Cleaned up some duplicate code in preparation for making plugin dir configurable.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1270 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1,7 +1,8 @@
 package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
+import org.broadinstitute.sting.utils.cmdLine.ArgumentFactory;
+import org.broadinstitute.sting.utils.cmdLine.ArgumentCollection;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -11,6 +12,8 @@ import java.io.FileNotFoundException;
 import java.util.List;
 import java.util.ArrayList;
 
+import net.sf.samtools.SAMFileReader;
+
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -44,20 +47,16 @@ import java.util.ArrayList;
  */
 public abstract class CommandLineExecutable extends CommandLineProgram {
 
-    // our argument collection, the collection of command line args we accept
-    protected GATKArgumentCollection argCollection = new GATKArgumentCollection();
-
-    /** the type of analysis to run - switch to the type of analysis */
-    private String analysisName = "SomaticCoverageWalker";
-
     // our genome analysis engine
     private GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
 
     // get the analysis name
     protected abstract String getAnalysisName();
 
+    protected abstract GATKArgumentCollection getArgumentCollection();
+
     // override select arguments
-    protected abstract void overrideArguments();
+    protected void overrideArguments() { }
 
     /**
      * this is the function that the inheriting class can expect to have called
@@ -66,18 +65,20 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @return the return code to exit the program with
      */
     protected int execute() {
-        Walker<?,?> mWalker = GATKEngine.getWalkerByName(analysisName);
+        Walker<?,?> mWalker = GATKEngine.getWalkerByName(getAnalysisName());
+
+        GATKArgumentCollection arguments = getArgumentCollection();
 
         // load the arguments into the walkers
-        loadArgumentsIntoObject(argCollection);
+        loadArgumentsIntoObject(arguments);
         loadArgumentsIntoObject(mWalker);
 
         // process any arguments that need a second pass
-        processArguments(argCollection);
+        processArguments(arguments);
 
         // set the analysis name in the argument collection
-        this.argCollection.analysisName = this.analysisName;
+        arguments.analysisName = getAnalysisName();
-        GATKEngine.execute(argCollection, mWalker);
+        GATKEngine.execute(arguments, mWalker);
 
         return 0;
     }
@@ -93,17 +94,20 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
     }
 
     /**
-     * GATK provides the walker as an argument source.  As a side-effect, initializes the walker variable.
+     * GATK provides the walker as an argument source.
-     *
      * @return List of walkers to load dynamically.
      */
     @Override
     protected Class[] getArgumentSources() {
         // No walker info?  No plugins.
-        if (analysisName == null) return new Class[] {};
+        if (getAnalysisName() == null) return new Class[] {};
-        return new Class[] { GATKEngine.getWalkerByName(analysisName).getClass() };
+        return new Class[] { GATKEngine.getWalkerByName(getAnalysisName()).getClass() };
     }
 
+    @Override
+    protected String getArgumentSourceName( Class argumentSource ) {
+        return WalkerManager.getWalkerName((Class<Walker>) argumentSource);
+    }    
 
     /**
      * Preprocess the arguments before submitting them to the GATK engine.
@@ -111,7 +115,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      * @param argCollection Collection of arguments to preprocess.
      */
     private void processArguments( GATKArgumentCollection argCollection ) {
-        argCollection.samFiles = unpackReads(argCollection.samFiles);
+        argCollection.samFiles = unpackReads( argCollection.samFiles );
     }
 
     /**
@@ -124,33 +128,37 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      */
     private List<File> unpackReads( List<File> inputFiles ) {
         List<File> unpackedReads = new ArrayList<File>();
-        for (File inputFile : inputFiles) {
+        for( File inputFile: inputFiles ) {
-            if (inputFile.getName().endsWith(".list")) {
+            if (inputFile.getName().endsWith(".list") ) {
                 try {
-                    for (String fileName : new xReadLines(inputFile))
+                    for( String fileName : new xReadLines(inputFile) )
-                        unpackedReads.add(new File(fileName));
+                        unpackedReads.add( new File(fileName) );
                 }
-                catch (FileNotFoundException ex) {
+                catch( FileNotFoundException ex ) {
                     throw new StingException("Unable to find file while unpacking reads", ex);
                 }
-            } else
+            }
-                unpackedReads.add(inputFile);
+            else
+                unpackedReads.add( inputFile );
         }
         return unpackedReads;
     }
 
+    /**
+     * Get a custom factory for instantiating specialty GATK arguments.
+     * @return An instance of the command-line argument of the specified type.
+     */
     @Override
-    protected String getArgumentSourceName( Class argumentSource ) {
+    protected ArgumentFactory getCustomArgumentFactory() {
-        return WalkerManager.getWalkerName((Class<Walker>) argumentSource);
+        return new ArgumentFactory() {
+            public Object createArgument( Class type, List<String> repr ) {
+                if (type == SAMFileReader.class && repr.size() == 1) {
+                    SAMFileReader samFileReader = new SAMFileReader(new File(repr.get(0)),true);
+                    samFileReader.setValidationStringency(getArgumentCollection().strictnessLevel);
+                    return samFileReader;
+                }
+                return null;
+            }
+        };
     }
-
-    public GATKArgumentCollection getArgCollection() {
-        return argCollection;
-    }
-
-    public void setArgCollection( GATKArgumentCollection argCollection ) {
-        this.argCollection = argCollection;
-    }
-
-
 }

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

@@ -1,12 +1,7 @@
 package org.broadinstitute.sting.gatk;
 
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.utils.cmdLine.*;
 
-import java.io.FileNotFoundException;
-import java.io.File;
 import java.util.List;
 import java.util.ArrayList;
 
@@ -40,49 +35,18 @@ import net.sf.samtools.SAMFileReader;
  * gatk all the parsed out information.  Pretty much anything dealing with the underlying system should go here,
  * the gatk engine should  deal with any data related information.
  */
-public class CommandLineGATK extends CommandLineProgram {
+public class CommandLineGATK extends CommandLineExecutable {
 
     @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
     public String analysisName = null;
 
-    @ArgumentCollection // our argument collection, the collection of command line args we accept
+    // our argument collection, the collection of command line args we accept
-    public GATKArgumentCollection argCollection = new GATKArgumentCollection();
+    @ArgumentCollection
-
+    protected GATKArgumentCollection argCollection = new GATKArgumentCollection();    
-    /** our genome analysis engine */
-    GenomeAnalysisEngine GATKEngine = new GenomeAnalysisEngine();
-
-    /** Required main method implementation. */
-    public static void main(String[] argv) {
-        try {
-            CommandLineGATK instance = new CommandLineGATK();
-            start(instance, argv);
-        } catch (Exception e) {
-            exitSystemWithError(e);
-        }
-    }
-
-    /**
-     * this is the function that the inheriting class can expect to have called
-     * when the command line system has initialized.
-     *
-     * @return the return code to exit the program with
-     */
-    protected int execute() {
-        Walker<?,?> mWalker = GATKEngine.getWalkerByName(analysisName);
-
-        loadArgumentsIntoObject(argCollection);
-        loadArgumentsIntoObject(mWalker);
-
-        processArguments(argCollection);
-
-        this.argCollection.analysisName = this.analysisName;
-        GATKEngine.execute(argCollection, mWalker);
-        return 0;
-    }
 
     /**
      * Get pleasing info about the GATK.
-     * @return
+     * @return A list of Strings that contain pleasant info about the GATK.
      */
     @Override
     protected List<String> getApplicationHeader() {
@@ -95,90 +59,23 @@ public class CommandLineGATK extends CommandLineProgram {
         return header;
     }
 
-    /**
-     * GATK can add arguments dynamically based on analysis type.
-     *
-     * @return true
-     */
     @Override
-    protected boolean canAddArgumentsDynamically() {
+    protected String getAnalysisName() {
-        return true;
+        return analysisName;
-    }
-
-    /**
-     * GATK provides the walker as an argument source.  As a side-effect, initializes the walker variable.
-     *
-     * @return List of walkers to load dynamically.
-     */
-    @Override
-    protected Class[] getArgumentSources() {
-        // No walker info?  No plugins.
-        if (analysisName == null) return new Class[] {};
-        return new Class[] { GATKEngine.getWalkerByName(analysisName).getClass() };
     }
 
     @Override
-    protected String getArgumentSourceName(Class argumentSource) {
+    protected GATKArgumentCollection getArgumentCollection() {
-        return WalkerManager.getWalkerName((Class<Walker>) argumentSource);
-    }
-
-    public GATKArgumentCollection getArgCollection() {
         return argCollection;
     }
 
-    public void setArgCollection(GATKArgumentCollection argCollection) {
+    /** Required main method implementation. */
-        this.argCollection = argCollection;
+    public static void main(String[] argv) {
-    }
+        try {
-
+            CommandLineGATK instance = new CommandLineGATK();
-    /**
+            start(instance, argv);
-     * Get a custom factory for instantiating specialty GATK arguments.
+        } catch (Exception e) {
-     * @return An instance of the command-line argument of the specified type.
+            exitSystemWithError(e);
-     */
-    @Override
-    protected ArgumentFactory getCustomArgumentFactory() {
-        return new ArgumentFactory() {
-            public Object createArgument( Class type, List<String> repr ) {
-                if (type == SAMFileReader.class && repr.size() == 1) {
-                    SAMFileReader samFileReader = new SAMFileReader(new File(repr.get(0)),true);
-                    samFileReader.setValidationStringency(argCollection.strictnessLevel);
-                    return samFileReader;
-                }
-                return null;
-            }
-        };
-    }
-
-    /**
-     * Preprocess the arguments before submitting them to the GATK engine.
-     * @param argCollection Collection of arguments to preprocess.
-     */
-    private void processArguments( GATKArgumentCollection argCollection ) {
-        argCollection.samFiles = unpackReads( argCollection.samFiles );    
-    }
-
-    /**
-     * Unpack the files to be processed, given a list of files.  That list of files can
-     * itself contain lists of other files to be read.
-     * @param inputFiles
-     * @return
-     */
-    private List<File> unpackReads( List<File> inputFiles ) {
-        List<File> unpackedReads = new ArrayList<File>();
-        for( File inputFile: inputFiles ) {
-            if( inputFile.getName().endsWith(".list") ) {
-                try {
-                    for( String fileName : new xReadLines(inputFile) )
-                        unpackedReads.add( new File(fileName) );
-                }
-                catch( FileNotFoundException ex ) {
-                    throw new StingException("Unable to find file while unpacking reads", ex);
-                }
-            }
-            else
-                unpackedReads.add( inputFile );
         }
-        return unpackedReads;
     }
-
-
 }

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

@@ -90,6 +90,8 @@ public class WalkerManager {
     public Walker createWalkerByName(String walkerName)
             throws InstantiationException, IllegalAccessException {
         Class<? extends Walker> walker = walkersByName.get(walkerName);
+        if( walker == null )
+            throw new StingException(String.format("Could not find walker with name: %s", walkerName));
         return walker.newInstance();
     }
 

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

@@ -47,7 +47,6 @@ public class SomaticCoverageTool extends CommandLineExecutable {
     @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>();
 
-
     /** Required main method implementation. */
     public static void main( String[] argv ) {
         try {
@@ -69,8 +68,9 @@ public class SomaticCoverageTool extends CommandLineExecutable {
     }
 
     /** override any arguments we see fit. */
-    protected void overrideArguments() {
+    protected GATKArgumentCollection getArgumentCollection() {
-        this.argCollection = GATKArgumentCollection.unmarshal(getClass().getClassLoader().getResourceAsStream("SomaticCoverage.xml"));
+        GATKArgumentCollection argCollection = GATKArgumentCollection.unmarshal(getClass().getClassLoader().getResourceAsStream("SomaticCoverage.xml"));
-        this.argCollection.samFiles = samFiles;
+        argCollection.samFiles = samFiles;
+        return argCollection;
     }
 }