diff --git a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index cf190835e..6aeb42faa 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java @@ -33,9 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.help.DescriptionTaglet; -import org.broadinstitute.sting.utils.help.DisplayNameTaglet; -import org.broadinstitute.sting.utils.help.SummaryTaglet; +import org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; @@ -82,19 +80,10 @@ public class WalkerManager extends PluginManager { * @return A suitable display name for the package. */ public String getPackageDisplayName(String packageName) { - // Try to find an override for the display name of this package. - String displayNameKey = String.format("%s.%s",packageName,DisplayNameTaglet.NAME); - String displayName; - if(helpText.containsKey(displayNameKey)) { - displayName = helpText.getString(displayNameKey); - } - else { - // If no override exists... - // ...try to compute the override from the text of the package name, while accounting for - // unpackaged walkers. - displayName = packageName.substring(packageName.lastIndexOf('.')+1); - if(displayName.trim().equals("")) displayName = ""; - } + // ...try to compute the override from the text of the package name, while accounting for + // unpackaged walkers. + String displayName = packageName.substring(packageName.lastIndexOf('.')+1); + if (displayName.trim().equals("")) displayName = ""; return displayName; } @@ -104,7 +93,7 @@ public class WalkerManager extends PluginManager { * @return Package help text, or "" if none exists. */ public String getPackageSummaryText(String packageName) { - String key = String.format("%s.%s",packageName,SummaryTaglet.NAME); + String key = String.format("%s.%s",packageName, ResourceBundleExtractorDoclet.SUMMARY_TAGLET_NAME); if(!helpText.containsKey(key)) return ""; return helpText.getString(key); @@ -116,7 +105,7 @@ public class WalkerManager extends PluginManager { * @return Walker summary description, or "" if none exists. */ public String getWalkerSummaryText(Class walkerType) { - String walkerSummary = String.format("%s.%s",walkerType.getName(), SummaryTaglet.NAME); + String walkerSummary = String.format("%s.%s",walkerType.getName(), ResourceBundleExtractorDoclet.SUMMARY_TAGLET_NAME); if(!helpText.containsKey(walkerSummary)) return ""; return helpText.getString(walkerSummary); @@ -137,7 +126,7 @@ public class WalkerManager extends PluginManager { * @return Walker full description, or "" if none exists. */ public String getWalkerDescriptionText(Class walkerType) { - String walkerDescription = String.format("%s.%s",walkerType.getName(), DescriptionTaglet.NAME); + String walkerDescription = String.format("%s.%s",walkerType.getName(), ResourceBundleExtractorDoclet.DESCRIPTION_TAGLET_NAME); if(!helpText.containsKey(walkerDescription)) return ""; return helpText.getString(walkerDescription); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java index 8c6539f8d..775cde1f4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java @@ -58,6 +58,8 @@ import java.util.List; import java.util.Map; /** + * First pass of the recalibration. Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide). + * * This walker is designed to work as the first pass in a two-pass processing step. * It does a by-locus traversal operating only at sites that are not in dbSNP. * We assume that all reference mismatches we see are therefore errors and indicative of poor base quality. @@ -72,7 +74,6 @@ import java.util.Map; * * @author rpoplin * @since Nov 3, 2009 - * @help.summary First pass of the recalibration. Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide). */ @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java index 0277fda0d..fec7ee4e6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java @@ -54,8 +54,10 @@ import java.util.ResourceBundle; import java.util.regex.Pattern; /** + * Second pass of the recalibration. Uses the table generated by CountCovariates to update the base quality scores of the input bam file using a sequential table calculation making the base quality scores more accurately reflect the actual quality of the bases as measured by reference mismatch rate. + * * This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. - + * * For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) * Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. * This walker then outputs a new bam file with these updated (recalibrated) reads. @@ -65,7 +67,6 @@ import java.util.regex.Pattern; * * @author rpoplin * @since Nov 3, 2009 - * @help.summary Second pass of the recalibration. Uses the table generated by CountCovariates to update the base quality scores of the input bam file using a sequential table calculation making the base quality scores more accurately reflect the actual quality of the bases as measured by reference mismatch rate. */ @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 403c67d3e..b195fd35f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -49,8 +49,6 @@ import java.util.*; * * @author rpoplin * @since Mar 14, 2011 - * - * @help.summary Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration */ public class ApplyRecalibration extends RodWalker { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 8179463eb..76c888640 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -53,8 +53,6 @@ import java.util.*; * * User: rpoplin * Date: 3/12/11 - * - * @help.summary Takes variant calls as .vcf files, learns a Gaussian mixture model over the variant annotations and evaluates the variant -- assigning an informative lod score */ public class VariantRecalibrator extends RodWalker, ExpandingArrayList> implements TreeReducible> { diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java deleted file mode 100644 index 65c332048..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java +++ /dev/null @@ -1,59 +0,0 @@ -package org.broadinstitute.sting.utils.help; - -import com.sun.tools.doclets.Taglet; - -import java.util.Map; - -/** - * Provide an alternate description for the given help system. - * - * @author mhanna - * @version 0.1 - */ -public class DescriptionTaglet extends HelpTaglet { - /** - * The key tag for this taglet. - */ - public static final String NAME = "help.description"; - - /** - * Return the name of this custom tag. - */ - @Override - public String getName() { - return NAME; - } - - /** - * Will return false since overviews are always named - * by the @WalkerName tag. - * @return false always - */ - @Override - public boolean inOverview() { - return true; - } - - /** - * Will return true to indicate that packages can be given useful - * description. - * @return true always - */ - @Override - public boolean inPackage() { - return true; - } - - /** - * Register this Taglet. - * @param tagletMap the map to register this tag to. - */ - public static void register(Map tagletMap) { - DescriptionTaglet tag = new DescriptionTaglet(); - Taglet t = (Taglet)tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } -} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java deleted file mode 100644 index 6c6dad736..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java +++ /dev/null @@ -1,49 +0,0 @@ -package org.broadinstitute.sting.utils.help; - -import com.sun.tools.doclets.Taglet; - -import java.util.Map; - -/** - * Provide a display name in the help for packages - * - * @author mhanna - * @version 0.1 - */ -public class DisplayNameTaglet extends HelpTaglet { - /** - * The display name for this taglet. - */ - public static final String NAME = "help.display.name"; - - /** - * Return the name of this custom tag. - */ - @Override - public String getName() { - return NAME; - } - - /** - * Will return true to indicate that packages can be given useful - * display text. - * @return true always - */ - @Override - public boolean inPackage() { - return true; - } - - /** - * Register this Taglet. - * @param tagletMap the map to register this tag to. - */ - public static void register(Map tagletMap) { - DisplayNameTaglet tag = new DisplayNameTaglet(); - Taglet t = (Taglet)tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java deleted file mode 100644 index b350b1a29..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java +++ /dev/null @@ -1,91 +0,0 @@ -package org.broadinstitute.sting.utils.help; - -import com.sun.javadoc.Tag; -import com.sun.tools.doclets.Taglet; - -/** - * Basic functionality for the help taglet. - * - * @author mhanna - * @version 0.1 - */ -public abstract class HelpTaglet implements Taglet { - /** - * Return the name of this custom tag. - */ - public abstract String getName(); - - /** - * Will return false since this tag cannot be applied - * to a field. - * @return false since this tag cannot be applied to a field. - */ - public boolean inField() { - return false; - } - - /** - * Will return false since by default, help tags cannot be applied to a constructor. - * @return false since by default, help tags cannot be applied to a constructor. - */ - public boolean inConstructor() { - return false; - } - - /** - * Will return false since by default, help tags cannot be applied to a method. - * @return false since by default, this tag cannot be applied to a method. - */ - public boolean inMethod() { - return false; - } - - /** - * Will return false since by default, help tags cannot be applied to an overview. - * @return false since by default, help tags cannot be applied to an overview. - */ - public boolean inOverview() { - return false; - } - - /** - * Will return false since by default, help tags cannot be applied to a package. - * description. - * @return false since by default, help tags cannot be applied to a package. - */ - public boolean inPackage() { - return false; - } - - /** - * Will return false since help tags are by default not inline. - * @return false since help tags are by default not inline. - */ - public boolean inType() { - return false; - } - - /** - * Will return false since help tags are by default not inline. - * @return false since help tags are by default not inline. - */ - public boolean isInlineTag() { - return false; - } - - /** - * Create a string representation of this tag. Since this tag is only - * used by the help system, don't output any HTML. - */ - public String toString(Tag tag) { - return null; - } - - /** - * Create a string representation of this tag. Since this tag is only - * used by the help system, don't output any HTML. - */ - public String toString(Tag[] tags) { - return null; - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java index 4f4c411a3..c7b8b045e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java @@ -47,7 +47,9 @@ public class ResourceBundleExtractorDoclet { /** * Taglet for the particular version number. */ - protected static final String VERSION_TAGLET_NAME = "version"; + public static final String VERSION_TAGLET_NAME = "version"; + public static final String SUMMARY_TAGLET_NAME = "help.summary"; + public static final String DESCRIPTION_TAGLET_NAME = "help.description"; /** * Maintains a collection of resources in memory as they're accumulated. @@ -250,39 +252,26 @@ public class ResourceBundleExtractorDoclet { String description = element.commentText(); for(Tag tag: element.tags()) { - if(tag.name().equals("@"+DisplayNameTaglet.NAME)) { - if(name != null) - throw new ReviewedStingException("Only one display name tag can be used per package / walker."); - name = tag.text(); - } - else if(tag.name().equals("@"+VERSION_TAGLET_NAME)) { + if(tag.name().equals("@"+VERSION_TAGLET_NAME)) { if ( absoluteVersion != null ) { version = absoluteVersion; } else { version = String.format("%s%s%s", (versionPrefix != null) ? versionPrefix : "", - tag.text(), - (versionSuffix != null) ? versionSuffix : ""); + tag.text(), + (versionSuffix != null) ? versionSuffix : ""); } } - else if(tag.name().equals("@"+SummaryTaglet.NAME)) - summary = tag.text(); - else if(tag.name().equals("@"+DescriptionTaglet.NAME)) - description = tag.text(); } - // Write out an alternate element name, if exists. - if(name != null) - resourceText.setProperty(String.format("%s.%s",elementName,DisplayNameTaglet.NAME),name); - if(version != null) resourceText.setProperty(String.format("%s.%s",elementName,VERSION_TAGLET_NAME),version); // Write out an alternate element summary, if exists. - resourceText.setProperty(String.format("%s.%s",elementName,SummaryTaglet.NAME),formatText(summary)); + resourceText.setProperty(String.format("%s.%s",elementName,SUMMARY_TAGLET_NAME),formatText(summary)); // Write out an alternate description, if present. - resourceText.setProperty(String.format("%s.%s",elementName,DescriptionTaglet.NAME),formatText(description)); + resourceText.setProperty(String.format("%s.%s",elementName,DESCRIPTION_TAGLET_NAME),formatText(description)); } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java deleted file mode 100644 index db8b55940..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java +++ /dev/null @@ -1,58 +0,0 @@ -package org.broadinstitute.sting.utils.help; - -import com.sun.tools.doclets.Taglet; - -import java.util.Map; - -/** - * Provide an alternate brief summary for this walker / package. - * Acts as an alternative to the first sentence employed by default. - * @author mhanna - * @version 0.1 - */ -public class SummaryTaglet extends HelpTaglet { - /** - * The key tag for this taglet. - */ - public static final String NAME = "help.summary"; - - /** - * Return the name of this custom tag. - */ - @Override - public String getName() { - return NAME; - } - - /** - * Will return false since overviews are always named - * by the @WalkerName tag. - * @return false always - */ - @Override - public boolean inOverview() { - return true; - } - - /** - * Will return true to indicate that packages can be given useful summary. - * @return true always - */ - @Override - public boolean inPackage() { - return true; - } - - /** - * Register this Taglet. - * @param tagletMap the map to register this tag to. - */ - public static void register(Map tagletMap) { - SummaryTaglet tag = new SummaryTaglet(); - Taglet t = (Taglet)tagletMap.get(tag.getName()); - if (t != null) { - tagletMap.remove(tag.getName()); - } - tagletMap.put(tag.getName(), tag); - } -} \ No newline at end of file