IntelliJ no longer complains that my methods are too complex to analyze.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2708 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java

@@ -8,8 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
-import java.io.IOException;
-
 /*
  * Copyright (c) 2010 The Broad Institute
  *

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
+import java.io.IOException;
 import java.io.PrintStream;
 import java.io.FileNotFoundException;
 
@@ -47,7 +48,7 @@ public class AnnotationDataManager {
         data = new HashMap<String, TreeSet<AnnotationDatum>>();
     }
 
-    public void addAnnotations( RodVCF variant, String sampleName ) {
+    public void addAnnotations( final RodVCF variant, final String sampleName ) {
 
         if( sampleName != null ) { // Only process variants that are found in the sample with this sampleName
             if( variant.getGenotype(sampleName).isNoCall() ) { // This variant isn't found in this sample so break out
@@ -60,14 +61,10 @@ public class AnnotationDataManager {
         for( String annotationKey : infoField.keySet() ) {
 
             float value = 0.0f;
-            boolean skipThisAnnotation = false;
             try {
                 value = Float.parseFloat( infoField.get( annotationKey ) );
             } catch( NumberFormatException e ) {
-                skipThisAnnotation = true; // Skip over annotations that aren't floats, like older versions of "AC" and "DB"
+                continue; // Skip over annotations that aren't floats, like "DB"
-            }
-            if( skipThisAnnotation ) {
-                continue; // Skip over annotations that aren't floats, like older versions of "AC" and "DB"
             }
 
             TreeSet<AnnotationDatum> treeSet = data.get( annotationKey );
@@ -76,17 +73,17 @@ public class AnnotationDataManager {
                 data.put( annotationKey, treeSet );
             }
             AnnotationDatum datum = new AnnotationDatum( value );
-            if( treeSet.contains(datum) ) {
+            if( treeSet.contains(datum) ) { // contains uses AnnotationDatum's equals function, so it only checks if the value field is already present
                 datum = treeSet.tailSet(datum).first();
             } else {
                 treeSet.add(datum);
             }
 
             final boolean isNovelVariant = variant.getID().equals(".");
-            final boolean isTrueVariant = false;
+            final boolean isTrueVariant = false; //BUGBUG: Check truth input file to see if this variant is in the truth set
 
-            // Decide if it was a Ti or a Tv
+            // Decide if the variant is a transition or transversion
-            if( BaseUtils.isTransition(variant.getReferenceForSNP(), variant.getAlternativeBaseForSNP()) ) {
+            if( BaseUtils.isTransition( variant.getReferenceForSNP(), variant.getAlternativeBaseForSNP()) ) {
                 datum.incrementTi( isNovelVariant, isTrueVariant );
             } else {
                 datum.incrementTv( isNovelVariant, isTrueVariant );
@@ -97,6 +94,7 @@ public class AnnotationDataManager {
     public void plotCumulativeTables( final String PATH_TO_RSCRIPT, final String PATH_TO_RESOURCES, final String OUTPUT_PREFIX,
                                       final int MIN_VARIANTS_PER_BIN, final int MAX_VARIANTS_PER_BIN ) {
 
+        final AnnotationDatum thisAnnotationBin = new AnnotationDatum();
         System.out.println( "\nExecuting RScript commands:" );
 
         // For each annotation we've seen
@@ -113,8 +111,8 @@ public class AnnotationDataManager {
             // Output a header line
             output.println("value\ttitv\tnumVariants\tcategory");
 
-            // Bin SNPs and calculate truth metrics for each bin, right now this is just TiTv
+            // Bin SNPs and calculate truth metrics for each bin
-            AnnotationDatum thisAnnotationBin = new AnnotationDatum();
+            thisAnnotationBin.clearBin();
             for( AnnotationDatum datum : data.get( annotationKey ) ) {
                 thisAnnotationBin.combine( datum );
                 if( thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) >= MAX_VARIANTS_PER_BIN ) { // This annotation bin is full
@@ -126,24 +124,26 @@ public class AnnotationDataManager {
                 // else, continue accumulating variants because this bin isn't full yet
             }
 
-            if( thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) != 0 ) { // one final bin that may not have been dumped out
+            if( thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) != 0 ) { // One final bin that may not have been dumped out
                 output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.FULL_SET ) + "\t" + thisAnnotationBin.numVariants( AnnotationDatum.FULL_SET ) + "\tall");
                 output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.NOVEL_SET ) + "\t" + thisAnnotationBin.numVariants( AnnotationDatum.NOVEL_SET ) + "\tnovel");
                 output.println( thisAnnotationBin.value + "\t" + thisAnnotationBin.calcTiTv( AnnotationDatum.DBSNP_SET ) + "\t" + thisAnnotationBin.numVariants( AnnotationDatum.DBSNP_SET ) + "\tdbsnp");
 
             }
 
+            // Close the PrintStream
             output.close();
 
-            System.out.println(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTiTv.R" + " " +
+            // Print out the command line to make it clear to the user what is being executed and how one might modify it
-                                   OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationKey + " " + MIN_VARIANTS_PER_BIN);
+            final String rScriptCommandLine = PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTiTv.R" + " " +
+                                   OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationKey + " " + MIN_VARIANTS_PER_BIN;
+            System.out.println( rScriptCommandLine );
 
             // Execute the RScript command to plot the table of TiTv values
             try {
-                final Process p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_Annotations_BinnedTiTv.R" + " " +
+                Runtime.getRuntime().exec( rScriptCommandLine );
-                                        OUTPUT_PREFIX + annotationKey + ".dat" + " " + annotationKey + " " + MIN_VARIANTS_PER_BIN);
+            } catch ( IOException e ) {
-            } catch ( Exception e ) {
+                throw new StingException( "Unable to execute RScript command: " + rScriptCommandLine );
-                throw new StingException( "Unable to execute RScript command" );
             }
         }
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDatum.java

@@ -98,7 +98,7 @@ public class AnnotationDatum implements Comparator<AnnotationDatum> {
             this.ti[iii] += that.ti[iii];
             this.tv[iii] += that.tv[iii];
         }
-        this.value = that.value; // overwrite this bin's value
+        this.value = that.value; // Overwrite this bin's value
     }
 
     final public float calcTiTv( final int INDEX ) {