diff --git a/java/src/org/broadinstitute/sting/utils/doc/DescriptionTaglet.java b/java/src/org/broadinstitute/sting/utils/doc/DescriptionTaglet.java deleted file mode 100644 index 7b5a419f5..000000000 --- a/java/src/org/broadinstitute/sting/utils/doc/DescriptionTaglet.java +++ /dev/null @@ -1,120 +0,0 @@ -package org.broadinstitute.sting.utils.doc; - -import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.Tag; - -import java.util.Map; - -/** - * Provide an alternate description for the given help system. - * - * @author mhanna - * @version 0.1 - */ -public class DescriptionTaglet implements Taglet { - /** - * The key tag for this taglet. - */ - public static final String NAME = "help.description"; - - /** - * Return the name of this custom tag. - */ - public String getName() { - return NAME; - } - - /** - * Will return false since this tag cannot be applied - * to a field. - * @return false since this tag cannot be applied to a field. - */ - public boolean inField() { - return false; - } - - /** - * Will return false since this tag cannot be applied - * to a constructor. - * @return false since this tag cannot be applied to a constructor. - */ - public boolean inConstructor() { - return false; - } - - /** - * Will return false since this tag cannot be applied - * to a method. - * @return false since this tag cannot be applied to a method. - */ - public boolean inMethod() { - return false; - } - - /** - * Will return false since overviews are always named - * by the @WalkerName tag. - * @return false always - */ - public boolean inOverview() { - return true; - } - - /** - * Will return true to indicate that packages can be given useful - * description. - * @return true always - */ - public boolean inPackage() { - return true; - } - - /** - * Will return false indicating that types cannot be given - * alternate description. - * @return false always. - */ - public boolean inType() { - return false; - } - - /** - * Will return false since @todo - * is not an inline tag. - * @return false since @todo - * is not an inline tag. - */ - - public boolean isInlineTag() { - return false; - } - - /** - * Register this Taglet. - * @param tagletMap the map to register this tag to. - */ - public static void register(Map tagletMap) { - DescriptionTaglet tag = new DescriptionTaglet(); - Taglet t = (Taglet)tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } - - /** - * Create a string representation of this tag. Since this tag is only - * used by the help system, don't output any HTML. - */ - public String toString(Tag tag) { - return null; - } - - /** - * Create a string representation of this tag. Since this tag is only - * used by the help system, don't output any HTML. - */ - public String toString(Tag[] tags) { - return null; - } -} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/doc/DisplayNameTaglet.java b/java/src/org/broadinstitute/sting/utils/doc/DisplayNameTaglet.java deleted file mode 100644 index 2837a2237..000000000 --- a/java/src/org/broadinstitute/sting/utils/doc/DisplayNameTaglet.java +++ /dev/null @@ -1,120 +0,0 @@ -package org.broadinstitute.sting.utils.doc; - -import com.sun.tools.doclets.Taglet; -import com.sun.javadoc.Tag; - -import java.util.Map; - -/** - * Provide a display name in the help for packages - * - * @author mhanna - * @version 0.1 - */ -public class DisplayNameTaglet implements Taglet { - /** - * The display name for this taglet. - */ - public static final String NAME = "help.display.name"; - - /** - * Return the name of this custom tag. - */ - public String getName() { - return NAME; - } - - /** - * Will return false since this tag cannot be applied - * to a field. - * @return false since this tag cannot be applied to a field. - */ - public boolean inField() { - return false; - } - - /** - * Will return false since this tag cannot be applied - * to a constructor. - * @return false since this tag cannot be applied to a constructor. - */ - public boolean inConstructor() { - return false; - } - - /** - * Will return false since this tag cannot be applied - * to a method. - * @return false since this tag cannot be applied to a method. - */ - public boolean inMethod() { - return false; - } - - /** - * Will return false since overviews are always named - * by the @WalkerName tag. - * @return false always - */ - public boolean inOverview() { - return false; - } - - /** - * Will return true to indicate that packages can be given useful - * display text. - * @return true always - */ - public boolean inPackage() { - return true; - } - - /** - * Will return false indicating that types cannot be given - * alternate display names. - * @return false always. - */ - public boolean inType() { - return false; - } - - /** - * Will return false since @todo - * is not an inline tag. - * @return false since @todo - * is not an inline tag. - */ - - public boolean isInlineTag() { - return false; - } - - /** - * Register this Taglet. - * @param tagletMap the map to register this tag to. - */ - public static void register(Map tagletMap) { - DisplayNameTaglet tag = new DisplayNameTaglet(); - Taglet t = (Taglet)tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } - - /** - * Create a string representation of this tag. Since this tag is only - * used by the help system, don't output any HTML. - */ - public String toString(Tag tag) { - return null; - } - - /** - * Create a string representation of this tag. Since this tag is only - * used by the help system, don't output any HTML. - */ - public String toString(Tag[] tags) { - return null; - } -} diff --git a/java/src/org/broadinstitute/sting/utils/doc/HelpExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/doc/HelpExtractorDoclet.java deleted file mode 100644 index 2daf960e5..000000000 --- a/java/src/org/broadinstitute/sting/utils/doc/HelpExtractorDoclet.java +++ /dev/null @@ -1,113 +0,0 @@ -package org.broadinstitute.sting.utils.doc; - -import com.sun.javadoc.*; - -import java.util.HashSet; -import java.util.Set; -import java.util.Scanner; -import java.io.PrintStream; -import java.io.FileNotFoundException; - -import org.broadinstitute.sting.utils.StingException; - -/** - * Extracts certain types of javadoc (specifically package and class descriptions) and makes them available - * to applications at runtime. - * - * @author mhanna - * @version 0.1 - */ -public class HelpExtractorDoclet { - /** - * Extracts the contents of certain types of javadoc and adds them to an XML file. - * @param rootDoc The documentation root. - * @return Whether the JavaDoc run succeeded. - * @throws FileNotFoundException if output can't be written. - */ - public static boolean start(RootDoc rootDoc) throws FileNotFoundException { - PrintStream out = System.out; - - for(String[] options: rootDoc.options()) { - if(options[0].equals("-out")) - out = new PrintStream(options[1]); - } - - // Cache packages as we see them, since there's no direct way to iterate over packages. - Set packages = new HashSet(); - - for(ClassDoc currentClass: rootDoc.classes()) { - PackageDoc containingPackage = currentClass.containingPackage(); - packages.add(containingPackage); - String className = containingPackage.name().length() > 0 ? - String.format("%s.%s",containingPackage.name(),currentClass.name()) : - String.format("%s",currentClass.name()); - - renderHelpText(className,currentClass,out); - } - - for(PackageDoc currentPackage: packages) - renderHelpText(currentPackage.name(),currentPackage,out); - - return true; - } - - /** - * Validate the given options against options supported by this doclet. - * @param option Option to validate. - * @return Number of potential parameters; 0 if not supported. - */ - public static int optionLength(String option) { - if(option.equals("-out")) { - return 2; - } - return 0; - } - - /** - * Renders all the help text required for a given name. - * @param elementName element name to use as the key - * @param element Doc element to process. - * @param out Output stream to which to write. - */ - private static void renderHelpText(String elementName, Doc element, PrintStream out) { - // Extract overrides from the doc tags. - String overrideName = null; - String overrideDescription = element.commentText(); - for(Tag tag: element.tags()) { - if(tag.name().equals("@"+DisplayNameTaglet.NAME)) { - if(overrideName != null) - throw new StingException("Only one display name tag can be used per package / walker."); - overrideName = tag.text(); - } - else if(tag.name().equals("@"+DescriptionTaglet.NAME)) - overrideDescription = tag.text(); - } - - // Write out an alternate element name, if exists. - if(overrideName != null) - out.printf("%s.%s=%s%n",elementName,DisplayNameTaglet.NAME,overrideName); - - // Write out an alternate description, if present. - String description = formatText(overrideDescription); - if(description.length() > 0) - out.printf("%s=%s%n",elementName,description); - } - - /** - * Format text for consumption by the properties file. - * @param text Text to format. - * @return Formatted text; string trimmed, newlines removed. - */ - private static String formatText(String text) { - Scanner scanner = new Scanner(text); - StringBuilder output = new StringBuilder(); - - while(scanner.hasNextLine()) { - if(output.length() > 0) - output.append(' '); - output.append(scanner.nextLine().trim()); - } - - return output.toString(); - } -}