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Removed now unused @version tags from walker docs.

This commit is contained in:
Mark DePristo 2011-07-22 09:57:03 -04:00
parent 421b70ca4f
commit 9e88d51db9
3 changed files with 5 additions and 26 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
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@ -115,7 +115,6 @@ import java.util.List;
* *
* @author Mark DePristo * @author Mark DePristo
* @since 7/4/11 * @since 7/4/11
* @version 0.1
*/ */
@Requires(value={}) @Requires(value={})
public class DiffObjectsWalker extends RodWalker<Integer, Integer> { public class DiffObjectsWalker extends RodWalker<Integer, Integer> {

1
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
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@ -40,7 +40,6 @@ import java.util.List;
* of paired reads. * of paired reads.
* *
* @author mhanna * @author mhanna
* @version 0.1
*/ */
public class CountPairsWalker extends ReadPairWalker<Integer,Long> { public class CountPairsWalker extends ReadPairWalker<Integer,Long> {
@Output @Output

29
public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
View File

@ -61,7 +61,7 @@ public class ResourceBundleExtractorDoclet {
*/ */
protected final Set<String> undocumentedWalkers = new HashSet<String>(); protected final Set<String> undocumentedWalkers = new HashSet<String>();
protected String buildTimestamp = null, versionPrefix = null, versionSuffix = null, absoluteVersion = null; protected String buildTimestamp = null, absoluteVersion = null;
/** /**
* Extracts the contents of certain types of javadoc and adds them to an XML file. * Extracts the contents of certain types of javadoc and adds them to an XML file.
@ -93,10 +93,6 @@ public class ResourceBundleExtractorDoclet {
} }
if(options[0].equals("-build-timestamp")) if(options[0].equals("-build-timestamp"))
buildTimestamp = options[1]; buildTimestamp = options[1];
if(options[0].equals("-version-prefix"))
versionPrefix = options[1];
if(options[0].equals("-version-suffix"))
versionSuffix = options[1];
if (options[0].equals("-absolute-version")) if (options[0].equals("-absolute-version"))
absoluteVersion = options[1]; absoluteVersion = options[1];
} }
@ -144,7 +140,7 @@ public class ResourceBundleExtractorDoclet {
* @return Number of potential parameters; 0 if not supported. * @return Number of potential parameters; 0 if not supported.
*/ */
public static int optionLength(String option) { public static int optionLength(String option) {
if(option.equals("-build-timestamp") || option.equals("-version-prefix") || option.equals("-version-suffix") || option.equals("-out") || option.equals("-absolute-version") ) { if(option.equals("-build-timestamp") || option.equals("-out") || option.equals("-absolute-version") ) {
return 2; return 2;
} }
return 0; return 0;
@ -242,30 +238,15 @@ public class ResourceBundleExtractorDoclet {
* @param element Doc element to process. * @param element Doc element to process.
*/ */
private void renderHelpText(String elementName, Doc element) { private void renderHelpText(String elementName, Doc element) {
// Extract overrides from the doc tags.
String name = null;
String version = null;
StringBuilder summaryBuilder = new StringBuilder(); StringBuilder summaryBuilder = new StringBuilder();
for(Tag tag: element.firstSentenceTags()) for(Tag tag: element.firstSentenceTags())
summaryBuilder.append(tag.text()); summaryBuilder.append(tag.text());
String summary = summaryBuilder.toString(); String summary = summaryBuilder.toString();
String description = element.commentText(); String description = element.commentText();
for(Tag tag: element.tags()) { // this might seem unnecessary, but the GATK command line program uses this tag to determine the version when running
if(tag.name().equals("@"+VERSION_TAGLET_NAME)) { if(absoluteVersion != null)
if ( absoluteVersion != null ) { resourceText.setProperty(String.format("%s.%s",elementName,VERSION_TAGLET_NAME),absoluteVersion);
version = absoluteVersion;
}
else {
version = String.format("%s%s%s", (versionPrefix != null) ? versionPrefix : "",
tag.text(),
(versionSuffix != null) ? versionSuffix : "");
}
}
}
if(version != null)
resourceText.setProperty(String.format("%s.%s",elementName,VERSION_TAGLET_NAME),version);
// Write out an alternate element summary, if exists. // Write out an alternate element summary, if exists.
resourceText.setProperty(String.format("%s.%s",elementName,SUMMARY_TAGLET_NAME),formatText(summary)); resourceText.setProperty(String.format("%s.%s",elementName,SUMMARY_TAGLET_NAME),formatText(summary));