From 6b501e267bfb770f21f21048ac85551ee2ee3d8c Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 23 Jul 2011 22:15:01 -0400 Subject: [PATCH] Includes non-concrete classes in docs CommandLineGATK has extraDocs to ReadFilter and UserException as well --- .../broadinstitute/sting/gatk/CommandLineGATK.java | 5 ++--- .../utils/help/GenericDocumentationHandler.java | 13 +++++++------ 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 905e75584..2af29ea70 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -49,9 +49,8 @@ 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 }) + summary = "Features and arguments for the GATK engine itself, available to all walkers.", + extraDocs = { ReadFilter.class, UserException.class }) public class CommandLineGATK extends CommandLineExecutable { @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run") private String analysisName = null; diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java index d85e86bfe..8b0a33887 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java @@ -43,12 +43,13 @@ import java.util.*; public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { @Override public boolean shouldBeProcessed(ClassDoc doc) { - 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; +// } }