From f5d7cabb209352e57b7bc5f08cb2e1a97432f83b Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 18 Aug 2011 11:20:12 -0400 Subject: [PATCH] Fix for reintroducing an already solved problem. --- .../sting/gatk/CommandLineGATK.java | 2 +- .../help/DocumentedGATKFeatureHandler.java | 2 +- .../sting/utils/help/GATKDocUtils.java | 44 +++++++++++++++++++ .../sting/utils/help/HelpUtils.java | 15 ------- 4 files changed, 46 insertions(+), 17 deletions(-) create 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 7c567f511..8a13dadbf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -175,7 +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", HelpUtils.helpLinksToGATKDocs(walkerType)); + formatter.format("%s%n", GATKDocUtils.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 214a1716a..ce03c8093 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 HelpUtils.htmlFilenameForClass(clazz); + return GATKDocUtils.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 new file mode 100644 index 000000000..e2909cf15 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java @@ -0,0 +1,44 @@ +/* + * 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; + +public class GATKDocUtils { + 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/"; + + 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 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 da4e7bdaf..d72d2e83c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java @@ -32,9 +32,6 @@ 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) @@ -79,16 +76,4 @@ public class HelpUtils { 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