Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@201 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/BasicLociWalker.java

@@ -1,45 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers;
-
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: mdepristo
- * Date: Feb 22, 2009
- * Time: 3:22:14 PM
- * To change this template use File | Settings | File Templates.
- */
-public abstract class BasicLociWalker<MapType, ReduceType> implements LocusWalker<MapType, ReduceType> {
-    public String getName() {
-        // Return name of class, trimming 'Walker' from the end if present.
-        // TODO: Duplicate of BasicReadWalker.getName().  Eliminate duplication.
-        String className = getClass().getSimpleName();
-        if(className.endsWith(Walker.class.getSimpleName()))
-            return className.substring(0,className.lastIndexOf(Walker.class.getSimpleName()));
-        else
-            return className;
-    }
-
-    public void initialize() {
-        ;
-    }
-
-    // Do we actually want to operate on the context?
-    public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
-        return true;    // We are keeping all the reads
-    }
-
-    public void onTraversalDone() {
-        ;
-    }
-
-    // These three capabilities must be overidden
-    public abstract MapType map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
-    public abstract ReduceType reduceInit();
-    public abstract ReduceType reduce(MapType value, ReduceType sum);
-
-}

java/src/org/broadinstitute/sting/gatk/walkers/BasicReadWalker.java

@@ -1,41 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers;
-
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-
-/**
- * Created by IntelliJ IDEA.
- * User: mdepristo
- * Date: Feb 22, 2009
- * Time: 2:52:28 PM
- * To change this template use File | Settings | File Templates.
- */
-public abstract class BasicReadWalker<MapType, ReduceType> implements ReadWalker<MapType, ReduceType> {
-    public String getName() {
-        // Return name of class, trimming 'Walker' from the end if present.
-        // TODO: Duplicate of BasicLociWalker.getName().  Eliminate duplication.
-        String className = getClass().getSimpleName();
-        if(className.endsWith(Walker.class.getSimpleName()))
-            return className.substring(0,className.lastIndexOf(Walker.class.getSimpleName()));
-        else
-            return className;
-    }
-
-    public void initialize() { }
-    public boolean requiresOrderedReads() { return false; }
-
-    public boolean filter(LocusContext context, SAMRecord read) {
-        // We are keeping all the reads
-        return true;
-    }
-
-    public void onTraversalDone() {
-        ;
-    }
-
-    // Three basic abstract function that *must* be overridden
-    public abstract MapType map(LocusContext context, SAMRecord read);
-    public abstract ReduceType reduceInit();
-    public abstract ReduceType reduce(MapType value, ReduceType sum);
-}

java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java

@@ -12,7 +12,7 @@ import java.util.List;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class CountLociWalker extends BasicLociWalker<Integer, Integer> {
+public class CountLociWalker extends LocusWalker<Integer, Integer> {
     public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
         return 1;
     }

java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java

@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
 
-public class CountReadsWalker extends BasicReadWalker<Integer, Integer> {
+public class CountReadsWalker extends ReadWalker<Integer, Integer> {
     public Integer map(LocusContext context, SAMRecord read) {
         return 1;
     }

java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java

@@ -12,7 +12,7 @@ import java.util.List;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class DepthOfCoverageWalker extends BasicLociWalker<Integer, Integer> {
+public class DepthOfCoverageWalker extends LocusWalker<Integer, Integer> {
     public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
         System.out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
         return 1;

java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java

@@ -12,14 +12,16 @@ import java.util.List;
  * Time: 2:52:28 PM
  * To change this template use File | Settings | File Templates.
  */
-public interface LocusWalker<MapType, ReduceType> extends Walker {
+public abstract class LocusWalker<MapType, ReduceType> extends Walker {
     // Do we actually want to operate on the context?
-    boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
+    public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+        return true;    // We are keeping all the reads
+    }
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
-    MapType map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
+    public abstract MapType map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context);
 
     // Given result of map function
-    ReduceType reduceInit();
+    public abstract ReduceType reduceInit();
-    ReduceType reduce(MapType value, ReduceType sum);
+    public abstract ReduceType reduce(MapType value, ReduceType sum);
 }

java/src/org/broadinstitute/sting/gatk/walkers/NullWalker.java

@@ -9,11 +9,7 @@ import java.util.List;
 // Null traversal. For ATK performance measuring.
 // j.maguire 3-7-2009
 
-public class NullWalker implements LocusWalker<Integer, Integer> {
+public class NullWalker extends LocusWalker<Integer, Integer> {
-    public String getName() {
-        return "Null";
-    }
-
     public void initialize() {
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java

@@ -14,7 +14,7 @@ import java.util.List;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class PileupWalker extends BasicLociWalker<Integer, Integer> {
+public class PileupWalker extends LocusWalker<Integer, Integer> {
     public void initialize() {
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java

@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
 
-public class PrintReadsWalker extends BasicReadWalker<Integer, Integer> {
+public class PrintReadsWalker extends ReadWalker<Integer, Integer> {
     public Integer map(LocusContext context, SAMRecord read) {
         System.out.println(read.format());
         return 1;

java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java

@@ -10,16 +10,19 @@ import org.broadinstitute.sting.gatk.LocusContext;
  * Time: 2:52:28 PM
  * To change this template use File | Settings | File Templates.
  */
-public interface ReadWalker<MapType, ReduceType> extends Walker {
+public abstract class ReadWalker<MapType, ReduceType> extends Walker {
-    boolean requiresOrderedReads();
+    public boolean requiresOrderedReads() { return false; }
     
     // Do we actually want to operate on the context?
-    boolean filter(LocusContext context, SAMRecord read);
+    public boolean filter(LocusContext context, SAMRecord read) {
+        // We are keeping all the reads
+        return true;
+    }
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
-    MapType map(LocusContext context, SAMRecord read);
+    public abstract MapType map(LocusContext context, SAMRecord read);
 
     // Given result of map function
-    ReduceType reduceInit();
+    public abstract ReduceType reduceInit();
-    ReduceType reduce(MapType value, ReduceType sum);
+    public abstract ReduceType reduce(MapType value, ReduceType sum);
 }

java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -7,9 +7,17 @@ package org.broadinstitute.sting.gatk.walkers;
  * Time: 1:53:31 PM
  * To change this template use File | Settings | File Templates.
  */
-public interface Walker {
+public abstract class Walker {
     // TODO: Can a walker be templatized so that map and reduce live here?
-    String getName();
+    public String getName() {
-    void initialize();
+        // Return name of class, trimming 'Walker' from the end if present.
-    void onTraversalDone();
+        String className = getClass().getSimpleName();
+        if(className.endsWith(Walker.class.getSimpleName()))
+            return className.substring(0,className.lastIndexOf(Walker.class.getSimpleName()));
+        else
+            return className;
+    }
+
+    public void initialize() { }
+    public void onTraversalDone() { }
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**
@@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class AlignedReadsHistoWalker extends BasicReadWalker<Integer, Integer> {
+public class AlignedReadsHistoWalker extends ReadWalker<Integer, Integer> {
     long[] alignCounts = new long[51];
 
     public String getName() {

java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java

@@ -3,7 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.refdata.rodGFF;
-import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
 import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
@@ -18,7 +18,7 @@ import java.util.List;
  * To change this template use File | Settings | File Templates.
  */
 
-public class AlleleFrequencyMetricsWalker extends BasicLociWalker<AlleleFrequencyEstimate, String> 
+public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEstimate, String> 
 {
 
     long dbsnp_hits=0;

java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java

@@ -3,14 +3,14 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 import java.util.Arrays;
 
-public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstimate, Integer> {
+public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, Integer> {
 
     int N=2;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -10,7 +10,7 @@ import java.util.Iterator;
 import java.util.List;
 import static java.lang.reflect.Array.*;
 
-public class BaseQualityDumpWalker extends BasicReadWalker<Integer, Integer> {
+public class BaseQualityDumpWalker extends ReadWalker<Integer, Integer> {
 
     protected final int MIN_TARGET_EDIT_DISTANCE = 0; //5;
     protected final int MAX_TARGET_EDIT_DISTANCE = 4; //10;

java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**
@@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class BaseQualityHistoWalker extends BasicReadWalker<Integer, Integer> {
+public class BaseQualityHistoWalker extends ReadWalker<Integer, Integer> {
     long[] qualCounts = new long[100];
 
     public String getName() {

java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -10,7 +10,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
-public class MismatchCounterWalker extends BasicReadWalker<Integer, Integer> {
+public class MismatchCounterWalker extends ReadWalker<Integer, Integer> {
     public String getName() {
         return "CountMismatches";
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -10,7 +10,7 @@ import java.util.Iterator;
 import java.util.List;
 import static java.lang.reflect.Array.*;
 
-public class MismatchHistoWalker extends BasicReadWalker<Integer, Integer> {
+public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
 
     protected long[] mismatchCounts = new long[0];
     protected final int MIN_TARGET_EDIT_DISTANCE = 5;

java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java

@@ -3,7 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
 
@@ -12,7 +12,7 @@ import java.util.List;
 // Draft single sample genotyper
 // j.maguire 3-7-2009
 
-public class SingleSampleGenotyper extends BasicLociWalker<Integer, Integer> {
+public class SingleSampleGenotyper extends LocusWalker<Integer, Integer> {
     public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
     }

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

@@ -134,7 +134,6 @@ public class ArgumentParser {
      */
     private void AddToOptionStorage( List<Pair<Option,Pair<Object,Field>>> options ) {
         OptionGroup optionGroup = new OptionGroup();
-        boolean isRequired = true;
 
         for( Pair<Option,Pair<Object,Field>> option: options ) {
             if (m_options.hasOption(option.first.getOpt()) )
@@ -142,10 +141,9 @@ public class ArgumentParser {
 
             optionGroup.addOption(option.first);
             m_storageLocations.put( option.first.getLongOpt(), option.second );
-            isRequired &= option.first.isRequired();
+            optionGroup.setRequired( optionGroup.isRequired() & option.first.isRequired() );
         }
 
-        optionGroup.setRequired(isRequired);
         m_options.addOptionGroup(optionGroup);
     }