diff --git a/build.xml b/build.xml
index 35ddb091f..80e685ab4 100644
--- a/build.xml
+++ b/build.xml
@@ -6,7 +6,7 @@
-
+
@@ -99,10 +99,10 @@
-
+ additionalparam="-out ${build.dir}/${resource.file}">
@@ -124,7 +124,7 @@
-
+
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index bd6dc5e9d..fb3d9f2c3 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -58,19 +58,11 @@ public class WalkerManager extends PluginManager {
/**
* A collection of help text for walkers and their enclosing packages.
*/
- private Properties helpText = new Properties();
+ private ResourceBundle helpText;
public WalkerManager() {
super(Walker.class,"walker","Walker");
- InputStream helpSourceFile = getClass().getClassLoader().getResourceAsStream("help.properties");
- if(helpSourceFile != null) {
- try {
- helpText.load(helpSourceFile);
- }
- catch(IOException ex) {
- throw new StingException("Unable to process help data");
- }
- }
+ helpText = ResourceBundle.getBundle("StingText");
}
/**
@@ -100,7 +92,7 @@ public class WalkerManager extends PluginManager {
String displayNameKey = String.format("%s.%s",packageName,DisplayNameTaglet.NAME);
String displayName = null;
if(helpText.containsKey(displayNameKey)) {
- displayName = helpText.getProperty(displayNameKey);
+ displayName = helpText.getString(displayNameKey);
}
else {
// If no override exists...
@@ -121,7 +113,7 @@ public class WalkerManager extends PluginManager {
String key = String.format("%s.%s",packageName,SummaryTaglet.NAME);
if(!helpText.containsKey(key))
return "";
- return helpText.getProperty(key);
+ return helpText.getString(key);
}
/**
@@ -133,7 +125,7 @@ public class WalkerManager extends PluginManager {
String walkerSummary = String.format("%s.%s",walkerType.getName(), SummaryTaglet.NAME);
if(!helpText.containsKey(walkerSummary))
return "";
- return helpText.getProperty(walkerSummary);
+ return helpText.getString(walkerSummary);
}
/**
@@ -145,7 +137,7 @@ public class WalkerManager extends PluginManager {
String walkerDescription = String.format("%s.%s",walkerType.getName(), DescriptionTaglet.NAME);
if(!helpText.containsKey(walkerDescription))
return "";
- return helpText.getProperty(walkerDescription);
+ return helpText.getString(walkerDescription);
}
/**
diff --git a/java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
similarity index 91%
rename from java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java
rename to java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index a5edb412d..1ea8e2806 100644
--- a/java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java
+++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -17,7 +17,12 @@ import org.broadinstitute.sting.utils.StingException;
* @author mhanna
* @version 0.1
*/
-public class HelpExtractorDoclet {
+public class ResourceBundleExtractorDoclet {
+ /**
+ * Taglet for the particular version number.
+ */
+ private static final String VERSION_TAGLET_NAME = "version";
+
/**
* Extracts the contents of certain types of javadoc and adds them to an XML file.
* @param rootDoc The documentation root.
@@ -72,6 +77,7 @@ public class HelpExtractorDoclet {
private static void renderHelpText(String elementName, Doc element, PrintStream out) {
// Extract overrides from the doc tags.
String name = null;
+ String version = null;
StringBuilder summaryBuilder = new StringBuilder();
for(Tag tag: element.firstSentenceTags())
summaryBuilder.append(tag.text());
@@ -84,6 +90,8 @@ public class HelpExtractorDoclet {
throw new StingException("Only one display name tag can be used per package / walker.");
name = tag.text();
}
+ else if(tag.name().equals("@"+VERSION_TAGLET_NAME))
+ version = tag.text();
else if(tag.name().equals("@"+SummaryTaglet.NAME))
summary = tag.text();
else if(tag.name().equals("@"+DescriptionTaglet.NAME))
@@ -94,6 +102,9 @@ public class HelpExtractorDoclet {
if(name != null)
out.printf("%s.%s=%s%n",elementName,DisplayNameTaglet.NAME,name);
+ if(version != null)
+ out.printf("%s.%s=%s%n",elementName,VERSION_TAGLET_NAME,version);
+
// Write out an alternate element summary, if exists.
out.printf("%s.%s=%s%n",elementName,SummaryTaglet.NAME,formatText(summary));
diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index 7b1233007..b5e618cef 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -24,6 +24,10 @@
+
+
+
+
@@ -40,8 +44,11 @@
+
+
+
-
+
diff --git a/packages/FixBAMSortOrder.xml b/packages/FixBAMSortOrder.xml
index 51f30cab7..1c9491f32 100644
--- a/packages/FixBAMSortOrder.xml
+++ b/packages/FixBAMSortOrder.xml
@@ -4,8 +4,10 @@
GenomeAnalysisTK
org.broadinstitute.sting.gatk.CommandLineGATK
-
+
+ StingText.properties
+
org.broadinstitute.sting.gatk.walkers.FixBAMSortOrderTag
diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index 7ca07ad7c..9181d2382 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -7,6 +7,9 @@
GATK-GSA-Pipeline
org.broadinstitute.sting.gatk.CommandLineGATK
+
+ StingText.properties
+
org.broadinstitute.sting.gatk.filters
org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index 26f53d040..096fd54ed 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -8,6 +8,9 @@
GATK-Picard
org.broadinstitute.sting.gatk.CommandLineGATK
+
+ StingText.properties
+
org.broadinstitute.sting.gatk.filters
org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker
org.broadinstitute.sting.gatk.walkers.PileupWalker
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 9a32eb94d..4127c9e0e 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -5,7 +5,11 @@
GenomeAnalysisTK
org.broadinstitute.sting.gatk.CommandLineGATK
+
+ StingText.properties
+
org.broadinstitute.sting.gatk.filters
+
org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker
org.broadinstitute.sting.gatk.walkers.PileupWalker
org.broadinstitute.sting.gatk.walkers.PrintReadsWalker