Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple

source -> single definition mapping sets.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2417 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java

@@ -112,11 +112,12 @@ public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
         else
             shortName = null;
 
-        return new ArgumentDefinition( source,
+        return new ArgumentDefinition( fullName,
-                                       fullName,
                                        shortName,
                                        getDoc(source),
                                        isRequired(source),
+                                       false,
+                                       source.isMultiValued(),
                                        getExclusiveOf(source),
                                        getValidationRegex(source) );
     }
@@ -127,11 +128,12 @@ public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
      * @return Argument definition for the BAM file itself.  Will not be null.
      */
     private ArgumentDefinition createGenotypeFormatArgumentDefinition(ArgumentSource source) {
-        return new ArgumentDefinition( source,
+        return new ArgumentDefinition( "variant_output_format",
-                                       "variant_output_format",
                                        "vf",
                                        "Format to be used to represent variants; default is VCF",
                                        false,
+                                       false,
+                                       false,
                                        null,
                                        null );
     }

java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java

@@ -110,11 +110,12 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
         else
             shortName = null;
 
-        return new ArgumentDefinition( source,
+        return new ArgumentDefinition( fullName,
-                                       fullName,
                                        shortName,
                                        getDoc(source),
                                        isRequired(source),
+                                       false,
+                                       source.isMultiValued(),
                                        getExclusiveOf(source),
                                        getValidationRegex(source) );
     }
@@ -125,11 +126,12 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
      * @return Argument definition for the BAM file itself.  Will not be null.
      */
     private ArgumentDefinition createBAMCompressionArgumentDefinition(ArgumentSource source) {
-        return new ArgumentDefinition( source,
+        return new ArgumentDefinition( COMPRESSION_FULLNAME,
-                                       COMPRESSION_FULLNAME,
                                        COMPRESSION_SHORTNAME,
                                        "Compression level to use for writing BAM files",
                                        false,
+                                       false,
+                                       false,
                                        null,
                                        null );
     }

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentDefinition.java

@@ -51,6 +51,16 @@ public class ArgumentDefinition {
      */
     public final boolean required;
 
+    /**
+     * Is this argument a flag?  Users can't specify a value for a flag.
+     */
+    public final boolean isFlag;
+
+    /**
+     * Does this argument support multiple values (repeated "-arg value1 -arg value2"-style structures).
+     */
+    public final boolean isMultiValued;
+
     /**
      * Is this argument exclusive of other arguments?
      */
@@ -61,28 +71,31 @@ public class ArgumentDefinition {
      */
     public final String validation;
 
-    /**
-     * The target into which to inject arguments meeting this definition.
-     */
-    public final ArgumentSource source;
-
     /**
      * Creates a new argument definition.
-     * @param source Source information for defining the argument.
+     * @param fullName Full name for this argument definition.
+     * @param shortName Short name for this argument definition.
+     * @param doc Doc string for this argument.
+     * @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 exclusiveOf Whether this command line argument is mutually exclusive of other arguments.
+     * @param validation A regular expression for command-line argument validation.
      */
-    public ArgumentDefinition( ArgumentSource source,
+    public ArgumentDefinition( String fullName,
-                               String fullName,
                                String shortName,
                                String doc,
                                boolean required,
+                               boolean isFlag,
+                               boolean isMultiValued,
                                String exclusiveOf,
                                String validation ) {
-        this.source = source;
-
         this.fullName = fullName;
         this.shortName = shortName;
         this.doc = doc;
         this.required = required;
+        this.isFlag = isFlag;
+        this.isMultiValued = isMultiValued;
         this.exclusiveOf = exclusiveOf;
         this.validation = validation;
     }
@@ -110,6 +123,8 @@ public class ArgumentDefinition {
                Utils.equals(shortName,other.shortName) &&
                Utils.equals(doc,other.doc) &&
                required == other.required &&
+               isFlag == other.isFlag &&
+               isMultiValued == other.isMultiValued &&
                Utils.equals(exclusiveOf,other.exclusiveOf) &&
                Utils.equals(validation,other.validation);
     }

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentMatches.java

@@ -100,9 +100,11 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
      */
 
     ArgumentMatches findMatches( ArgumentSource argumentSource ) {
+        List<ArgumentDefinition> sourceDefinitions = ArgumentTypeDescriptor.create(argumentSource.field.getType()).createArgumentDefinitions(argumentSource);
+
         ArgumentMatches matches = new ArgumentMatches();
         for( ArgumentMatch argumentMatch: getUniqueMatches() ) {
-            if( argumentMatch.definition != null && argumentMatch.definition.source.equals( argumentSource ) )
+            if( sourceDefinitions.contains(argumentMatch.definition) )
                 matches.mergeInto( argumentMatch );
         }
         return matches;
@@ -374,6 +376,6 @@ class ArgumentMatch implements Iterable<ArgumentMatch> {
      * @return True if definition is known to be a flag; false if not known to be a flag.
      */
     private boolean isArgumentFlag() {
-        return definition != null && definition.source.isFlag();
+        return definition != null && definition.isFlag;
     }
 }

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentTypeDescriptor.java

@@ -100,11 +100,12 @@ public abstract class ArgumentTypeDescriptor {
      * @return The default definition for this argument source.
      */
     protected ArgumentDefinition createDefaultArgumentDefinition( ArgumentSource source ) {
-        return new ArgumentDefinition( source,
+        return new ArgumentDefinition( getFullName(source),
-                                       getFullName(source),
                                        getShortName(source),
                                        getDoc(source),
                                        isRequired(source),
+                                       source.isFlag(),
+                                       source.isMultiValued(),
                                        getExclusiveOf(source),
                                        getValidationRegex(source) );
     }

java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java

@@ -214,7 +214,7 @@ public class ParsingEngine {
             Collection<ArgumentMatch> overvaluedArguments = new ArrayList<ArgumentMatch>();
             for( ArgumentMatch argumentMatch: argumentMatches.findSuccessfulMatches() ) {
                 // Warning: assumes that definition is not null (asserted by checks above).
-                if( !argumentMatch.definition.source.isMultiValued() && argumentMatch.values().size() > 1 )
+                if( !argumentMatch.definition.isMultiValued && argumentMatch.values().size() > 1 )
                     overvaluedArguments.add(argumentMatch);
             }
 

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

@@ -75,7 +75,7 @@ public class HelpFormatter {
                     lineFormatter.format("-%s", argumentDefinition.shortName);
                 else
                     lineFormatter.format("--%s", argumentDefinition.fullName);
-                if( !argumentDefinition.source.isFlag() )
+                if( !argumentDefinition.isFlag )
                     lineFormatter.format(" <%s>", argumentDefinition.fullName);
                 if( !argumentDefinition.required ) lineFormatter.format("]");
             }
@@ -157,7 +157,7 @@ public class HelpFormatter {
         if( argumentDefinition.shortName != null )
             formatter.format("-%s,", argumentDefinition.shortName);
         formatter.format("--%s", argumentDefinition.fullName);
-        if( !argumentDefinition.source.isFlag() )
+        if( !argumentDefinition.isFlag )
             formatter.format(" <%s>", argumentDefinition.fullName);
 
         return builder.toString();