Farewell, functionalj. You promised much, but you could not deliver.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@847 348d0f76-0448-11de-a6fe-93d51630548a

ivy.xml

@@ -1,7 +1,6 @@
 <ivy-module version="1.0">
   <info organisation="org.broadinstitute" module="Sting"/>
   <dependencies>
-    <dependency org="net.sf" name="functionalj" rev="latest.integration" />
     <dependency org="net.sf" name="sam" rev="latest.integration" />
     <dependency org="edu.mit.broad" name="picard" rev="latest.integration" />
     <dependency org="junit" name="junit" rev="4.4" />

java/src/org/broadinstitute/sting/gatk/WalkerManager.java

@@ -1,10 +1,5 @@
 package org.broadinstitute.sting.gatk;
 
-import net.sf.functionalj.reflect.StdReflect;
-import net.sf.functionalj.reflect.JdkStdReflect;
-import net.sf.functionalj.FunctionN;
-import net.sf.functionalj.Functions;
-
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -41,7 +36,7 @@ public class WalkerManager {
      */
     private static Logger logger = Logger.getLogger(WalkerManager.class);
 
-    private Map<String, Class> walkers;
+    private Map<String, Class<? extends Walker>> walkersByName;
 
     public WalkerManager(String pluginDirectory) {
         try {
@@ -67,12 +62,12 @@ public class WalkerManager {
                 }
             }
 
-            walkerCandidates = filterWalkers(walkerCandidates);
+            List<Class<? extends Walker>> walkers = filterWalkers(walkerCandidates);
 
             if (walkerCandidates.isEmpty())
                 throw new RuntimeException("No walkers were found.");
 
-            walkers = createWalkerDatabase(walkerCandidates);
+            walkersByName = createWalkerDatabase(walkers);
         }
         // IOExceptions here are suspect; they indicate that the WalkerManager can't open its containing jar.
         // Wrap in a RuntimeException.
@@ -88,7 +83,7 @@ public class WalkerManager {
      * @return True if the walker exists, false otherwise.
      */
     public boolean doesWalkerExist(String walkerName) {
-        return walkers.containsKey(walkerName);
+        return walkersByName.containsKey(walkerName);
     }
 
     /**
@@ -99,8 +94,8 @@ public class WalkerManager {
      */
     public Walker createWalkerByName(String walkerName)
             throws InstantiationException, IllegalAccessException {
-        Class walker = walkers.get(walkerName);
+        Class<? extends Walker> walker = walkersByName.get(walkerName);
-        return (Walker) walker.newInstance();
+        return walker.newInstance();
     }
 
     /**
@@ -109,7 +104,7 @@ public class WalkerManager {
      * @return Class representing the walker.
      */
     public Class getWalkerClassByName(String walkerName) {
-        return walkers.get(walkerName);
+        return walkersByName.get(walkerName);
     }
 
     /**
@@ -213,10 +208,13 @@ public class WalkerManager {
      * @param classes Arbitrary list of classes.
      * @return List of classes extending from Walker.
      */
-    private List<Class> filterWalkers(List<Class> classes) {
+    private List<Class<? extends Walker>> filterWalkers(List<Class> classes) {
-        StdReflect reflect = new JdkStdReflect();
+        List<Class<? extends Walker>> walkerClasses = new ArrayList<Class<? extends Walker>>();
-        FunctionN<Boolean> filterFunc = reflect.instanceFunction(new JVMUtils.ClassFilter(Walker.class), "filter", Class.class);
+        for( Class clazz: classes ) {
-        return Functions.findAll(filterFunc.f1(), classes);
+            if( JVMUtils.isConcreteImplementationOf(clazz,Walker.class) )
+                walkerClasses.add( (Class<? extends Walker>)clazz );
+        }
+        return walkerClasses;
     }
 
     /**
@@ -225,10 +223,10 @@ public class WalkerManager {
      * @param walkerClasses Classes to instantiate.
      * @return map of walker name to walker.
      */
-    private Map<String, Class> createWalkerDatabase(List<Class> walkerClasses) {
+    private Map<String, Class<? extends Walker>> createWalkerDatabase(List<Class<? extends Walker>> walkerClasses) {
-        Map<String, Class> walkers = new HashMap<String, Class>();
+        Map<String, Class<? extends Walker>> walkers = new HashMap<String, Class<? extends Walker>>();
 
-        for (Class<Walker> walkerClass : walkerClasses) {
+        for (Class<? extends Walker> walkerClass : walkerClasses) {
             String walkerName = getWalkerName(walkerClass);
             logger.info(String.format("* Adding module %s", walkerName));
             walkers.put(walkerName, walkerClass);

java/src/org/broadinstitute/sting/utils/GenomeLoc.java

@@ -3,12 +3,6 @@ package org.broadinstitute.sting.utils;
 import edu.mit.broad.picard.directed.IntervalList;
 import edu.mit.broad.picard.reference.ReferenceSequenceFile;
 import edu.mit.broad.picard.util.Interval;
-import net.sf.functionalj.Function1;
-import net.sf.functionalj.FunctionN;
-import net.sf.functionalj.Functions;
-import net.sf.functionalj.reflect.JdkStdReflect;
-import net.sf.functionalj.reflect.StdReflect;
-import net.sf.functionalj.util.Operators;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
@@ -203,23 +197,21 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
      * @param str String representation of genome locs.  Null string corresponds to no filter.
      * @return Array of GenomeLoc objects corresponding to the locations in the string, sorted by coordinate order
      */
-    public static ArrayList<GenomeLoc> parseGenomeLocs(final String str) {
+    public static List<GenomeLoc> parseGenomeLocs(final String str) {
         // Null string means no filter.
         if( str == null ) return null;
 
         // Of the form: loc1;loc2;...
         // Where each locN can be:
         // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
-        StdReflect reflect = new JdkStdReflect();
-        FunctionN<GenomeLoc> parseOne = reflect.staticFunction(GenomeLoc.class, "parseGenomeLoc", String.class);
-        Function1<GenomeLoc, String> f1 = parseOne.f1();
         try {
-            Collection<GenomeLoc> result = Functions.map(f1, Arrays.asList(str.split(";")));
+            List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
-            ArrayList<GenomeLoc> locs = new ArrayList(result);
+            for( String loc: str.split(";") )
+                locs.add( parseGenomeLoc(loc.trim()) );
             Collections.sort(locs);
             //logger.info(String.format("Going to process %d locations", locs.length));
             locs = mergeOverlappingLocations(locs);
-            logger.info("Locations are:" + Utils.join(", ", Functions.map(Operators.toString, locs)));
+            logger.info("Locations are:" + Utils.join(", ", locs));
             return locs;
         } catch (Exception e) {
             e.printStackTrace();
@@ -228,8 +220,8 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
         }
     }
 
-    public static ArrayList<GenomeLoc> mergeOverlappingLocations(final ArrayList<GenomeLoc> raw) {
+    public static List<GenomeLoc> mergeOverlappingLocations(final List<GenomeLoc> raw) {
-        logger.debug("  Raw locations are:\n" + Utils.join("\n", Functions.map(Operators.toString, raw)));        
+        logger.debug("  Raw locations are:\n" + Utils.join("\n", raw));        
         if ( raw.size() <= 1 )
             return raw;
         else {
@@ -561,11 +553,11 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
      *
      * @param file_name
      */
-    public static ArrayList<GenomeLoc> IntervalFileToList(final String file_name) {
+    public static List<GenomeLoc> IntervalFileToList(final String file_name) {
 // first try to read it as an interval file since that's well structured
         // we'll fail quickly if it's not a valid file.  Then try to parse it as
         // a location string file
-        ArrayList<GenomeLoc> ret = null;
+        List<GenomeLoc> ret = null;
         try {
             IntervalList il = IntervalList.fromFile(new File(file_name));
 

java/src/org/broadinstitute/sting/utils/JVMUtils.java

@@ -101,20 +101,15 @@ public class JVMUtils {
     }
 
     /**
-     * A functor returning true for classes which extend from baseClass.
+     * Is the specified class a concrete implementation of baseClass?
+     * @param clazz Class to check.
+     * @param baseClass Base class to check against.
+     * @return True if clazz implements baseClass and is not abstract / an interface.  False otherwise.
      */
-    public static class ClassFilter {
+    public static boolean isConcreteImplementationOf( Class clazz, Class baseClass ) {
-        private Class baseClass;
+        return baseClass.isAssignableFrom(clazz) &&
-
+                !Modifier.isAbstract(clazz.getModifiers()) &&
-        public ClassFilter(Class baseClass) {
+                !Modifier.isInterface(clazz.getModifiers());
-            this.baseClass = baseClass;
-        }
-
-        public Boolean filter(Class clazz) {
-            return baseClass.isAssignableFrom(clazz) &&
-                    !Modifier.isAbstract(clazz.getModifiers()) &&
-                    !Modifier.isInterface(clazz.getModifiers());
-        }
     }
 
     /**

settings/repository/net.sf/functionalj-1.0.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="functionalj" revision="1.0" status="release" />
-</ivy-module>