A mechanism for supplying attribution text -- mainly useful for external

walkers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4402 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -95,7 +95,9 @@ public abstract class CommandLineProgram {
      */
     protected ApplicationDetails getApplicationDetails() {
         return new ApplicationDetails(ApplicationDetails.createDefaultHeader(getClass()),
-                                      ApplicationDetails.createDefaultRunningInstructions(getClass()));
+                                      Collections.<String>emptyList(),
+                                      ApplicationDetails.createDefaultRunningInstructions(getClass()),
+                                      null);
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
+import org.broadinstitute.sting.gatk.walkers.Attribution;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
@@ -61,6 +62,7 @@ public class CommandLineGATK extends CommandLineExecutable {
     @Override
     protected ApplicationDetails getApplicationDetails() {
         return new ApplicationDetails(createApplicationHeader(),
+                getAttribution(),
                 ApplicationDetails.createDefaultRunningInstructions(getClass()),
                 getAdditionalHelp());
     }
@@ -98,7 +100,7 @@ public class CommandLineGATK extends CommandLineExecutable {
     public static List<String> createApplicationHeader() {
         List<String> header = new ArrayList<String>();
         header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
-        header.add("Copyright (c) 2009 The Broad Institute");
+        header.add("Copyright (c) 2010 The Broad Institute");
         header.add("Please view our documentation at http://www.broadinstitute.org/gsa/wiki");
         header.add("For support, please view our support site at http://getsatisfaction.com/gsa");
         return header;
@@ -114,6 +116,24 @@ public class CommandLineGATK extends CommandLineExecutable {
         return headerInfo.containsKey("build.timestamp") ? headerInfo.getString("build.timestamp") : "<unknown>";
     }
 
+    /**
+     * If the user supplied any additional attribution, return it here.
+     * @return Additional attribution if supplied by the user.  Empty (non-null) list otherwise.
+     */
+    private List<String> getAttribution() {
+        List<String> attributionLines = new ArrayList<String>();
+
+        // If no analysis name is present, fill in extra help on the walkers.
+        WalkerManager walkerManager = engine.getWalkerManager();
+        String analysisName = getAnalysisName();
+        if(analysisName != null && walkerManager.exists(analysisName)) {
+            Class<? extends Walker> walkerType = walkerManager.getWalkerClassByName(analysisName);
+            if(walkerType.isAnnotationPresent(Attribution.class))
+                attributionLines.addAll(Arrays.asList(walkerType.getAnnotation(Attribution.class).value()));
+        }
+        return attributionLines;
+    }
+
     /**
      * Retrieves additional information about GATK walkers.
      * the code in HelpFormatter and supply it as a helper to this method.

java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java

@@ -47,6 +47,11 @@ public class ApplicationDetails {
      */
     final List<String> applicationHeader;
 
+    /**
+     * Stores additional attribution for a given walker.
+     */
+    final List<String> attribution;
+
     /**
      * Extract details covering exactly how to run this executable.
      */
@@ -57,12 +62,9 @@ public class ApplicationDetails {
      */
     final String additionalHelp;
 
-    public ApplicationDetails( List<String> applicationHeader, String runningInstructions ) {
+    public ApplicationDetails( List<String> applicationHeader, List<String> attribution, String runningInstructions, String additionalHelp ) {
-        this(applicationHeader,runningInstructions,null);    
-    }
-
-    public ApplicationDetails( List<String> applicationHeader, String runningInstructions, String additionalHelp ) {
         this.applicationHeader = applicationHeader;
+        this.attribution = attribution;
         this.runningInstructions = runningInstructions;
         this.additionalHelp = additionalHelp;
     }

java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java

@@ -65,6 +65,9 @@ public class HelpFormatter {
         for(String headerLine: header)
             System.out.printf("%s%n",headerLine);
         System.out.printf("%s%n",barrier);
+        for(String attributionLine: applicationDetails.attribution)
+            System.out.printf("%s%n",attributionLine);
+        System.out.printf("%s%n",barrier);
 
         String synopsis = getSynopsis(applicationDetails.runningInstructions,argumentGroups);
         String additionalDetails = applicationDetails.additionalHelp != null ? applicationDetails.additionalHelp : "";
@@ -293,6 +296,10 @@ public class HelpFormatter {
         logger.info("Program Args: " + output);
         logger.info("Date/Time: " + dateFormat.format(date));
         logger.info(barrier);
+
+        for(String attribution: applicationDetails.attribution)
+            logger.info(attribution);
+        logger.info(barrier);
     }
 
     /**