added some sample annotations to VariantEval2 analysis modules, and some changes to the report system.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3067 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java

@@ -5,39 +5,61 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
 import java.util.Arrays;
 
+@Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
 public class CountVariants extends VariantEvaluator {
+    @DataPoint(description = "Number of processed loci")
     long nProcessedLoci = 0;
+    @DataPoint(description = "Number of called loci")
     long nCalledLoci = 0;
+    @DataPoint(description = "Number of variant loci")
     long nVariantLoci = 0;
+    @DataPoint(description = "Number of reference loci")
     long nRefLoci = 0;
 
+    @DataPoint(description = "Number of snp loci")
     long nSNPs = 0;
+    @DataPoint(description = "Number of insertions")
     long nInsertions = 0;
+    @DataPoint(description = "Number of deletions")
     long nDeletions = 0;
+    @DataPoint(description = "Number of complex loci")
     long nComplex = 0;
 
+    @DataPoint(description = "Number of no calls loci")
     long nNoCalls = 0;
+    @DataPoint(description = "Number of het loci")
     long nHets = 0;
+    @DataPoint(description = "Number of hom ref loci")
     long nHomRef = 0;
+    @DataPoint(description = "Number of hom var loci")
     long nHomVar = 0;
 
     public CountVariants(VariantEval2Walker parent) {
         // don't do anything
     }
 
-    private double perLocusRate(long n)      { return rate(n, nProcessedLoci); }
+    private double perLocusRate(long n) {
-    private long perLocusRInverseRate(long n) { return inverseRate(n, nProcessedLoci); }
+        return rate(n, nProcessedLoci);
+    }
+
+    private long perLocusRInverseRate(long n) {
+        return inverseRate(n, nProcessedLoci);
+    }
 
     public String getName() {
         return "counter";
     }
 
-    public boolean enabled() { return true; }
+    public boolean enabled() {
+        return true;
+    }
 
     public int getComparisonOrder() {
         return 1;   // we only need to see each eval track
@@ -53,25 +75,41 @@ public class CountVariants extends VariantEvaluator {
 
         if (vc1.isVariant()) nVariantLoci++;
         switch (vc1.getType()) {
-            case NO_VARIATION: nRefLoci++; break;
+            case NO_VARIATION:
-            case SNP: nSNPs++; break;
+                nRefLoci++;
-            case INDEL:
+                break;
-                if ( vc1.isInsertion() ) nInsertions++; else nDeletions++;
+            case SNP:
+                nSNPs++;
+                break;
+            case INDEL:
+                if (vc1.isInsertion()) nInsertions++;
+                else nDeletions++;
+                break;
+            case MIXED:
+                nComplex++;
                 break;
-            case MIXED: nComplex++; break;
         }
 
         for (Genotype g : vc1.getGenotypes().values()) {
             switch (g.getType()) {
-                case NO_CALL: nNoCalls++; break;
+                case NO_CALL:
-                case HOM_REF: nHomRef++; break;
+                    nNoCalls++;
-                case HET:     nHets++; break;
+                    break;
-                case HOM_VAR: nHomVar++; break;
+                case HOM_REF:
-                default: throw new StingException("BUG: Unexpected genotype type: " + g);
+                    nHomRef++;
+                    break;
+                case HET:
+                    nHets++;
+                    break;
+                case HOM_VAR:
+                    nHomVar++;
+                    break;
+                default:
+                    throw new StingException("BUG: Unexpected genotype type: " + g);
             }
         }
 
-        return null; // we don't capture any intersting sites
+        return null; // we don't capture any interesting sites
     }
 
     public String toString() {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java

@@ -5,6 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 
 import java.util.List;
 import java.util.Arrays;
@@ -18,10 +20,15 @@ import java.util.Arrays;
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
+@Analysis(name = "dbOverlap", description = "the overlap between DbSNP sites and other SNP tracks")
 public class DbSNPPercentage extends VariantEvaluator {
+    @DataPoint(name = "DbSNP_count", description = "number of DPSNP sites")
     private long nDBSNPs = 0;
+    @DataPoint(name = "total_count", description = "number of total snp sites")
     private long nEvalSNPs = 0;
+    @DataPoint(name = "number_snps_at_dbsnp", description = "number of SNP sites at DPSNP sites")
     private long nSNPsAtdbSNPs = 0;
+    @DataPoint(name = "number_concordant", description = "number of concordant sites")
     private long nConcordant = 0;
 
     public DbSNPPercentage(VariantEval2Walker parent) {
@@ -36,11 +43,25 @@ public class DbSNPPercentage extends VariantEvaluator {
         return 2;   // we need to see each eval track and each comp track
     }
 
-    public long nDBSNPs()        { return nDBSNPs; }
+    public long nDBSNPs() {
-    public long nEvalSNPs()      { return nEvalSNPs; }
+        return nDBSNPs;
-    public long nSNPsAtdbSNPs()  { return nSNPsAtdbSNPs; }
+    }
-    public long nConcordant()    { return nConcordant; }
+
-    public long nNovelSites()    { return Math.abs(nEvalSNPs() - nSNPsAtdbSNPs()); }
+    public long nEvalSNPs() {
+        return nEvalSNPs;
+    }
+
+    public long nSNPsAtdbSNPs() {
+        return nSNPsAtdbSNPs;
+    }
+
+    public long nConcordant() {
+        return nConcordant;
+    }
+
+    public long nNovelSites() {
+        return Math.abs(nEvalSNPs() - nSNPsAtdbSNPs());
+    }
 
 
     /**
@@ -48,8 +69,13 @@ public class DbSNPPercentage extends VariantEvaluator {
      *
      * @return db rate
      */
-    public double dbSNPRate()           { return rate(nSNPsAtdbSNPs(), nEvalSNPs()); }
+    public double dbSNPRate() {
-    public double concordanceRate()     { return rate(nConcordant(), nSNPsAtdbSNPs()); }
+        return rate(nSNPsAtdbSNPs(), nEvalSNPs());
+    }
+
+    public double concordanceRate() {
+        return rate(nConcordant(), nSNPsAtdbSNPs());
+    }
 
     public String toString() {
         return getName() + ": " + summaryLine();
@@ -65,11 +91,14 @@ public class DbSNPPercentage extends VariantEvaluator {
                     "n_novel_snps", "percent_eval_in_comp", "concordance_rate");
 
     // making it a table
+
     public List<String> getTableHeader() {
         return HEADER;
     }
 
-    public boolean enabled() { return true; }
+    public boolean enabled() {
+        return true;
+    }
 
     public List<List<String>> getTableRows() {
         return Arrays.asList(Arrays.asList(summaryLine().split(" ")));

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/GenotypeConcordance.java

@@ -3,6 +3,10 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
+import org.broadinstitute.sting.playground.utils.report.tags.Param;
+import org.broadinstitute.sting.playground.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.StingException;
 import org.apache.log4j.Logger;
 
@@ -17,17 +21,44 @@ import java.util.*;
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
+@Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
 public class GenotypeConcordance extends VariantEvaluator {
     protected static Logger logger = Logger.getLogger(GenotypeConcordance.class);
 
+    // a mapping from allele count to stats
+    @DataPoint(description = "the frequency statistics for each allele")
+    private HashMap<Integer, FrequencyStats> alleleCountStats = new HashMap<Integer, FrequencyStats>();
+
+    // a mapping from sample to stats
+    @DataPoint(description = "the concordance statistics for each sample")
+    private HashMap<String, SampleStats> concordanceStats = null;
+
     private static final int MAX_MISSED_VALIDATION_DATA = 10000;
 
     private static final int nGenotypeTypes = Genotype.Type.values().length;
 
-    class SampleStats {
+    class SampleStats implements TableType {
 
         long[][] concordance = new long[nGenotypeTypes][nGenotypeTypes];
 
+        // TableType methods
+
+        public Object[] getRowKeys() {
+            return Genotype.Type.values();
+        }
+
+        public Object[] getColumnKeys() {
+            return Genotype.Type.values();
+        }
+
+        public String getCell(int x, int y) {
+            return String.valueOf(concordance[x][y]);
+        }
+
+        public String getName() {
+            return "SampleStats";
+        }
+
         public String toString() {
             StringBuffer sb = new StringBuffer();
             for (int truth = 0; truth < nGenotypeTypes; truth++) {
@@ -48,22 +79,33 @@ public class GenotypeConcordance extends VariantEvaluator {
         }
     }
 
-    class FrequencyStats {
+    class FrequencyStats implements TableType {
         long nFound = 0;
         long nMissed = 0;
 
+        public Object[] getRowKeys() {
+            return new String[]{"sample"};
+        }
+
+        public Object[] getColumnKeys() {
+            return new String[]{"number_found", "number_missing"};
+        }
+
+        public String getName() {
+            return "FrequencyStats";
+        }
+
+        public String getCell(int x, int y) {
+            if (y == 0) return String.valueOf(nFound);
+            else return String.valueOf(nMissed);
+        }
+
         public String toString() {
             long total = nFound + nMissed;
             return String.format("%d %d %.2f ", nFound, nMissed, total == 0 ? 0.0 : (100.0 * rate(nFound, total)));
         }
     }
 
-    // a mapping from allele count to stats
-    private HashMap<Integer, FrequencyStats> alleleCountStats = new HashMap<Integer, FrequencyStats>();
-
-    // a mapping from sample to stats
-    private HashMap<String, SampleStats> concordanceStats = null;
-
     // keep a list of the validation data we saw before the first eval data
     private HashSet<VariantContext> missedValidationData = new HashSet<VariantContext>();
 
@@ -80,7 +122,9 @@ public class GenotypeConcordance extends VariantEvaluator {
         return 2;   // we need to see each eval track and each comp track
     }
 
-    public boolean enabled() { return true; }
+    public boolean enabled() {
+        return true;
+    }
 
     public String toString() {
         return getName() + ": " + getTableRows();
@@ -99,6 +143,7 @@ public class GenotypeConcordance extends VariantEvaluator {
             Arrays.asList("alleleCount", "n_found", "n_missed", "%_found");
 
     // making it a table
+
     public List<String> getTableHeader() {
         ArrayList<String> header = new ArrayList<String>();
         header.addAll(SAMPLE_HEADER);
@@ -123,6 +168,7 @@ public class GenotypeConcordance extends VariantEvaluator {
     }
 
     private boolean warnedAboutValidationData = false;
+
     public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         String interesting = null;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java

@@ -6,6 +6,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
@@ -15,36 +17,51 @@ import java.util.regex.Matcher;
 
 /**
  * Mendelian violation detection and counting
- *
+ * <p/>
  * a violation looks like:
  * Suppose dad = A/B and mom = C/D
  * The child can be [A or B] / [C or D].
  * If the child doesn't match this, the site is a violation
- *
+ * <p/>
  * Some examples:
- *
+ * <p/>
  * mom = A/A, dad = C/C
  * child can be A/C only
- *
+ * <p/>
  * mom = A/C, dad = C/C
  * child can be A/C or C/C
- *
+ * <p/>
  * mom = A/C, dad = A/C
  * child can be A/A, A/C, C/C
- *
+ * <p/>
  * The easiest way to do this calculation is to:
- *
+ * <p/>
  * Get alleles for mom => A/B
  * Get alleles for dad => C/D
  * Make allowed genotypes for child: A/C, A/D, B/C, B/D
  * Check that the child is one of these.
  */
+@Analysis(name = "Mendelian Violation Evaluator", description = "Mendelian Violation Evaluator")
 public class MendelianViolationEvaluator extends VariantEvaluator {
-    long nVariants, nViolations;
+
-    TrioStructure trio;
+    @DataPoint(name = "number_variants", description = "Number of mendelian variants found")
+    long nVariants;
+
+    @DataPoint(name = "number_violations", description = "Number of mendelian violations found")
+    long nViolations;
+
+    @DataPoint(description = "number of child hom ref calls where the parent was hom variant")
+    long KidHomRef_ParentHomVar;
+    @DataPoint(description = "number of child het calls where the parent was hom ref")
+    long KidHet_ParentsHomRef;
+    @DataPoint(description = "number of child het calls where the parent was hom variant")
+    long KidHet_ParentsHomVar;
+    @DataPoint(description = "number of child hom variant calls where the parent was hom ref")
+    long KidHomVar_ParentHomRef;
+
     VariantEval2Walker parent;
 
-    long KidHomRef_ParentHomVar, KidHet_ParentsHomRef, KidHet_ParentsHomVar, KidHomVar_ParentHomRef;
+    TrioStructure trio;
 
     private static Pattern FAMILY_PATTERN = Pattern.compile("(.*)\\+(.*)=(.*)");
 
@@ -173,6 +190,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
             Arrays.asList("nVariants", "nViolations", "KidHomRef_ParentHomVar", "KidHet_ParentsHomRef", "KidHet_ParentsHomVar", "KidHomVar_ParentHomRef");
 
     // making it a table
+
     public List<String> getTableHeader() {
         return HEADER;
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java

@@ -4,19 +4,31 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
+import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 
 import java.util.List;
 import java.util.Arrays;
 
+@Analysis(name = "Ti/Tv Variant Evaluator", description = "Ti/Tv Variant Evaluator")
 public class TiTvVariantEvaluator extends VariantEvaluator {
-    long nTi = 0, nTv = 0;
+
-    long nTiInStd = 0, nTvInStd = 0;
+    @DataPoint(name = "ti_count", description = "number of transition loci")
+    long nTi = 0;
+    @DataPoint(name = "tv_count", description = "number of transversion loci")
+    long nTv = 0;
+    @DataPoint(name = "ti_count_std", description = "number of transition sites in the std")
+    long nTiInStd = 0;
+    @DataPoint(name = "tv_count_std", description = "number of transversion sites in the std")
+    long nTvInStd = 0;
 
     public TiTvVariantEvaluator(VariantEval2Walker parent) {
         // don't do anything
     }
 
-    public boolean enabled() { return true; }
+    public boolean enabled() {
+        return true;
+    }
 
     public String getName() {
         return "titv";
@@ -29,9 +41,11 @@ public class TiTvVariantEvaluator extends VariantEvaluator {
     public void updateTiTv(VariantContext vc, boolean updateStandard) {
         if (vc != null && vc.isSNP() && vc.isBiallelic()) {
             if (vc.isTransition()) {
-                if ( updateStandard ) nTiInStd++; else nTi++;
+                if (updateStandard) nTiInStd++;
+                else nTi++;
             } else {
-                if ( updateStandard ) nTvInStd++; else nTv++;
+                if (updateStandard) nTvInStd++;
+                else nTv++;
             }
         }
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/ValidationRate.java

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 
 import java.util.List;
 import java.util.Arrays;
@@ -17,6 +18,7 @@ import java.util.Arrays;
  * This software is supplied without any warranty or guaranteed support whatsoever. Neither
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
+@Analysis(name = "Validation Rate", description = "Validation Rate")
 public class ValidationRate extends VariantEvaluator {
 
     // todo -- subset validation data by list of samples, if provided
@@ -26,7 +28,9 @@ public class ValidationRate extends VariantEvaluator {
     class SiteStats {
         long nPoly = 0, nMono = 0, nNoCall = 0;
 
-        double polyPercent() { return 100 * rate(nPoly, nPoly + nMono + nNoCall); }
+        double polyPercent() {
+            return 100 * rate(nPoly, nPoly + nMono + nNoCall);
+        }
     }
 
     private SiteStats validationStats = new SiteStats();
@@ -68,11 +72,14 @@ public class ValidationRate extends VariantEvaluator {
                     "PPV", "Sensitivity");
 
     // making it a table
+
     public List<String> getTableHeader() {
         return HEADER;
     }
 
-    public boolean enabled() { return true; }
+    public boolean enabled() {
+        return true;
+    }
 
     public List<List<String>> getTableRows() {
         return Arrays.asList(Arrays.asList(summaryLine().split(" ")));
@@ -89,8 +96,7 @@ public class ValidationRate extends VariantEvaluator {
                 overlap = evalOverlapAtPoly;
                 if (eval == null || eval.isMonomorphic())
                     interesting = "ValidationStatus=FN";
-            }
+            } else {
-            else {
                 validationStats.nMono++;
                 overlap = evalOverlapAtMono;
 

java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java

@@ -33,10 +33,7 @@ import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.lang.reflect.Field;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
 
 
 /**
@@ -52,6 +49,7 @@ public class ReportMarshaller {
     // the aggregation of all our analyses
     private Node root;
     private File writeLocation;
+
     /**
      * create a marshaled object
      *
@@ -64,10 +62,8 @@ public class ReportMarshaller {
     }
 
     private void init(String reportName, File filename) {
-        root = new Node(reportName);
+        root = new Node("report", reportName, "the overarching report object");
-        Node title= new Node("title");
+        root.addChild(new Node("title", reportName, "title of the report"));
-        title.addChild(new Node(reportName));
-        root.addChild(title);
         this.writeLocation = filename;
     }
 
@@ -101,12 +97,40 @@ public class ReportMarshaller {
         root.addChild(analysis);
     }
 
+    /**
+     * add an analysis module to the output source
+     *
+     * @param toMarshall the object to marshall
+     */
+    public void write(List<Node> prependNodes, Object toMarshall) {
+        // Create a context to add data to
+        HashMap analysisMap = new HashMap();
+        AnalysisModuleScanner moduleScanner = new AnalysisModuleScanner(toMarshall);
+
+        Node analysis = addAnalysis(moduleScanner);
+
+        analysis.addAllChildren(getParameterNodes(toMarshall, moduleScanner));
+        analysis.addAllChildren(getDataPointNodes(toMarshall, moduleScanner));
+
+        // prepend the list of nodes passed in
+        Node currChild = null;
+        for (Node n : prependNodes) {
+            if (currChild == null) {
+                root.addChild(n);
+                currChild = n;
+            } else {
+                currChild.addChild(n);
+                currChild = n;
+            }
+        }
+        // add this analysis to the root node
+        if (currChild == null) root.addChild(analysis);
+        else currChild.addChild(analysis);
+    }
+
+
     private Node addAnalysis(AnalysisModuleScanner moduleScanner) {
-        Node analysis = new Node(moduleScanner.getAnalysis().name());
+        return new Node("analysis", moduleScanner.getAnalysis().name(), moduleScanner.getAnalysis().description());
-        Node description = new Node("description");
-        description.createSubNode(moduleScanner.getAnalysis().description());
-        analysis.addChild(description);
-        return analysis;
     }
 
     /**
@@ -119,7 +143,9 @@ public class ReportMarshaller {
     private Collection<Node> getParameterNodes(Object toMarshall, AnalysisModuleScanner moduleScanner) {
         Collection<Node> nodes = new ArrayList<Node>();
         for (Field f : moduleScanner.getParameters().keySet()) {
-            Node node = new Node(moduleScanner.getParameters().get(f).name().equals("") ? f.getName() : moduleScanner.getParameters().get(f).name());
+            Node node = new Node("parameter",
+                    moduleScanner.getParameters().get(f).name().equals("") ? f.getName() : moduleScanner.getParameters().get(f).name(),
+                    moduleScanner.getParameters().get(f).description());
             addChildNodeFromField(toMarshall, f, node);
             nodes.add(node);
         }
@@ -136,14 +162,18 @@ public class ReportMarshaller {
     private Collection<Node> getDataPointNodes(Object toMarshall, AnalysisModuleScanner moduleScanner) {
         Collection<Node> nodes = new ArrayList<Node>();
         for (Field f : moduleScanner.getData().keySet()) {
-            Node node = new Node(moduleScanner.getData().get(f).name().equals("") ? f.getName() : moduleScanner.getData().get(f).name());
+            Node node = new Node("data_point",
+                    moduleScanner.getData().get(f).name().equals("") ? f.getName() : moduleScanner.getData().get(f).name(),
+                    moduleScanner.getData().get(f).description());
             addChildNodeFromField(toMarshall, f, node);
             nodes.add(node);
         }
         return nodes;
     }
 
-    /** call the method to finalize the report */
+    /**
+     * call the method to finalize the report
+     */
     public void close() {
         Writer out = null;
         try {
@@ -174,7 +204,7 @@ public class ReportMarshaller {
         cfg.setObjectWrapper(new DefaultObjectWrapper());
         Template temp = null;
         try {
-            temp = cfg.getTemplate("machineReadable.ftl");
+            temp = cfg.getTemplate("myTestTemp.ftl");  // TODO: obviously this has to be changed to a factory or something like that
         } catch (IOException e) {
             e.printStackTrace();
         }
@@ -183,6 +213,7 @@ public class ReportMarshaller {
 
     /**
      * helper method for adding a Node to the specified node, given the field
+     *
      * @param toMarshall the object which contains the specified field
      * @param f          the field
      * @param node       the node to add a child node to

java/src/org/broadinstitute/sting/playground/utils/report/TableFormatter.java

@@ -1,99 +0,0 @@
-/*
- * Copyright (c) 2010.  The Broad Institute
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.playground.utils.report;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
-
-/**
- * 
- * @author aaron 
- * 
- * Class TableFormatter
- *
- * a helper class for formatting a table of data.  Given a collection, it formats it into rows and columns.
- * If it's a Map, values are emited as key, value, key, value, so it may make sense to have colums set to 2.
- *
- * TODO: Needs some cleanup
- *
- */
-public class TableFormatter {
-    public Object tableEntries;                 // data storage
-    private int columns = 2;                    // default to two columns of data, overridden in the constructor
-
-
-    public TableFormatter(Collection<Object> tbl, int columns) {
-        tableEntries = tbl;
-        this.columns = columns;
-    }
-
-    public TableFormatter(Object tbl) {
-        tableEntries = tbl;        
-    }
-
-    /**
-     * convert the underlying object to a list of lists, for convenient output
-     * @return a list of list of objects (a list for each row, then a list of row members)
-     */
-    public List<List<Object>> toRows() {
-        if (tableEntries instanceof Collection)
-            return collectionToTable(((Collection)tableEntries));
-        else if (tableEntries instanceof Map)
-            return mapToTable(((Map)tableEntries));
-        else
-            throw new UnsupportedOperationException("underlying collection must be an instance of type Collection or of type Map");
-    }
-
-    private List<List<Object>> mapToTable(Map collection) {
-        ArrayList<List<Object>> list = new ArrayList<List<Object>>();        
-        for (Object obj : collection.keySet()) {
-            List<Object> currentRow = new ArrayList<Object>();
-            currentRow.add(obj);
-            Object data = collection.get(obj);
-            currentRow.add(data.toString());
-
-            list.add(currentRow);
-        }
-
-        return list;
-    }
-
-    private List<List<Object>> collectionToTable(Collection collection) {
-        ArrayList<List<Object>> list = new ArrayList<List<Object>>();
-        List<Object> currentRow = new ArrayList<Object>();
-        for (Object obj : collection) {
-            if (currentRow.size() >= columns) {
-                list.add(currentRow);
-                currentRow = new ArrayList<Object>();
-            }
-            currentRow.add(obj);
-        }
-        list.add(currentRow);
-        return list;
-    }
-
-}

java/src/org/broadinstitute/sting/playground/utils/report/utils/ComplexDataUtils.java

@@ -1,20 +1,22 @@
 package org.broadinstitute.sting.playground.utils.report.utils;
 
+import org.broadinstitute.sting.utils.Utils;
+
 import java.util.*;
 
 
 /**
- * 
  * @author aaron
- * 
+ *         <p/>
  *         Class ComplexDataUtils
- *
+ *         <p/>
  *         This class contains methods and techniques for breaking down complex data in the output system
  */
 public class ComplexDataUtils {
 
     /**
      * convert any string -> object pairing into a string keyed tree
+     *
      * @param obj the object
      * @return a mapping of the name to the associated value tree.  All non-leaf nodes will be Strings
      */
@@ -22,12 +24,13 @@ public class ComplexDataUtils {
         Collection<Node> nodes = new ArrayList<Node>();
 
         // the simplest case
-        if (obj == null) nodes.add(new Node("<null>")); // throw new IllegalStateException("object is null");
+        if (obj == null)
+            nodes.add(new Node("<null>", "<null>", "<null>")); // throw new IllegalStateException("object is null");
         else if (obj instanceof TableType)
             nodes.add(tableToNode((TableType) obj, ((TableType) obj).getName()));
         else if (obj instanceof Map) {
             for (Object key : ((Map) obj).keySet()) {
-                Node keyNode = new Node(key.toString());
+                Node keyNode = new Node("key", key.toString(), "map key");
                 nodes.add(keyNode);
                 keyNode.addAllChildren(resolveObjects(((Map) obj).get(key)));
             }
@@ -36,27 +39,35 @@ public class ComplexDataUtils {
         else if (obj.getClass().isArray())
             nodes.addAll(listToNode(Arrays.asList(obj), "array"));
         else
-            nodes.add(new Node(obj.toString()));
+            nodes.add(new Node(obj.getClass().getSimpleName(), obj.toString(), "value"));
         return nodes;
     }
 
 
     /**
      * given a TableType object, make it into a tree using maps.
+     *
      * @param table the table type to convert into a map
      * @return
      */
     private static Node tableToNode(TableType table, String name) {
-        Node root = new Node(name);
+        Node root = new Node("table", name, "Table");
         Object[] rows = table.getRowKeys();
         Object[] cols = table.getColumnKeys();
+
+        // add the columns names
+        Node col_names = new Node("col_names", "col_names", "the column names, ~ seperated", false);
+        for (Object col : cols)
+            col_names.addChild(new Node("col", col.toString(), "a column name", false));
+        root.addChild(col_names);
+
         for (int x = 0; x < table.getRowKeys().length; x++) {
-            Node row = new Node(rows[x].toString());
+            Node row = new Node("row", rows[x].toString(), "a row");
             root.addChild(row);
-            for (int y = 0; y < table.getRowKeys().length; y++) {
+            for (int y = 0; y < table.getColumnKeys().length; y++) {
-                Node col = new Node(cols[y].toString());
+                Node col = new Node("column", cols[y].toString(), "a column");
                 row.addChild(col);
-                col.addChild(new Node(table.getCell(x,y)));
+                col.addChild(new Node("cell(" + x + "," + y + ")", table.getCell(x, y), "a cell"));
             }
         }
         return root;
@@ -64,6 +75,7 @@ public class ComplexDataUtils {
 
     /**
      * given a Collection object, make it into a tree using maps.
+     *
      * @param coll the collection to iterate, and turn into a list
      * @return a mapping of String to Object
      */
@@ -71,11 +83,10 @@ public class ComplexDataUtils {
         Collection<Node> nodes = new ArrayList<Node>();
         Iterator<Object> iter = coll.iterator();
         for (int x = 0; x < coll.size(); x++) {
-            Node value = new Node(String.valueOf(x));
+            Node value = new Node("column " + x, String.valueOf(x), "column");
-            value.addChild(new Node(iter.next().toString()));
+            value.addChild(new Node("value " + x, iter.next().toString(), "value"));
             nodes.add(value);
         }
         return nodes;
     }
-
 }

java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java

@@ -7,12 +7,24 @@ import java.util.LinkedHashSet;
  * a node, extracted using the new report output system.
  */
 public class Node {
-    public String value;
+    public final String name;
-    public String description; // if one is available 
+    public final String value;
+    public final String description;
+    public final boolean display; // is this node an output node, or a node for tracking internal data? true if output node
     public Collection<Node> children;
 
-    public Node(String value) {
+    public Node(String name, String value, String description) {
         this.value = value;
+        this.name = name;
+        this.description = description;
+        display = true;
+    }
+
+    public Node(String name, String value, String description, boolean display) {
+        this.value = value;
+        this.name = name;
+        this.description = description;
+        this.display = display;
     }
 
     public void addChild(Node child) {
@@ -25,20 +37,27 @@ public class Node {
         this.children.addAll(children);
     }
 
-    public Boolean getComplex() { return (children != null && children.size() > 0); }
+    public Boolean getComplex() {
+        return (children != null && children.size() > 0);
+    }
 
     /**
      * a convenience method for adding a new sub-node with the specified value
+     *
      * @param value the value of the sub-node
      */
-    public void createSubNode(String value) {
+    public void createSubNode(String name, String value, String description) {
-        addChild(new Node(value));
+        addChild(new Node(name, value, description));
     }
 
     public String getValue() {
         return value;
     }
 
+    public String getName() {
+        return name;
+    }
+
     public String getDescription() {
         return description;
     }
@@ -46,4 +65,8 @@ public class Node {
     public Collection<Node> getChildren() {
         return children;
     }
+
+    public boolean getDisplay() {
+        return display;
+    }
 }