From 8dafd261003b4734f5f3fd64937f67bfa13fa2f8 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Jan 2010 21:58:36 +0000
Subject: [PATCH] Print out the current version number in the application
 header.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2633 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml                                     |  2 +-
 .../sting/gatk/CommandLineGATK.java           |  8 ++++--
 .../sting/utils/help/HelpFormatter.java       | 27 ++++++++++++++++---
 3 files changed, 31 insertions(+), 6 deletions(-)

diff --git a/build.xml b/build.xml
index ae21f1580..a9edc6b94 100644
--- a/build.xml
+++ b/build.xml
@@ -75,7 +75,7 @@
         <arg value="--no-newline"/>
       </exec>
       <tstamp>
-        <format property="build.timestamp" pattern="dd MMMM yyyy hh:mm aa"/>
+        <format property="build.timestamp" pattern="yyyy/MM/dd HH:mm:ss"/>
       </tstamp>
 
       <echo message="Compiling module: ${target}"/>
diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 6256bb02b..0950a381a 100755
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -99,12 +99,16 @@ public class CommandLineGATK extends CommandLineExecutable {
      * @return The application header.
      */
     public static List<String> createApplicationHeader() {
+        ResourceBundle headerInfo = ResourceBundle.getBundle("StingText");
+
+        String versionNumber = headerInfo.getString("org.broadinstitute.sting.gatk.version");
+        String timestamp = headerInfo.getString("build.timestamp");
+
         List<String> header = new ArrayList<String>();
-        header.add("The Genome Analysis Toolkit (GATK)");
+        header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",versionNumber,timestamp));
         header.add("Copyright (c) 2009 The Broad Institute");
         header.add("Please view our documentation at http://www.broadinstitute.org/gsa/wiki");
         header.add("For support, email gsahelp@broadinstitute.org");
-        header.add("");
         return header;
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java b/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
index 498f44ae5..e7fd4983f 100755
--- a/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
+++ b/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting.utils.help;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentDefinition;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentDefinitionGroup;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentDefinitions;
-import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
 import org.broadinstitute.sting.utils.TextFormattingUtils;
 import org.apache.log4j.Logger;
 
@@ -46,6 +45,14 @@ public class HelpFormatter {
     public void printHelp( ApplicationDetails applicationDetails, ArgumentDefinitions argumentDefinitions ) {
         List<ArgumentDefinitionGroup> argumentGroups = prepareArgumentGroups( argumentDefinitions );
 
+        List<String> header = applicationDetails.applicationHeader;
+        String barrier = createBarrier(header);
+
+        System.out.printf("%s%n",barrier);
+        for(String headerLine: header)
+            System.out.printf("%s%n",headerLine);
+        System.out.printf("%s%n",barrier);
+
         String synopsis = getSynopsis(applicationDetails.runningInstructions,argumentGroups);
         String additionalDetails = applicationDetails.additionalHelp != null ? applicationDetails.additionalHelp : "";
         String detailedDescription = getDetailed(argumentGroups);
@@ -234,7 +241,9 @@ public class HelpFormatter {
         DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
         java.util.Date date = new java.util.Date();
 
-        logger.info("-------------------------------------------------------");
+        String barrier = createBarrier(applicationDetails.applicationHeader);
+
+        logger.info(barrier);
         for (String headerLine : applicationDetails.applicationHeader)
             logger.info(headerLine);
         String output = "";
@@ -243,6 +252,18 @@ public class HelpFormatter {
         }
         logger.info("Program Args: " + output);
         logger.info("Date/Time: " + dateFormat.format(date));
-        logger.info("-------------------------------------------------------");
+        logger.info(barrier);
+    }
+
+    /**
+     * Create a barrier to use to distinguish the header from the rest of the output.
+     * @param text A collection of lines to output as part of a header.
+     * @return A barrier consisting of the '-' character.
+     */
+    private static String createBarrier(List<String> text) {
+        int barrierWidth = 0;
+        for(String headerLine: text)
+            barrierWidth = Math.max(headerLine.length(),barrierWidth);
+        return String.format("%0" + barrierWidth + "d",0).replace('0','-');
     }
 }