Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1287 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -2,8 +2,6 @@ package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentFactory;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -47,10 +45,9 @@ import net.sf.samtools.SAMFileReader;
 public abstract class CommandLineExecutable extends CommandLineProgram {
 
     /**
-     * Get an instance of the GATK engine.
+     * The actual engine which performs the analysis.
-     * @return The GATK engine that will power the requested traversal.
      */
-    protected abstract GenomeAnalysisEngine getGATKEngine();
+    protected GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
 
     // get the analysis name
     protected abstract String getAnalysisName();
@@ -71,7 +68,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @return the return code to exit the program with
      */
     protected int execute() {
-        GenomeAnalysisEngine GATKEngine = getGATKEngine();
         GATKArgumentCollection arguments = getArgumentCollection();
 
         Walker<?,?> mWalker = GATKEngine.getWalkerByName(getAnalysisName());
@@ -108,7 +104,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
     protected Class[] getArgumentSources() {
         // No walker info?  No plugins.
         if (getAnalysisName() == null) return new Class[] {};
-        return new Class[] { getGATKEngine().getWalkerByName(getAnalysisName()).getClass() };
+        return new Class[] { GATKEngine.getWalkerByName(getAnalysisName()).getClass() };
     }
 
     @Override

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

@@ -5,8 +5,6 @@ import org.broadinstitute.sting.utils.cmdLine.*;
 import java.util.List;
 import java.util.ArrayList;
 
-import net.sf.samtools.SAMFileReader;
-
 /**
  *
  * User: aaron
@@ -61,19 +59,6 @@ public class CommandLineGATK extends CommandLineExecutable {
         return header;
     }
 
-    /**
-     * Lazy load the GATK engine.  This current CANNOT happen until after the command-line arguments are populated.
-     * TODO: Make this chain of events more explicit.  Perhaps an abstract initialize method after clp arguments are parsed?
-     * @return The GATK engine that will power the requested traversal.
-     */
-    @Override
-    protected GenomeAnalysisEngine getGATKEngine() {
-        if( GATKEngine == null )
-            GATKEngine = new GenomeAnalysisEngine();
-        return GATKEngine;
-    }
-
-
     @Override
     protected String getAnalysisName() {
         return analysisName;

java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverageTool.java

@@ -2,11 +2,9 @@ package org.broadinstitute.sting.playground.somaticcoverage;
 
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.GATKArgumentCollection;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.io.File;
-import java.io.IOException;
 import java.util.List;
 import java.util.ArrayList;
 
@@ -43,9 +41,6 @@ import java.util.ArrayList;
  * a executable command line for the Somatic Coverage Walker.
  */
 public class SomaticCoverageTool extends CommandLineExecutable {    
-    // our genome analysis engine
-    private GenomeAnalysisEngine GATKEngine = null;
-
     // the two sam/bam files, one for cancer, one for normal
     @Argument(fullName = "bam_file", shortName = "I", doc = "The bam files, one for the tumor one for the normal", required = true)
     public List<File> samFiles = new ArrayList<File>();
@@ -60,14 +55,6 @@ public class SomaticCoverageTool extends CommandLineExecutable {
         }
     }
 
-    @Override
-    protected GenomeAnalysisEngine getGATKEngine() {
-        if( GATKEngine == null )
-            GATKEngine = new GenomeAnalysisEngine();
-        return GATKEngine;
-    }
-
-
     /**
      * a required method, returns the analysis name.  This is usually the walker
      * name with 'Walker' stripped off.