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Includes non-concrete classes in docs 

CommandLineGATK has extraDocs to ReadFilter and UserException as well
This commit is contained in:
Mark DePristo 2011-07-23 22:15:01 -04:00
parent 7420ed098e
commit 6b501e267b
2 changed files with 9 additions and 9 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -49,9 +49,8 @@ import java.util.*;
*/ */
@DocumentedGATKFeature( @DocumentedGATKFeature(
groupName = "GATK Engine", groupName = "GATK Engine",
summary = "Features and arguments for the GATK engine itself, available to all walkers." ) summary = "Features and arguments for the GATK engine itself, available to all walkers.",
//, extraDocs = { ReadFilter.class, UserException.class })
// extraDocs = { ReadFilter.class, UserException.class })
public class CommandLineGATK extends CommandLineExecutable { public class CommandLineGATK extends CommandLineExecutable {
@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run") @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
private String analysisName = null; private String analysisName = null;

13
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
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@ -43,12 +43,13 @@ import java.util.*;
public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
@Override @Override
public boolean shouldBeProcessed(ClassDoc doc) { public boolean shouldBeProcessed(ClassDoc doc) {
try { return true;
Class type = HelpUtils.getClassForDoc(doc); // try {
return JVMUtils.isConcrete(type); // Class type = HelpUtils.getClassForDoc(doc);
} catch ( ClassNotFoundException e ) { // return JVMUtils.isConcrete(type);
return false; // } catch ( ClassNotFoundException e ) {
} // return false;
// }
} }