Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions.

Also increased the line width as much as I could tolerate (100 characters -> 120 characters).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2336 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java

@@ -5,8 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 /**
- * Basic example of a locus-backed analysis.  Walks over the input data set, calculating the number of
+ * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
- * covered loci for diagnostic purposes.
+ * Simplest example of a locus walker.
  */
 public class CountLociWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java

@@ -3,9 +3,9 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Basic example of a read-backed analysis.  Walks over the input data set, calculating the number of
+ * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
- * reads seen for diagnostic purposes.  Can also count the number of reads matching a given criterion using
+ * Can also count the number of reads matching a given criterion using read filters (see the
- *  read filters (see the --read-filter command line argument).
+ * --read-filter command line argument).  Simplest example of a read-backed analysis.  
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReadsWalker extends ReadWalker<Integer, Integer> {

java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java

@@ -11,7 +11,7 @@ import java.util.Arrays;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Diagnostics analysis.  At each locus in the input data set, prints the reference base, genomic location, and
+ * At each locus in the input data set, prints the reference base, genomic location, and
  * all aligning reads in a compact but human-readable form. 
  */
 public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {

java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java

@@ -37,7 +37,7 @@ import java.util.ArrayList;
  */
 
 /**
- * Diagnostics analysis.  Checks all reads passed through the system to ensure that
+ * Checks all reads passed through the system to ensure that
  * the same read is not passed to the walker multiple consecutive times.
  * @author aaron
  */

java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java

@@ -14,7 +14,7 @@ import org.broadinstitute.sting.utils.StingException;
 import java.util.Arrays;
 
 /**
- * Diagnostics analysis.  At every locus in the input set, compares the pileup data (reference base, aligned base from
+ * At every locus in the input set, compares the pileup data (reference base, aligned base from
  * each overlapping read, and quality score) to the reference pileup data generated by samtools.  Samtools' pileup data
  * should be specified using the command-line argument '-B pileup,SAMPileup,<your sam pileup file>'.
  */

java/src/org/broadinstitute/sting/utils/TextFormattingUtils.java

@@ -16,7 +16,7 @@ public class TextFormattingUtils {
     /**
      * The default line width, for GATK output written to the screen.
      */
-    public static final int DEFAULT_LINE_WIDTH = 100;
+    public static final int DEFAULT_LINE_WIDTH = 120;
 
     /**
      * Simple implementation of word-wrap for a line of text.  Idea and

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

@@ -72,7 +72,7 @@ public class HelpExtractorDoclet {
     private static void renderHelpText(String elementName, Doc element, PrintStream out) {
         // Extract overrides from the doc tags.
         String overrideName = null;
-        String overrideDescription = element.commentText();
+        String overrideDescription = element.firstSentenceTags().length > 0 ? element.firstSentenceTags()[0].text() : "";
         for(Tag tag: element.tags()) {
             if(tag.name().equals("@"+DisplayNameTaglet.NAME)) {
                 if(overrideName != null)