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84 changes: 41 additions & 43 deletions
84
src/main/java/org/broadinstitute/hellbender/utils/help/GATKDocWorkUnit.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,41 @@ | ||
| package org.broadinstitute.hellbender.utils.help; | ||
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| import org.broadinstitute.barclay.help.DocWorkUnit; | ||
| import org.broadinstitute.barclay.help.DocWorkUnitHandler; | ||
| import org.broadinstitute.barclay.help.DocumentedFeature; | ||
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| import org.broadinstitute.hellbender.utils.runtime.RuntimeUtils; | ||
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| import javax.lang.model.element.Element; | ||
|
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| /** | ||
| * Custom DocWorkUnit used for generating GATK help/documentation. Overrides the defaults to provide tool | ||
| * names that are annotated with a " (Picard)" suffix for Picard tools. | ||
| * | ||
| * NOTE: Methods in this class are intended to be called by Gradle/Javadoc only, and should not be called | ||
| * by methods that are used by the GATK runtime. This class has a dependency on com.sun.javadoc classes, | ||
| * which may not be present since they're not provided as part of the normal GATK runtime classpath. | ||
| */ | ||
| @SuppressWarnings("removal") | ||
| public class GATKDocWorkUnit extends DocWorkUnit { | ||
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| public GATKDocWorkUnit( | ||
| final DocWorkUnitHandler workUnitHandler, | ||
| final Element classElement, | ||
| final Class<?> clazz, | ||
| final DocumentedFeature documentedFeatureAnnotation) { | ||
| super(workUnitHandler, classElement, clazz, documentedFeatureAnnotation); | ||
| } | ||
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| @Override | ||
| public String getName() { | ||
| // Override getName to return a display name that annotates Picard tool names with " (Picard)" | ||
| return RuntimeUtils.toolDisplayName(getClazz()); | ||
| } | ||
|
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| /** | ||
| * Sort in order of the name of this WorkUnit | ||
| */ | ||
| @Override | ||
| public int compareTo(DocWorkUnit other) { | ||
| return this.getName().compareTo(other.getName()); | ||
| } | ||
| } | ||
| //package org.broadinstitute.hellbender.utils.help; | ||
| // | ||
| //import org.broadinstitute.barclay.help.DocWorkUnit; | ||
| //import org.broadinstitute.barclay.help.DocWorkUnitHandler; | ||
| //import org.broadinstitute.barclay.help.DocumentedFeature; | ||
| // | ||
| //import org.broadinstitute.hellbender.utils.runtime.RuntimeUtils; | ||
| // | ||
| ///** | ||
| // * Custom DocWorkUnit used for generating GATK help/documentation. Overrides the defaults to provide tool | ||
| // * names that are annotated with a " (Picard)" suffix for Picard tools. | ||
| // * | ||
| // * NOTE: Methods in this class are intended to be called by Gradle/Javadoc only, and should not be called | ||
| // * by methods that are used by the GATK runtime. This class has a dependency on com.sun.javadoc classes, | ||
| // * which may not be present since they're not provided as part of the normal GATK runtime classpath. | ||
| // */ | ||
| //@SuppressWarnings("removal") | ||
| //public class GATKDocWorkUnit extends DocWorkUnit { | ||
| // | ||
| // public GATKDocWorkUnit( | ||
| // final DocWorkUnitHandler workUnitHandler, | ||
| // final DocumentedFeature documentedFeatureAnnotation, | ||
| // final com.sun.javadoc.ClassDoc classDoc, | ||
| // final Class<?> clazz) { | ||
| // super(workUnitHandler, documentedFeatureAnnotation, classDoc, clazz); | ||
| // } | ||
| // | ||
| // @Override | ||
| // public String getName() { | ||
| // // Override getName to return a display name that annotates Picard tool names with " (Picard)" | ||
| // return RuntimeUtils.toolDisplayName(getClazz()); | ||
| // } | ||
| // | ||
| // /** | ||
| // * Sort in order of the name of this WorkUnit | ||
| // */ | ||
| // @Override | ||
| // public int compareTo(DocWorkUnit other) { | ||
| // return this.getName().compareTo(other.getName()); | ||
| // } | ||
| //} |
34 changes: 17 additions & 17 deletions
34
src/main/java/org/broadinstitute/hellbender/utils/help/GATKGSONWorkUnit.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,17 @@ | ||
| package org.broadinstitute.hellbender.utils.help; | ||
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| import org.broadinstitute.barclay.help.GSONWorkUnit; | ||
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| /** | ||
| * Class representing a GSONWorkUnit for GATK work units. | ||
| * | ||
| * Adds "walkertype" to the base gson object created by Barclay. | ||
| */ | ||
| public class GATKGSONWorkUnit extends GSONWorkUnit { | ||
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| private String walkerType; | ||
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| public void setWalkerType(final String walkerType){ | ||
| this.walkerType = walkerType; | ||
| } | ||
| } | ||
| //package org.broadinstitute.hellbender.utils.help; | ||
| // | ||
| //import org.broadinstitute.barclay.help.GSONWorkUnit; | ||
| // | ||
| ///** | ||
| // * Class representing a GSONWorkUnit for GATK work units. | ||
| // * | ||
| // * Adds "walkertype" to the base gson object created by Barclay. | ||
| // */ | ||
| //public class GATKGSONWorkUnit extends GSONWorkUnit { | ||
| // | ||
| // private String walkerType; | ||
| // | ||
| // public void setWalkerType(final String walkerType){ | ||
| // this.walkerType = walkerType; | ||
| // } | ||
| //} |
122 changes: 61 additions & 61 deletions
122
src/main/java/org/broadinstitute/hellbender/utils/help/GATKHelpDocWorkUnitHandler.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,61 +1,61 @@ | ||
| package org.broadinstitute.hellbender.utils.help; | ||
|
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| import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; | ||
| import org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler; | ||
| import org.broadinstitute.barclay.help.DocWorkUnit; | ||
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| import org.broadinstitute.barclay.help.HelpDoclet; | ||
|
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| /** | ||
| * The GATK Documentation work unit handler class that is the companion to GATKHelpDoclet. | ||
| * | ||
| * NOTE: Methods in this class are intended to be called by Gradle/Javadoc only, and should not be called | ||
| * by methods that are used by the GATK runtime, as this class assumes a dependency on com.sun.javadoc classes | ||
| * which may not be present. | ||
| */ | ||
| public class GATKHelpDocWorkUnitHandler extends DefaultDocWorkUnitHandler { | ||
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| private final static String GATK_JAVADOC_TAG_PREFIX = "GATK"; // prefix for custom javadoc tags used by GATK | ||
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| private final static String GATK_FREEMARKER_TEMPLATE_NAME = "generic.template.html"; | ||
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| public GATKHelpDocWorkUnitHandler(final HelpDoclet doclet) { | ||
| super(doclet); | ||
| } | ||
| /** | ||
| * @return Prefix for custom GATK tags that should be lifted from the javadoc and stored in the | ||
| * FreeMarker map. These will be available in the template returned by {@link #getTemplateName}. | ||
| */ | ||
| @Override | ||
| protected String getTagFilterPrefix() { return GATK_JAVADOC_TAG_PREFIX; } | ||
|
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| /** | ||
| * @param workUnit the classdoc object being processed | ||
| * @return the name of a the freemarker template to be used for the class being documented. | ||
| * Must reside in the folder passed to the Barclay Doclet via the "-settings-dir" parameter to | ||
| * Javadoc. | ||
| */ | ||
| @Override | ||
| public String getTemplateName(final DocWorkUnit workUnit) { return GATK_FREEMARKER_TEMPLATE_NAME; } | ||
|
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|
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| /** | ||
| * Add any custom freemarker bindings discovered via custom javadoc tags. Subclasses can override this to | ||
| * provide additional custom bindings. | ||
| * | ||
| * @param currentWorkUnit the work unit for the feature being documented | ||
| */ | ||
| @Override | ||
| protected void addCustomBindings(final DocWorkUnit currentWorkUnit) { | ||
| super.addCustomBindings(currentWorkUnit); | ||
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| // Picard tools use the summary line for the long overview section, so extract that | ||
| // from Picard tools only, and put it in the freemarker map. | ||
| Class<?> toolClass = currentWorkUnit.getClazz(); | ||
| if (picard.cmdline.CommandLineProgram.class.isAssignableFrom(toolClass)) { | ||
| final CommandLineProgramProperties clpProperties = currentWorkUnit.getCommandLineProperties(); | ||
| currentWorkUnit.setProperty("picardsummary", clpProperties.summary()); | ||
| } | ||
| } | ||
|
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| } | ||
| //package org.broadinstitute.hellbender.utils.help; | ||
| // | ||
| //import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; | ||
| //import org.broadinstitute.barclay.help.DefaultDocWorkUnitHandler; | ||
| //import org.broadinstitute.barclay.help.DocWorkUnit; | ||
| // | ||
| //import org.broadinstitute.barclay.help.HelpDoclet; | ||
| // | ||
| ///** | ||
| // * The GATK Documentation work unit handler class that is the companion to GATKHelpDoclet. | ||
| // * | ||
| // * NOTE: Methods in this class are intended to be called by Gradle/Javadoc only, and should not be called | ||
| // * by methods that are used by the GATK runtime, as this class assumes a dependency on com.sun.javadoc classes | ||
| // * which may not be present. | ||
| // */ | ||
| //public class GATKHelpDocWorkUnitHandler extends DefaultDocWorkUnitHandler { | ||
| // | ||
| // private final static String GATK_JAVADOC_TAG_PREFIX = "GATK"; // prefix for custom javadoc tags used by GATK | ||
| // | ||
| // private final static String GATK_FREEMARKER_TEMPLATE_NAME = "generic.template.html"; | ||
| // | ||
| // public GATKHelpDocWorkUnitHandler(final HelpDoclet doclet) { | ||
| // super(doclet); | ||
| // } | ||
| // /** | ||
| // * @return Prefix for custom GATK tags that should be lifted from the javadoc and stored in the | ||
| // * FreeMarker map. These will be available in the template returned by {@link #getTemplateName}. | ||
| // */ | ||
| // @Override | ||
| // protected String getTagFilterPrefix() { return GATK_JAVADOC_TAG_PREFIX; } | ||
| // | ||
| // /** | ||
| // * @param workUnit the classdoc object being processed | ||
| // * @return the name of a the freemarker template to be used for the class being documented. | ||
| // * Must reside in the folder passed to the Barclay Doclet via the "-settings-dir" parameter to | ||
| // * Javadoc. | ||
| // */ | ||
| // @Override | ||
| // public String getTemplateName(final DocWorkUnit workUnit) { return GATK_FREEMARKER_TEMPLATE_NAME; } | ||
| // | ||
| // | ||
| // /** | ||
| // * Add any custom freemarker bindings discovered via custom javadoc tags. Subclasses can override this to | ||
| // * provide additional custom bindings. | ||
| // * | ||
| // * @param currentWorkUnit the work unit for the feature being documented | ||
| // */ | ||
| // @Override | ||
| // protected void addCustomBindings(final DocWorkUnit currentWorkUnit) { | ||
| // super.addCustomBindings(currentWorkUnit); | ||
| // | ||
| // // Picard tools use the summary line for the long overview section, so extract that | ||
| // // from Picard tools only, and put it in the freemarker map. | ||
| // Class<?> toolClass = currentWorkUnit.getClazz(); | ||
| // if (picard.cmdline.CommandLineProgram.class.isAssignableFrom(toolClass)) { | ||
| // final CommandLineProgramProperties clpProperties = currentWorkUnit.getCommandLineProperties(); | ||
| // currentWorkUnit.setProperty("picardsummary", clpProperties.summary()); | ||
| // } | ||
| // } | ||
| // | ||
| //} |
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