Okay, I caved in:

CallsetConcordance now gets possible concordance types by looking at classes that implement ConcordanceType instead of having them hard-coded in.
Thanks to Kiran this was pretty easy...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1939 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/CallsetConcordanceWalker.java

@@ -26,32 +26,23 @@ public class CallsetConcordanceWalker extends RefWalker<Integer, Integer> {
 
     private ArrayList<ConcordanceType> requestedTypes;
 
-    private HashMap<String, ConcordanceType> initializeConcordanceTypes(String prefix) {
-        HashMap<String, ConcordanceType> types = new HashMap<String, ConcordanceType>();
-
-        //
-        // Add new concordance types here!
-        //
-        types.put("SNPGenotypeConcordance", new SNPGenotypeConcordance(prefix));
-        types.put("SimpleVenn", new SimpleVenn(prefix));
-        types.put("IndelSubsets", new IndelSubsets(prefix));
-
-        return types;
-    }
-
     /**
      * Prepare the output file and the list of available features.
      */
     public void initialize() {
-        HashMap<String, ConcordanceType> concordanceTypes = initializeConcordanceTypes(OUTPUT_PATH);
 
+        // get the possible concordance types
+        List<Class<? extends ConcordanceType>> classes = PackageUtils.getClassesImplementingInterface(ConcordanceType.class);
+
+        // print and exit if that's what was requested
         if (LIST_ONLY) {
-            Iterator<String> types = concordanceTypes.keySet().iterator();
             out.println("\nAvailable concordance types:");
-            while ( types.hasNext() )
+            for (int i = 0; i < classes.size(); i++)
-                out.println("\t" + types.next());
+                out.println("\t" + classes.get(i).getSimpleName());
+            out.println();
             System.exit(0);
         }
+
         requestedTypes = new ArrayList<ConcordanceType>();
 
         // initialize requested concordance types
@@ -59,22 +50,37 @@ public class CallsetConcordanceWalker extends RefWalker<Integer, Integer> {
             for ( String requestedTypeString : TYPES ) {
                 String[] requestedPieces = requestedTypeString.split(":");
                 String requestedType = requestedPieces[0];
-                ConcordanceType type = concordanceTypes.get(requestedType);
-                if ( type == null )
-                    throw new StingException("The requested concordance type (" + requestedType + ") isn't a valid option");
 
-                HashMap<String,String> requestedArgs = new HashMap<String,String>();
+                boolean foundClass = false;
-                if ( requestedPieces.length == 2 ) {
+                for ( Class type : classes ) {
-                    String[] argStrings = requestedPieces[1].split(",");
+
-                    for (int i = 0; i < argStrings.length; i++ ) {
+                    if (requestedType.equalsIgnoreCase(type.getSimpleName())) {
-                        String[] arg = argStrings[i].split("=");
+                        foundClass = true;
-                        if ( arg.length == 2 )
+                        try {
-                            requestedArgs.put(arg[0], arg[1]);
+                            ConcordanceType concordance = (ConcordanceType)type.newInstance();
+                            HashMap<String,String> requestedArgs = new HashMap<String,String>();
+                            if ( requestedPieces.length == 2 ) {
+                                String[] argStrings = requestedPieces[1].split(",");
+                                for (int i = 0; i < argStrings.length; i++ ) {
+                                    String[] arg = argStrings[i].split("=");
+                                    if ( arg.length == 2 )
+                                        requestedArgs.put(arg[0], arg[1]);
+                                }
+                            }
+
+                            concordance.initialize(OUTPUT_PATH, requestedArgs);
+                            requestedTypes.add(concordance);
+                            break;
+                        } catch (InstantiationException e) {
+                            throw new StingException(String.format("Cannot instantiate concordance class '%s': must be concrete class", type.getSimpleName()));
+                        } catch (IllegalAccessException e) {
+                            throw new StingException(String.format("Cannot instantiate concordance class '%s': must have no-arg constructor", type.getSimpleName()));
+                        }
                     }
                 }
 
-                type.initialize(requestedArgs);
+                if ( !foundClass )
-                requestedTypes.add(type);
+                    throw new StingException("The requested concordance type (" + requestedType + ") isn't a valid concordance option");
             }
         }
      }

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/ConcordanceType.java

@@ -7,7 +7,7 @@ import java.util.HashMap;
 
 public interface ConcordanceType {
 
-    public void initialize(HashMap<String,String> args);
+    public void initialize(String prefix, HashMap<String,String> args);
     public void computeConcordance(RefMetaDataTracker tracker, ReferenceContext ref);
     public void cleanup();
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/IndelSubsets.java

@@ -23,13 +23,10 @@ public class IndelSubsets implements ConcordanceType {
     private int sizeCutoff = 2;
 
     private PrintWriter[][][][] writers = new PrintWriter[2][2][2][2];
-    private String prefix;
 
-    public IndelSubsets(String prefix) {
+    public IndelSubsets() {}
-        this.prefix = prefix;
-    }
 
-    public void initialize(HashMap<String,String> args) {        
+    public void initialize(String prefix, HashMap<String,String> args) {        
         if ( args.get("sizeCutoff") != null )
             sizeCutoff = Integer.valueOf(args.get("sizeCutoff"));
         if ( args.get("homopolymerCutoff") != null )

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java

@@ -28,13 +28,10 @@ public class SNPGenotypeConcordance implements ConcordanceType {
     private PrintWriter comboVarWriter = null;
     private PrintWriter coverageVar1Writer = null;
     private PrintWriter coverageVar2Writer = null;
-    private String prefix;
 
-    public SNPGenotypeConcordance(String prefix) {
+    public SNPGenotypeConcordance() {}
-        this.prefix = prefix;
-    }
 
-    public void initialize(HashMap<String,String> args) {
+    public void initialize(String prefix, HashMap<String,String> args) {
         try {
             sameVarWriter = new PrintWriter(prefix + ".snp_concordance.sameConfidentVariant.calls");
             oneVarWriter = new PrintWriter(prefix + ".snp_concordance.bothVariantOnlyOneIsConfident.calls");

java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java

@@ -21,13 +21,10 @@ public class SimpleVenn implements ConcordanceType {
     private PrintWriter discord_writer = null;
     private PrintWriter set1_writer = null;
     private PrintWriter set2_writer = null;
-    private String prefix;
 
-    public SimpleVenn(String prefix) {
+    public SimpleVenn() {}
-        this.prefix = prefix;
-    }
 
-    public void initialize(HashMap<String,String> args) {
+    public void initialize(String prefix, HashMap<String,String> args) {
         try {
             union_writer = new PrintWriter(prefix + ".venn.union.calls");
             intersect_writer = new PrintWriter(prefix + ".venn.intersection.calls");