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gatk-3.8
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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
This commit is contained in:
hanna 2010-01-19 21:58:36 +00:00
parent 9e0ae993c7
commit 8dafd26100
3 changed files with 31 additions and 6 deletions
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2
build.xml
View File

@ -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}"/>

8
java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -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;
}

27
java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
View File

@ -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','-');
}
}