions );
 
         System.out.printf("%s%s%n",
-                getSynopsis(mainArguments,pluginsByGroup),
+                getSynopsis(runningInstructions,mainArguments,pluginsByGroup),
                 getDetailed(mainArguments,pluginsByGroup) );
     }
 
@@ -89,15 +89,18 @@ public class HelpFormatter {
     /**
      * Gets the synopsis: the actual command to run.
      * @param mainArguments Main program arguments.
-     * @praam pluginArgumentGroups Groups of plugin arguments
+     * @param runningInstructions Instructions on how to run hte application.
+     * @param pluginArgumentGroups Groups of plugin arguments
      * @return A synopsis line.
      */
-    private String getSynopsis( SortedSet<ArgumentDefinition> mainArguments, Map<String,SortedSet<ArgumentDefinition>> pluginArgumentGroups ) {
+    private String getSynopsis( String runningInstructions,
+                                SortedSet<ArgumentDefinition> mainArguments,
+                                Map<String,SortedSet<ArgumentDefinition>> pluginArgumentGroups ) {
         // Build out the synopsis all as one long line.        
         StringBuilder lineBuilder = new StringBuilder();
         Formatter lineFormatter = new Formatter( lineBuilder );
 
-        lineFormatter.format("java -jar dist/GenomeAnalysisTK.jar");
+        lineFormatter.format("java %s", runningInstructions);
 
         List<ArgumentDefinition> argumentDefinitions = new ArrayList<ArgumentDefinition>();
         argumentDefinitions.addAll( mainArguments );

java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java

@@ -218,8 +218,8 @@ public class ParsingEngine {
     /**
      * Prints out the help associated with these command-line argument definitions.
      */
-    public void printHelp() {
-        new HelpFormatter().printHelp(argumentDefinitions);
+    public void printHelp( String runningInstructions ) {
+        new HelpFormatter().printHelp(runningInstructions,argumentDefinitions);
     }
 
     /**