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Only concrete classes are now documented

This commit is contained in:
Mark DePristo 2011-08-18 14:04:47 -04:00
parent 5772766dd5
commit faa3f8b6f6
2 changed files with 8 additions and 22 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -50,7 +50,7 @@ import java.util.*;
@DocumentedGATKFeature(
groupName = "GATK Engine",
summary = "Features and arguments for the GATK engine itself, available to all walkers.",
extraDocs = { ReadFilter.class, UserException.class })
extraDocs = { UserException.class })
public class CommandLineGATK extends CommandLineExecutable {
@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
private String analysisName = null;

28
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
View File

@ -52,13 +52,13 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
@Override
public boolean includeInDocs(ClassDoc doc) {
return true;
// try {
// Class type = HelpUtils.getClassForDoc(doc);
// return JVMUtils.isConcrete(type);
// } catch ( ClassNotFoundException e ) {
// return false;
// }
// return true;
try {
Class type = HelpUtils.getClassForDoc(doc);
return JVMUtils.isConcrete(type);
} catch ( ClassNotFoundException e ) {
return false;
}
}
@ -256,20 +256,6 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
}
root.put("extradocs", extraDocsData);
// List<Map<String, Object>> hierarchyDocs = new ArrayList<Map<String, Object>>();
// for (final GATKDocWorkUnit other : all ) {
// final String relation = classRelationship(toProcess.clazz, other.clazz);
// if ( relation != null )
// hierarchyDocs.add(
// new HashMap<String, Object>(){{
// put("filename", other.filename);
// put("relation", relation);
// put("name", other.name);}});
//
// }
// root.put("relatedDocs", hierarchyDocs);
}
private static final String classRelationship(Class me, Class other) {