From cdfe204d197ce71d054e8dab35865387ba2574a4 Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 11 Dec 2009 21:59:55 +0000 Subject: [PATCH] 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 --- .../broadinstitute/sting/gatk/walkers/CountLociWalker.java | 4 ++-- .../broadinstitute/sting/gatk/walkers/CountReadsWalker.java | 6 +++--- .../sting/gatk/walkers/qc/PrintLocusContextWalker.java | 2 +- .../sting/gatk/walkers/qc/ReadValidationWalker.java | 2 +- .../sting/gatk/walkers/qc/ValidatingPileupWalker.java | 2 +- .../org/broadinstitute/sting/utils/TextFormattingUtils.java | 2 +- .../sting/utils/help/HelpExtractorDoclet.java | 2 +- 7 files changed, 10 insertions(+), 10 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java index 83a491ebd..1241d18c2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java +++ b/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 - * covered loci for diagnostic purposes. + * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes. + * Simplest example of a locus walker. */ public class CountLociWalker extends LocusWalker implements TreeReducible { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java index 9aa35fac8..5915bcb1b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java +++ b/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 - * reads seen for diagnostic purposes. Can also count the number of reads matching a given criterion using - * read filters (see the --read-filter command line argument). + * Walks over the input data set, calculating the number of reads seen for diagnostic purposes. + * Can also count the number of reads matching a given criterion using read filters (see the + * --read-filter command line argument). Simplest example of a read-backed analysis. */ @Requires({DataSource.READS, DataSource.REFERENCE}) public class CountReadsWalker extends ReadWalker { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java index fb01a51d2..9d08d4081 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java +++ b/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 implements TreeReducible { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java index 59dc30070..32a5e97a1 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +++ b/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 */ diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java index eb077dbb4..0afab418d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +++ b/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,'. */ diff --git a/java/src/org/broadinstitute/sting/utils/TextFormattingUtils.java b/java/src/org/broadinstitute/sting/utils/TextFormattingUtils.java index 7c588989d..923c44dc1 100644 --- a/java/src/org/broadinstitute/sting/utils/TextFormattingUtils.java +++ b/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 diff --git a/java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java index 6a39144ae..8d8db5fa7 100644 --- a/java/src/org/broadinstitute/sting/utils/help/HelpExtractorDoclet.java +++ b/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)