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Added @Hidden annotation, a way to deliberately exclude experimental fields and 

walkers from the help system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3946 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-08-05 02:26:46 +00:00
parent 82d6c5073b
commit 78bfe6ac48
10 changed files with 124 additions and 9 deletions
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14
java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
View File

@ -70,6 +70,11 @@ public class ArgumentDefinition {
*/
public final boolean isMultiValued;
/**
* Is this argument hidden from the help system?
*/
public final boolean isHidden;
/**
* Is this argument exclusive of other arguments?
*/
@ -94,6 +99,7 @@ public class ArgumentDefinition {
* @param required Whether or not this argument is required.
* @param isFlag Whether or not this argument should be treated as a flag.
* @param isMultiValued Whether or not this argument supports multiple values.
* @param isHidden Whether or not this argument should be hidden from the command-line argument system.
* @param exclusiveOf Whether this command line argument is mutually exclusive of other arguments.
* @param validation A regular expression for command-line argument validation.
* @param validOptions is there a particular list of options that's valid for this argument definition? List them if so, otherwise set this to null.
@ -105,6 +111,7 @@ public class ArgumentDefinition {
boolean required,
boolean isFlag,
boolean isMultiValued,
boolean isHidden,
String exclusiveOf,
String validation,
List<String> validOptions) {
@ -115,6 +122,7 @@ public class ArgumentDefinition {
this.required = required;
this.isFlag = isFlag;
this.isMultiValued = isMultiValued;
this.isHidden = isHidden;
this.exclusiveOf = exclusiveOf;
this.validation = validation;
this.validOptions = validOptions;
@ -127,6 +135,7 @@ public class ArgumentDefinition {
* @param defaultShortName Default short name for this argument definition.
* @param isFlag Whether or not this argument should be treated as a flag.
* @param isMultiValued Whether or not this argument supports multiple values.
* @param isHidden Whether or not this argument should be hidden from the command-line argument system.
* @param validOptions is there a particular list of options that's valid for this argument definition? List them if so, otherwise set this to null.
*/
public ArgumentDefinition( Annotation annotation,
@ -134,6 +143,7 @@ public class ArgumentDefinition {
String defaultShortName,
boolean isFlag,
boolean isMultiValued,
boolean isHidden,
List<String> validOptions) {
String fullName = (String)getValue(annotation, "fullName");
@ -159,6 +169,7 @@ public class ArgumentDefinition {
this.required = isRequired(annotation, isFlag);
this.isFlag = isFlag;
this.isMultiValued = isMultiValued;
this.isHidden = isHidden;
this.exclusiveOf = getExclusiveOf(annotation);
this.validation = getValidationRegex(annotation);
this.validOptions = validOptions;
@ -170,12 +181,14 @@ public class ArgumentDefinition {
* @param fieldName Default full name for this argument definition.
* @param isFlag Whether or not this argument should be treated as a flag.
* @param isMultiValued Whether or not this argument supports multiple values.
* @param isHidden Whether or not this argument should be hidden from the command-line argument system.
* @param validOptions is there a particular list of options that's valid for this argument definition? List them if so, otherwise set this to null.
*/
public ArgumentDefinition( Annotation annotation,
String fieldName,
boolean isFlag,
boolean isMultiValued,
boolean isHidden,
List<String> validOptions) {
this.ioType = getIOType(annotation);
this.fullName = getFullName(annotation, fieldName);
@ -184,6 +197,7 @@ public class ArgumentDefinition {
this.required = isRequired(annotation, isFlag);
this.isFlag = isFlag;
this.isMultiValued = isMultiValued;
this.isHidden = isHidden;
this.exclusiveOf = getExclusiveOf(annotation);
this.validation = getValidationRegex(annotation);
this.validOptions = validOptions;

12
java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
View File

@ -86,4 +86,16 @@ public class ArgumentDefinitionGroup implements Iterable<ArgumentDefinition> {
public Iterator<ArgumentDefinition> iterator() {
return argumentDefinitions.iterator();
}
/**
* Reports whether all the arguments in this group are hidden.
* @return True if all are hidden, false if some or none are hidden.
*/
public boolean allHidden() {
for(ArgumentDefinition argumentDefinition: argumentDefinitions) {
if(!argumentDefinition.isHidden)
return false;
}
return true;
}
}

10
java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
View File

@ -25,6 +25,8 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.gatk.walkers.Hidden;
import java.lang.reflect.Field;
import java.util.Collection;
import java.util.List;
@ -147,6 +149,14 @@ public class ArgumentSource {
return Collection.class.isAssignableFrom(argumentType) || field.getType().isArray();
}
/**
* Should the given class be hidden from the command-line argument system.
* @return True if so. False otherwise.
*/
public boolean isHidden() {
return field.isAnnotationPresent(Hidden.class);
}
/**
* Gets a string representation of the argument source for debugging.
* @return String representation of the argument source.

11
java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.commandline;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.gatk.walkers.Hidden;
import org.apache.log4j.Logger;
import java.lang.annotation.Annotation;
@ -127,6 +128,7 @@ public abstract class ArgumentTypeDescriptor {
source.field.getName(),
source.isFlag(),
source.isMultiValued(),
source.isHidden(),
getValidOptions(source) );
}
@ -198,6 +200,15 @@ public abstract class ArgumentTypeDescriptor {
return true;
return false;
}
/**
* Returns true if the given annotation is hidden from the help system.
* @param field Field to test.
* @return True if argument should be hidden. False otherwise.
*/
public static boolean isArgumentHidden(Field field) {
return field.isAnnotationPresent(Hidden.class);
}
}
/**

2
java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
View File

@ -187,7 +187,7 @@ public class CommandLineGATK extends CommandLineExecutable {
int longestPackageName = 0;
int longestWalkerName = 0;
for(Map.Entry<String,Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage().entrySet()) {
for(Map.Entry<String,Collection<Class<? extends Walker>>> walkersByPackage: walkerManager.getWalkerNamesByPackage(true).entrySet()) {
// Get the display name.
String packageName = walkersByPackage.getKey();
String packageDisplayName = walkerManager.getPackageDisplayName(walkersByPackage.getKey());

15
java/src/org/broadinstitute/sting/gatk/WalkerManager.java
View File

@ -66,11 +66,15 @@ public class WalkerManager extends PluginManager<Walker> {
/**
* Get the list of walkers currently available to the GATK, organized
* by package.
* @param visibleWalkersOnly If true, return only the walker names that aren't hidden.
* @return Names of currently available walkers.
*/
public Map<String,Collection<Class<? extends Walker>>> getWalkerNamesByPackage() {
public Map<String,Collection<Class<? extends Walker>>> getWalkerNamesByPackage(boolean visibleWalkersOnly) {
Map<String,Collection<Class<? extends Walker>>> walkersByPackage = new HashMap<String,Collection<Class<? extends Walker>>>();
for(Class<? extends Walker> walker: pluginsByName.values()) {
if(visibleWalkersOnly && isHidden(walker))
continue;
// Extract the name for the package; if the walker is in the unnamed package, use the empty string
String walkerPackage = walker.getPackage() != null ? walker.getPackage().getName() : "";
if(!walkersByPackage.containsKey(walkerPackage))
@ -225,6 +229,15 @@ public class WalkerManager extends PluginManager<Walker> {
return Arrays.asList(requiresDataSource.referenceMetaData());
}
/**
* Reports whether this walker type is hidden -- in other words, whether it'll appear in the help output.
* @param walkerType Class to test for visibility.
* @return True if the walker should be hidden. False otherwise.
*/
public static boolean isHidden(Class<? extends Walker> walkerType) {
return walkerType.isAnnotationPresent(Hidden.class);
}
/**
* Extracts filters that the walker has requested be run on the dataset.
* @param walker Walker to inspect for filtering requests.

2
java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java
View File

@ -162,6 +162,7 @@ public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
"varout",
false,
source.isMultiValued(),
source.isHidden(),
null );
}
@ -179,6 +180,7 @@ public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
false,
false,
false,
source.isHidden(),
null,
null,
null );

2
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
View File

@ -101,6 +101,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
DEFAULT_ARGUMENT_SHORTNAME,
false,
source.isMultiValued(),
source.isHidden(),
null );
}
@ -118,6 +119,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
false,
false,
false,
source.isHidden(),
null,
null,
null );

40
java/src/org/broadinstitute/sting/gatk/walkers/Hidden.java 100644
View File

@ -0,0 +1,40 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers;
import java.lang.annotation.*;
/**
* Indicates that a walker or walker argument should not be presented in the help system.
*
* @author mhanna
* @version 0.1
*/
@Documented
@Inherited
@Retention(RetentionPolicy.RUNTIME)
@Target({ElementType.TYPE,ElementType.FIELD})
public @interface Hidden {
}

25
java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
View File

@ -89,6 +89,8 @@ public class HelpFormatter {
for( ArgumentDefinitionGroup argumentGroup: argumentGroups ) {
for( ArgumentDefinition argumentDefinition: argumentGroup.argumentDefinitions ) {
if(argumentDefinition.isHidden)
continue;
lineFormatter.format(" ");
if( !argumentDefinition.required ) lineFormatter.format("[");
if( argumentDefinition.shortName != null )
@ -125,24 +127,33 @@ public class HelpFormatter {
private String getDetailed( List<ArgumentDefinitionGroup> argumentGroups ) {
StringBuilder builder = new StringBuilder();
for( ArgumentDefinitionGroup argumentGroup: argumentGroups ) {
if( argumentGroup.groupName != null && argumentGroup.argumentDefinitions.size() != 0 )
builder.append( String.format("%nArguments for %s:%n", argumentGroup.groupName ) );
builder.append( getDetailForGroup( argumentGroup.argumentDefinitions ) );
}
for( ArgumentDefinitionGroup argumentGroup: argumentGroups )
builder.append( getDetailForGroup( argumentGroup ) );
return builder.toString();
}
/**
* Gets a detailed description for a given argument group.
* @param argumentDefinitions The argument definitions contained withina group.
* @param argumentDefinitionGroup The group of argument definitions to render.
* @return A string giving detailed info about the contents of this group.
*/
private String getDetailForGroup( List<ArgumentDefinition> argumentDefinitions ) {
private String getDetailForGroup( ArgumentDefinitionGroup argumentDefinitionGroup ) {
if(argumentDefinitionGroup.allHidden())
return "";
StringBuilder builder = new StringBuilder();
Formatter formatter = new Formatter( builder );
if( argumentDefinitionGroup.groupName != null && argumentDefinitionGroup.argumentDefinitions.size() != 0 )
builder.append( String.format("%nArguments for %s:%n", argumentDefinitionGroup.groupName ) );
List<ArgumentDefinition> argumentDefinitions = new ArrayList<ArgumentDefinition>();
for(ArgumentDefinition argumentDefinition: argumentDefinitionGroup.argumentDefinitions) {
if(!argumentDefinition.isHidden)
argumentDefinitions.add(argumentDefinition);
}
// Try to fit the entire argument definition across the screen, but impose an arbitrary cap of 3/4 *
// LINE_WIDTH in case the length of the arguments gets out of control.
int argWidth = Math.min( findLongestArgumentCallingInfo(argumentDefinitions), (TextFormattingUtils.DEFAULT_LINE_WIDTH*3)/4 - FIELD_SEPARATION_WIDTH );