From c30e1db744052c789de6726c259678509f6a91e8 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 18 Aug 2011 09:38:51 -0400 Subject: [PATCH] Better location for help utils --- .../sting/gatk/CommandLineGATK.java | 7 +-- .../help/DocumentedGATKFeatureHandler.java | 2 +- .../sting/utils/help/GATKDocUtils.java | 48 ------------------- .../sting/utils/help/HelpUtils.java | 17 +++++++ 4 files changed, 20 insertions(+), 54 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index 7e96b609e..7c567f511 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -34,10 +34,7 @@ import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.walkers.Attribution; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.ApplicationDetails; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.help.GATKDocUtils; -import org.broadinstitute.sting.utils.help.GATKDoclet; +import org.broadinstitute.sting.utils.help.*; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; @@ -178,7 +175,7 @@ public class CommandLineGATK extends CommandLineExecutable { Formatter formatter = new Formatter(additionalHelp); formatter.format("For a full description of this walker, see its GATKdocs at:%n"); - formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType)); + formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType)); return additionalHelp.toString(); } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java index ce03c8093..214a1716a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java @@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler { * @return */ public String getDestinationFilename(ClassDoc doc, Class clazz) { - return GATKDocUtils.htmlFilenameForClass(clazz); + return HelpUtils.htmlFilenameForClass(clazz); } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java deleted file mode 100644 index 8efeecd7b..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +++ /dev/null @@ -1,48 +0,0 @@ -/* - * Copyright (c) 2011, The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR - * OTHER DEALINGS IN THE SOFTWARE. - */ - -package org.broadinstitute.sting.utils.help; - -/** - * @author depristo - * @since 8/8/11 - */ -public class GATKDocUtils { - private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/"; - private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/"; - private final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; - - public static String htmlFilenameForClass(Class c) { - return c.getName().replace(".", "_") + ".html"; - } - - public static String helpLinksToGATKDocs(Class c) { - String classPath = htmlFilenameForClass(c); - StringBuilder b = new StringBuilder(); - b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n"); - b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n"); - b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n"); - return b.toString(); - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java index 4527c6afe..da4e7bdaf 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java @@ -32,6 +32,10 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils; import java.lang.reflect.Field; public class HelpUtils { + public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/"; + public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/"; + public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; + protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) { for (Class interfaceClass : interfaceClasses) if (assignableToClass(classDoc, interfaceClass, false)) @@ -74,4 +78,17 @@ public class HelpUtils { String.format("%s.%s", containingPackage.name(), doc.name()) : String.format("%s", doc.name()); } + + public static String htmlFilenameForClass(Class c) { + return c.getName().replace(".", "_") + ".html"; + } + + public static String helpLinksToGATKDocs(Class c) { + String classPath = htmlFilenameForClass(c); + StringBuilder b = new StringBuilder(); + b.append("release version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n"); + b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n"); + b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n"); + return b.toString(); + } } \ No newline at end of file