diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java index 752b99be9..a8b9cbbe5 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java @@ -15,7 +15,7 @@ import java.util.List; * To change this template use File | Settings | File Templates. */ public class DepthOfCoverageWalker extends LocusWalker> { - @Argument(fullName="suppressLocusPrinting",required=false,defaultValue="false") + @Argument(fullName="suppressLocusPrinting",doc="Suppress printing",required=false,defaultValue="false") public boolean suppressPrinting; public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index cbf865c2d..fc55872c1 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -15,10 +15,10 @@ import org.broadinstitute.sting.utils.ReadBackedPileup; * To change this template use File | Settings | File Templates. */ public class PileupWalker extends LocusWalker implements TreeReducible { - @Argument(fullName="verbose",required=false,defaultValue="false") + @Argument(fullName="verbose",doc="verbose",required=false,defaultValue="false") public boolean VERBOSE; - @Argument(fullName="extended",shortName="ext",required=false,defaultValue="false") + @Argument(fullName="extended",shortName="ext",doc="extended",required=false,defaultValue="false") public boolean EXTENDED; public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument? diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java index e2bac9449..9b4e5fbe1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java @@ -17,7 +17,7 @@ import org.broadinstitute.sting.utils.ReadBackedPileup; * To change this template use File | Settings | File Templates. */ public class ValidatingPileupWalker extends LocusWalker { - @Argument(fullName="continue_after_error",required=false,defaultValue="false") + @Argument(fullName="continue_after_error",doc="Continue after an error",required=false,defaultValue="false") public boolean CONTINUE_AFTER_AN_ERROR; public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java index 372f6dc9b..b1fe87fc8 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java @@ -21,7 +21,7 @@ import java.io.DataInputStream; public class AlleleFrequencyWalker extends LocusWalker// implements AllelicVariant { @Argument(doc="Number of chromosomes in data") public int N; - @Argument(required=false,defaultValue="0") public int DOWNSAMPLE; + @Argument(required=false,doc="downsample",defaultValue="0") public int DOWNSAMPLE; @Argument(doc="File to output GFF formatted allele frequency calls") public String GFF_OUTPUT_FILE; @Argument(shortName="met", doc="Turns on logging of metrics on the fly with AlleleFrequency calculation") public boolean LOG_METRICS; @Argument(required=false, defaultValue="metrics.out", doc="Name of file where metrics will output") public String METRICS_OUTPUT_FILE; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java index b053ac8b3..c74db3a50 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java @@ -15,10 +15,10 @@ import java.io.FileNotFoundException; @WalkerName("CountCovariates") public class CovariateCounterWalker extends LocusWalker { - @Argument(fullName="MAX_READ_LENGTH", shortName="mrl", required=false,defaultValue="101") + @Argument(fullName="MAX_READ_LENGTH", shortName="mrl", doc="max read length", required=false,defaultValue="101") public int MAX_READ_LENGTH; - @Argument(fullName="MAX_QUAL_SCORE", shortName="mqs", required=false,defaultValue="63") + @Argument(fullName="MAX_QUAL_SCORE", shortName="mqs", doc="max quality score", required=false,defaultValue="63") public int MAX_QUAL_SCORE; @Argument(fullName="OUTPUT_FILEROOT", shortName="outroot", required=false, defaultValue="output", doc="Filename root for the outputted logistic regression training files") diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java index 17b190313..8f524b86d 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/FindNonrandomSecondBestBasePiles.java @@ -21,7 +21,7 @@ import java.util.List; import java.util.ArrayList; public class FindNonrandomSecondBestBasePiles extends LocusWalker { - @Argument(fullName="verbose",required=false,defaultValue="false") + @Argument(fullName="verbose",doc="verbose",required=false,defaultValue="false") public boolean VERBOSE; private AlleleFrequencyWalker caller_1b; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java index ba8bc3f24..f9d71141b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java @@ -24,13 +24,13 @@ import java.io.File; * @author Kiran Garimella */ public class IOCrusherWalker extends ReadWalker> { - @Argument(shortName="nWaysOut",required=false,defaultValue="1") + @Argument(shortName="nWaysOut",doc="n ways out",required=false,defaultValue="1") public int nWaysOut; - @Argument(shortName="readScaling",required=false,defaultValue="1") + @Argument(shortName="readScaling",doc="read scaling",required=false,defaultValue="1") public float readScaling; - @Argument(shortName="outputBase", required=true) + @Argument(shortName="outputBase",doc="output base",required=true) public String outputBase; public long nReadsRead = 0; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java index a372420e5..bb6c5624c 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java @@ -17,9 +17,9 @@ import java.util.List; @WalkerName("IndelIntervals") public class IndelIntervalWalker extends ReadWalker { - @Argument(fullName="maxReadLength", shortName="maxRead", required=false, defaultValue="-1") + @Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false, defaultValue="-1") public int maxReadLength; - @Argument(fullName="minIndelsPerInterval", shortName="minIndels", required=false, defaultValue="1") + @Argument(fullName="minIndelsPerInterval", shortName="minIndels", doc="min indels per interval", required=false, defaultValue="1") public int minIntervalIndelCount; public void initialize() {} diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java index 07f3d7851..8c77754bf 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java @@ -19,7 +19,7 @@ import java.io.File; @WalkerName("IntervalCleaner") public class IntervalCleanerWalker extends LocusWindowWalker { - @Argument(fullName="maxReadLength", shortName="maxRead", required=false, defaultValue="-1") + @Argument(fullName="maxReadLength", shortName="maxRead", doc="max read length", required=false, defaultValue="-1") public int maxReadLength; @Argument(fullName="OutputCleaned", shortName="O", required=true, doc="Output file (sam or bam) for improved (realigned) reads") public String OUT; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java index 723d2d659..7b8ca424a 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java @@ -17,10 +17,10 @@ import java.io.FileNotFoundException; @WalkerName("LogisticRecalibration") public class LogisticRecalibrationWalker extends ReadWalker { - @Argument(shortName="logisticParams", required=true) + @Argument(shortName="logisticParams", doc="logistic params file", required=true) public String logisticParamsFile; - @Argument(shortName="outputBAM", required=false, defaultValue="") + @Argument(shortName="outputBAM", doc="output BAM file", required=false, defaultValue="") public String outputFile; HashMap regressors = new HashMap(); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java index 57701a2e8..ab3e08a4b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java @@ -14,9 +14,9 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; public class MendelianInheritanceWalker extends RefWalker { - @Argument(fullName="consensus_cutoff", shortName="XC",required=true ) public Double CONS_CUTOFF; - @Argument(fullName="snp_cutoff", shortName="XS",required=true ) public Double SNP_CUTOFF; - @Argument(fullName="indel_cutoff", shortName="XI",required=true ) public Double INDEL_CUTOFF; + @Argument(fullName="consensus_cutoff", shortName="XC", doc="consensus cutoff", required=true ) public Double CONS_CUTOFF; + @Argument(fullName="snp_cutoff", shortName="XS", doc="snp cutoff", required=true ) public Double SNP_CUTOFF; + @Argument(fullName="indel_cutoff", shortName="XI", doc="indel cutoff", required=true ) public Double INDEL_CUTOFF; @Argument(fullName="log_concordant", shortName="LC",doc="If set, all trio-concordant sites will be logged at level INFO") public boolean LOG_CONCORDANT; @Argument(fullName="log_discordant", shortName="LD",doc="If set, all trio-discordant sites will be logged at level INFO") public boolean LOG_DISCORDANT; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java index 6405f2c50..aa3fb2ac3 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java @@ -21,7 +21,7 @@ import edu.mit.broad.picard.PicardException; public class Pilot3CoverageWalker extends LocusWalker { - @Argument(fullName = "extended", shortName="ext", required=false, defaultValue = "false") + @Argument(fullName = "extended", shortName="ext", doc="extended output", required=false, defaultValue = "false") public boolean extendedOutput; @Argument(fullName="min_mapq", shortName="mmq", required=false, defaultValue="1", doc="Minimum mapping quality of reads to consider") public Integer MIN_MAPQ; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java index 656648342..7a348455d 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java @@ -24,7 +24,7 @@ public class PoolCaller extends LocusWalker List sample_names = null; //@Argument(required=false, shortName="log_metrics", defaultValue="true") public boolean LOG_METRICS; - @Argument(required=false, shortName="fractional_counts", defaultValue="false") public boolean FRACTIONAL_COUNTS; + @Argument(required=false, shortName="fractional_counts", doc="fractional counts", defaultValue="false") public boolean FRACTIONAL_COUNTS; private Random random; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java index 006625649..0cdb18f8d 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java @@ -24,10 +24,10 @@ public class PoolCallingExperiment extends LocusWalker sample_names = null; - @Argument(required=false, shortName="downsample", defaultValue="4") public int DOWNSAMPLE; - @Argument(required=false, shortName="downsample_noise", defaultValue="3") public int DOWNSAMPLE_NOISE; - @Argument(required=false, shortName="log_metrics", defaultValue="true") public boolean LOG_METRICS; - @Argument(required=false, shortName="fractional_counts", defaultValue="false") public boolean FRACTIONAL_COUNTS; + @Argument(required=false, shortName="downsample", doc="downsample", defaultValue="4") public int DOWNSAMPLE; + @Argument(required=false, shortName="downsample_noise", doc="downsample noise", defaultValue="3") public int DOWNSAMPLE_NOISE; + @Argument(required=false, shortName="log_metrics", doc="log metrics", defaultValue="true") public boolean LOG_METRICS; + @Argument(required=false, shortName="fractional_counts", doc="fractional counts", defaultValue="false") public boolean FRACTIONAL_COUNTS; private Random random; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java index 0824e8658..7a2f6f3a5 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java @@ -20,7 +20,7 @@ import edu.mit.broad.picard.PicardException; public class PopPriorWalker extends LocusWalker { - @Argument(fullName = "quality_score_cutoff", required = false) public Byte qualityScoreCutoff; + @Argument(fullName = "quality_score_cutoff", doc="quality score cutoff", required = false) public Byte qualityScoreCutoff; public PopPriorWalker() { } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java index 6fad04235..ae7b6a673 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java @@ -20,9 +20,9 @@ import java.util.Random; * @author Kiran Garimella */ public class ReadErrorRateWalker extends ReadWalker { - @Argument(fullName="printVisualHits", shortName="v", required=false, defaultValue="false") public boolean printVisualHits; - @Argument(fullName="useNextBestBase", shortName="nb", required=false, defaultValue="false") public boolean useNextBestBase; - @Argument(fullName="useNextRandomBase", shortName="nr", required=false, defaultValue="false") public boolean useNextRandomBase; + @Argument(fullName="printVisualHits", shortName="v", doc="print visual hits", required=false, defaultValue="false") public boolean printVisualHits; + @Argument(fullName="useNextBestBase", shortName="nb", doc="use next best base", required=false, defaultValue="false") public boolean useNextBestBase; + @Argument(fullName="useNextRandomBase", shortName="nr", doc="use next random base", required=false, defaultValue="false") public boolean useNextRandomBase; /** * Ignore reads with indels or clipping diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java index cd7c08d6c..03ddfa36b 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java @@ -19,15 +19,15 @@ import java.util.*; // j.maguire 3-7-2009 public class SingleSampleGenotyper extends LocusWalker { - @Argument(fullName="metrics", shortName="met", required=false, defaultValue="/dev/null") public String metricsFileName; - @Argument(fullName="metInterval", shortName="mi", required=false, defaultValue="50000") public Integer metricsInterval; - @Argument(fullName="printMetrics", shortName="printMetrics", required=false, defaultValue="true") public Boolean printMetrics; - @Argument(fullName="lodThreshold", shortName="lod", required=false, defaultValue="5.0") public Double lodThreshold; - @Argument(fullName="fourBaseMode", shortName="fb", required=false, defaultValue="false") public Boolean fourBaseMode; - @Argument(fullName="retest", shortName="re", required=false, defaultValue="false") public Boolean retest; - @Argument(fullName="qHom", shortName="qHom", required=false, defaultValue="0.04") public Double qHom; - @Argument(fullName="qHet", shortName="qHet", required=false, defaultValue="0.49") public Double qHet; - @Argument(fullName="qHomNonRef", shortName="qHomNonRef", required=false, defaultValue="0.97") public Double qHomNonRef; + @Argument(fullName="metrics", shortName="met", doc="metrics", required=false, defaultValue="/dev/null") public String metricsFileName; + @Argument(fullName="metInterval", shortName="mi", doc="metInterval", required=false, defaultValue="50000") public Integer metricsInterval; + @Argument(fullName="printMetrics", shortName="printMetrics", doc="printMetrics", required=false, defaultValue="true") public Boolean printMetrics; + @Argument(fullName="lodThreshold", shortName="lod", doc="lodThreshold", required=false, defaultValue="5.0") public Double lodThreshold; + @Argument(fullName="fourBaseMode", shortName="fb", doc="fourBaseMode", required=false, defaultValue="false") public Boolean fourBaseMode; + @Argument(fullName="retest", shortName="re", doc="retest", required=false, defaultValue="false") public Boolean retest; + @Argument(fullName="qHom", shortName="qHom", doc="qHom", required=false, defaultValue="0.04") public Double qHom; + @Argument(fullName="qHet", shortName="qHet", doc="qHet", required=false, defaultValue="0.49") public Double qHet; + @Argument(fullName="qHomNonRef", shortName="qHomNonRef", doc="qHomNonRef", required=false, defaultValue="0.97") public Double qHomNonRef; public AlleleMetrics metrics; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java index 72a8343cc..16d93c3a3 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java @@ -21,13 +21,13 @@ import edu.mit.broad.picard.PicardException; public class SomaticCoverageWalker extends LocusWalker { - @Argument(fullName = "tumor_sample_name", shortName = "s1", required = true) + @Argument(fullName = "tumor_sample_name", shortName = "s1", doc="tumor sample name", required = true) public String tumorSampleName; - @Argument(fullName = "normal_sample_name", shortName = "s2", required = true) + @Argument(fullName = "normal_sample_name", shortName = "s2", doc="normal sample name", required = true) public String normalSampleName; - @Argument(fullName = "extended", shortName="ext", required=false, defaultValue = "false") + @Argument(fullName = "extended", shortName="ext", doc="extended output", required=false, defaultValue = "false") public boolean extendedOutput; diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java b/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java index 7479796e0..a64cd1fa3 100755 --- a/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java +++ b/java/src/org/broadinstitute/sting/utils/cmdLine/Argument.java @@ -42,7 +42,7 @@ public @interface Argument { * --help argument is specified. * @return Doc string associated with this command-line argument. */ - String doc() default ""; + String doc(); /** * Is this command-line argument required. The application should exit diff --git a/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java b/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java index 5620b9f97..b8d03fe53 100755 --- a/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java +++ b/java/test/org/broadinstitute/sting/utils/cmdLine/ParsingEngineTest.java @@ -33,7 +33,7 @@ public class ParsingEngineTest extends BaseTest { } private class InputFileArgProvider { - @Argument(fullName="input_file",shortName="I") + @Argument(fullName="input_file",doc="input file",shortName="I") public String inputFile; } @@ -81,7 +81,7 @@ public class ParsingEngineTest extends BaseTest { private class MultiCharShortNameArgProvider { - @Argument(shortName="out") + @Argument(shortName="out", doc="output file") public String outputFile; } @@ -128,7 +128,7 @@ public class ParsingEngineTest extends BaseTest { } private class AllLociArgProvider { - @Argument(fullName="all_loci",shortName="A") + @Argument(fullName="all_loci",shortName="A", doc="all loci") public boolean allLoci = false; } @@ -149,7 +149,7 @@ public class ParsingEngineTest extends BaseTest { } private class MultiValueArgProvider { - @Argument(fullName="input_file",shortName="I") + @Argument(fullName="input_file",shortName="I", doc="input file") public String[] inputFile; } @@ -174,7 +174,7 @@ public class ParsingEngineTest extends BaseTest { } private class IntegerListArgProvider { - @Argument(fullName="integer_list",shortName="N") + @Argument(fullName="integer_list",shortName="N",doc="integer list") public List integers; } @@ -199,7 +199,7 @@ public class ParsingEngineTest extends BaseTest { } private class UntypedListArgProvider { - @Argument(fullName="untyped_list",shortName="N") + @Argument(fullName="untyped_list",shortName="N", doc="untyped list") public List integers; } @@ -213,7 +213,7 @@ public class ParsingEngineTest extends BaseTest { } private class RequiredArgProvider { - @Argument(required=true) + @Argument(required=true,doc="value") public Integer value; } @@ -232,7 +232,7 @@ public class ParsingEngineTest extends BaseTest { } private class UnrequiredArgProvider { - @Argument(required=false) + @Argument(required=false,doc="unrequired value") public Integer value; } @@ -251,10 +251,10 @@ public class ParsingEngineTest extends BaseTest { } private class DuplicateLongNameProvider { - @Argument(fullName="myarg") + @Argument(fullName="myarg",doc="my arg") public Integer foo; - @Argument(fullName="myarg") + @Argument(fullName="myarg", doc="my arg") public Integer bar; } @@ -265,10 +265,10 @@ public class ParsingEngineTest extends BaseTest { private class DuplicateShortNameProvider { - @Argument(shortName="myarg") + @Argument(shortName="myarg", doc="my arg") public Integer foo; - @Argument(shortName="myarg") + @Argument(shortName="myarg", doc="my arg") public Integer bar; } @@ -327,7 +327,7 @@ public class ParsingEngineTest extends BaseTest { } private class PackageProtectedArgProvider { - @Argument + @Argument(doc="foo") Integer foo; } @@ -342,7 +342,7 @@ public class ParsingEngineTest extends BaseTest { } private class CamelCaseArgProvider { - @Argument + @Argument(doc="my arg") Integer myArg; } }