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
This commit is contained in:
aaron
parent
1f451e17e5
commit
60dfba997b
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@ -5,39 +5,61 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
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import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
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import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.utils.StingException;
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import java.util.List;
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import java.util.Arrays;
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@Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
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public class CountVariants extends VariantEvaluator {
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@DataPoint(description = "Number of processed loci")
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long nProcessedLoci = 0;
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@DataPoint(description = "Number of called loci")
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long nCalledLoci = 0;
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@DataPoint(description = "Number of variant loci")
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long nVariantLoci = 0;
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@DataPoint(description = "Number of reference loci")
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long nRefLoci = 0;
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@DataPoint(description = "Number of snp loci")
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long nSNPs = 0;
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@DataPoint(description = "Number of insertions")
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long nInsertions = 0;
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@DataPoint(description = "Number of deletions")
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long nDeletions = 0;
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@DataPoint(description = "Number of complex loci")
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long nComplex = 0;
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@DataPoint(description = "Number of no calls loci")
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long nNoCalls = 0;
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@DataPoint(description = "Number of het loci")
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long nHets = 0;
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@DataPoint(description = "Number of hom ref loci")
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long nHomRef = 0;
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@DataPoint(description = "Number of hom var loci")
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long nHomVar = 0;
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public CountVariants(VariantEval2Walker parent) {
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// don't do anything
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}
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private double perLocusRate(long n) { return rate(n, nProcessedLoci); }
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private long perLocusRInverseRate(long n) { return inverseRate(n, nProcessedLoci); }
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private double perLocusRate(long n) {
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return rate(n, nProcessedLoci);
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}
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private long perLocusRInverseRate(long n) {
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return inverseRate(n, nProcessedLoci);
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}
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public String getName() {
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return "counter";
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}
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public boolean enabled() { return true; }
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public boolean enabled() {
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return true;
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}
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public int getComparisonOrder() {
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return 1; // we only need to see each eval track
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@ -51,27 +73,43 @@ public class CountVariants extends VariantEvaluator {
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//nProcessedLoci++;
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nCalledLoci++;
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if ( vc1.isVariant() ) nVariantLoci++;
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switch ( vc1.getType() ) {
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case NO_VARIATION: nRefLoci++; break;
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case SNP: nSNPs++; break;
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case INDEL:
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if ( vc1.isInsertion() ) nInsertions++; else nDeletions++;
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if (vc1.isVariant()) nVariantLoci++;
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switch (vc1.getType()) {
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case NO_VARIATION:
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nRefLoci++;
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break;
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case SNP:
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nSNPs++;
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break;
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case INDEL:
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if (vc1.isInsertion()) nInsertions++;
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else nDeletions++;
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break;
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case MIXED:
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nComplex++;
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break;
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case MIXED: nComplex++; break;
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}
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for ( Genotype g : vc1.getGenotypes().values() ) {
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switch ( g.getType() ) {
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case NO_CALL: nNoCalls++; break;
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case HOM_REF: nHomRef++; break;
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case HET: nHets++; break;
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case HOM_VAR: nHomVar++; break;
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default: throw new StingException("BUG: Unexpected genotype type: " + g);
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for (Genotype g : vc1.getGenotypes().values()) {
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switch (g.getType()) {
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case NO_CALL:
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nNoCalls++;
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break;
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case HOM_REF:
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nHomRef++;
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break;
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case HET:
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nHets++;
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break;
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case HOM_VAR:
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nHomVar++;
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break;
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default:
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throw new StingException("BUG: Unexpected genotype type: " + g);
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}
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}
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return null; // we don't capture any intersting sites
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return null; // we don't capture any interesting sites
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}
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public String toString() {
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@ -5,6 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
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import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
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import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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import java.util.List;
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import java.util.Arrays;
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@ -18,11 +20,16 @@ import java.util.Arrays;
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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@Analysis(name = "dbOverlap", description = "the overlap between DbSNP sites and other SNP tracks")
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public class DbSNPPercentage extends VariantEvaluator {
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private long nDBSNPs = 0;
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private long nEvalSNPs = 0;
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@DataPoint(name = "DbSNP_count", description = "number of DPSNP sites")
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private long nDBSNPs = 0;
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@DataPoint(name = "total_count", description = "number of total snp sites")
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private long nEvalSNPs = 0;
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@DataPoint(name = "number_snps_at_dbsnp", description = "number of SNP sites at DPSNP sites")
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private long nSNPsAtdbSNPs = 0;
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private long nConcordant = 0;
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@DataPoint(name = "number_concordant", description = "number of concordant sites")
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private long nConcordant = 0;
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public DbSNPPercentage(VariantEval2Walker parent) {
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// don't do anything
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@ -36,11 +43,25 @@ public class DbSNPPercentage extends VariantEvaluator {
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return 2; // we need to see each eval track and each comp track
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}
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public long nDBSNPs() { return nDBSNPs; }
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public long nEvalSNPs() { return nEvalSNPs; }
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public long nSNPsAtdbSNPs() { return nSNPsAtdbSNPs; }
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public long nConcordant() { return nConcordant; }
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public long nNovelSites() { return Math.abs(nEvalSNPs() - nSNPsAtdbSNPs()); }
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public long nDBSNPs() {
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return nDBSNPs;
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}
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public long nEvalSNPs() {
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return nEvalSNPs;
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}
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public long nSNPsAtdbSNPs() {
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return nSNPsAtdbSNPs;
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}
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public long nConcordant() {
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return nConcordant;
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}
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public long nNovelSites() {
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return Math.abs(nEvalSNPs() - nSNPsAtdbSNPs());
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}
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/**
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@ -48,9 +69,14 @@ public class DbSNPPercentage extends VariantEvaluator {
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*
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* @return db rate
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*/
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public double dbSNPRate() { return rate(nSNPsAtdbSNPs(), nEvalSNPs()); }
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public double concordanceRate() { return rate(nConcordant(), nSNPsAtdbSNPs()); }
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public double dbSNPRate() {
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return rate(nSNPsAtdbSNPs(), nEvalSNPs());
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}
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public double concordanceRate() {
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return rate(nConcordant(), nSNPsAtdbSNPs());
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}
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public String toString() {
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return getName() + ": " + summaryLine();
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}
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@ -65,12 +91,15 @@ public class DbSNPPercentage extends VariantEvaluator {
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"n_novel_snps", "percent_eval_in_comp", "concordance_rate");
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// making it a table
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public List<String> getTableHeader() {
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return HEADER;
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}
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public boolean enabled() { return true; }
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public boolean enabled() {
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return true;
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}
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public List<List<String>> getTableRows() {
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return Arrays.asList(Arrays.asList(summaryLine().split(" ")));
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}
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@ -78,13 +107,13 @@ public class DbSNPPercentage extends VariantEvaluator {
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/**
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* Returns true if every allele in eval is also in dbsnp
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*
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* @param eval eval context
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* @param dbsnp db context
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* @param eval eval context
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* @param dbsnp db context
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* @return true if eval and db are discordant
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*/
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public boolean discordantP(VariantContext eval, VariantContext dbsnp ) {
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for ( Allele a : eval.getAlleles() ) {
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if ( ! dbsnp.hasAllele(a, true) )
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public boolean discordantP(VariantContext eval, VariantContext dbsnp) {
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for (Allele a : eval.getAlleles()) {
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if (!dbsnp.hasAllele(a, true))
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return true;
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}
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@ -95,13 +124,13 @@ public class DbSNPPercentage extends VariantEvaluator {
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boolean dbSNPIsGood = dbsnp != null && dbsnp.isSNP() && dbsnp.isNotFiltered();
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boolean evalIsGood = eval != null && eval.isSNP();
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if ( dbSNPIsGood ) nDBSNPs++; // count the number of dbSNP events
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if ( evalIsGood ) nEvalSNPs++; // count the number of dbSNP events
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if (dbSNPIsGood) nDBSNPs++; // count the number of dbSNP events
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if (evalIsGood) nEvalSNPs++; // count the number of dbSNP events
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if ( dbSNPIsGood && evalIsGood ) {
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if (dbSNPIsGood && evalIsGood) {
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nSNPsAtdbSNPs++;
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if ( ! discordantP(eval, dbsnp) ) // count whether we're concordant or not with the dbSNP value
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if (!discordantP(eval, dbsnp)) // count whether we're concordant or not with the dbSNP value
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nConcordant++;
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}
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@ -3,6 +3,10 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
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import org.broadinstitute.sting.gatk.contexts.*;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
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import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
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import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.playground.utils.report.tags.Param;
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import org.broadinstitute.sting.playground.utils.report.utils.TableType;
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import org.broadinstitute.sting.utils.StingException;
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import org.apache.log4j.Logger;
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@ -17,29 +21,56 @@ import java.util.*;
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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@Analysis(name = "Genotype Concordance", description = "Determine the genotype concordance between the genotypes in difference tracks")
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public class GenotypeConcordance extends VariantEvaluator {
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protected static Logger logger = Logger.getLogger(GenotypeConcordance.class);
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// a mapping from allele count to stats
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@DataPoint(description = "the frequency statistics for each allele")
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private HashMap<Integer, FrequencyStats> alleleCountStats = new HashMap<Integer, FrequencyStats>();
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// a mapping from sample to stats
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@DataPoint(description = "the concordance statistics for each sample")
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private HashMap<String, SampleStats> concordanceStats = null;
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private static final int MAX_MISSED_VALIDATION_DATA = 10000;
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private static final int nGenotypeTypes = Genotype.Type.values().length;
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class SampleStats {
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class SampleStats implements TableType {
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long[][] concordance = new long[nGenotypeTypes][nGenotypeTypes];
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// TableType methods
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public Object[] getRowKeys() {
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return Genotype.Type.values();
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}
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public Object[] getColumnKeys() {
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return Genotype.Type.values();
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}
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public String getCell(int x, int y) {
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return String.valueOf(concordance[x][y]);
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}
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public String getName() {
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return "SampleStats";
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}
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public String toString() {
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StringBuffer sb = new StringBuffer();
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for (int truth = 0; truth < nGenotypeTypes; truth++ ) {
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for (int truth = 0; truth < nGenotypeTypes; truth++) {
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// don't print out when truth = no-call
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if ( truth == Genotype.Type.NO_CALL.ordinal() )
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if (truth == Genotype.Type.NO_CALL.ordinal())
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continue;
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long total = 0;
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for (int called = 0; called < nGenotypeTypes; called++ )
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for (int called = 0; called < nGenotypeTypes; called++)
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total += concordance[truth][called];
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sb.append(String.format("%d %d %.2f ", total, concordance[truth][truth], total == 0 ? 0.0 : (100.0 * (double)concordance[truth][truth] / (double)total)));
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for (int called = 0; called < nGenotypeTypes; called++ ) {
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if ( called != truth )
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sb.append(String.format("%d %d %.2f ", total, concordance[truth][truth], total == 0 ? 0.0 : (100.0 * (double) concordance[truth][truth] / (double) total)));
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for (int called = 0; called < nGenotypeTypes; called++) {
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if (called != truth)
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sb.append(String.format("%d ", concordance[truth][called]));
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}
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}
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@ -48,22 +79,33 @@ public class GenotypeConcordance extends VariantEvaluator {
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}
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}
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class FrequencyStats {
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class FrequencyStats implements TableType {
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long nFound = 0;
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long nMissed = 0;
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public Object[] getRowKeys() {
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return new String[]{"sample"};
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}
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public Object[] getColumnKeys() {
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return new String[]{"number_found", "number_missing"};
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}
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public String getName() {
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return "FrequencyStats";
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}
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public String getCell(int x, int y) {
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if (y == 0) return String.valueOf(nFound);
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else return String.valueOf(nMissed);
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}
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public String toString() {
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long total = nFound + nMissed;
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return String.format("%d %d %.2f ", nFound, nMissed, total == 0 ? 0.0 : (100.0 * rate(nFound, total)));
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}
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}
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// a mapping from allele count to stats
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private HashMap<Integer, FrequencyStats> alleleCountStats = new HashMap<Integer, FrequencyStats>();
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// a mapping from sample to stats
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private HashMap<String, SampleStats> concordanceStats = null;
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// keep a list of the validation data we saw before the first eval data
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private HashSet<VariantContext> missedValidationData = new HashSet<VariantContext>();
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@ -80,7 +122,9 @@ public class GenotypeConcordance extends VariantEvaluator {
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return 2; // we need to see each eval track and each comp track
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}
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public boolean enabled() { return true; }
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public boolean enabled() {
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return true;
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}
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public String toString() {
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return getName() + ": " + getTableRows();
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@ -99,6 +143,7 @@ public class GenotypeConcordance extends VariantEvaluator {
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Arrays.asList("alleleCount", "n_found", "n_missed", "%_found");
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// making it a table
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public List<String> getTableHeader() {
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ArrayList<String> header = new ArrayList<String>();
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header.addAll(SAMPLE_HEADER);
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@ -109,13 +154,13 @@ public class GenotypeConcordance extends VariantEvaluator {
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public List<List<String>> getTableRows() {
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ArrayList<List<String>> rows = new ArrayList<List<String>>();
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if ( concordanceStats != null ) {
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for ( Map.Entry<String, SampleStats> sample : concordanceStats.entrySet() )
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if (concordanceStats != null) {
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for (Map.Entry<String, SampleStats> sample : concordanceStats.entrySet())
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rows.add(Arrays.asList(String.format("%s %s", sample.getKey(), sample.getValue().toString()).split(" ")));
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}
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if ( alleleCountStats != null ) {
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for ( Map.Entry<Integer, FrequencyStats> alleleCount : alleleCountStats.entrySet() )
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if (alleleCountStats != null) {
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for (Map.Entry<Integer, FrequencyStats> alleleCount : alleleCountStats.entrySet())
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rows.add(Arrays.asList(String.format("%d %s", alleleCount.getKey(), alleleCount.getValue().toString()).split(" ")));
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}
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@ -123,26 +168,27 @@ public class GenotypeConcordance extends VariantEvaluator {
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}
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private boolean warnedAboutValidationData = false;
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public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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String interesting = null;
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// sanity check that we at least have either eval or validation data
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if ( eval == null && !isValidVC(validation) )
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if (eval == null && !isValidVC(validation))
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return interesting;
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if ( concordanceStats == null ) {
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if ( eval != null ) {
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if (concordanceStats == null) {
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if (eval != null) {
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// initialize the concordance table
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createConcordanceTable(eval);
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for ( VariantContext vc : missedValidationData )
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for (VariantContext vc : missedValidationData)
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determineStats(null, vc);
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missedValidationData = null;
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} else {
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// todo -- Eric, this results in a memory problem when eval is WEx data but you are using CG calls genome-wide
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// todo -- perhaps you need should extend the evaluators with an initialize
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// todo -- method that gets the header (or samples) for the first eval sites?
|
||||
if ( missedValidationData.size() > MAX_MISSED_VALIDATION_DATA) {
|
||||
if ( ! warnedAboutValidationData ) {
|
||||
if (missedValidationData.size() > MAX_MISSED_VALIDATION_DATA) {
|
||||
if (!warnedAboutValidationData) {
|
||||
logger.warn("Too many genotype sites missed before eval site appeared; ignoring");
|
||||
warnedAboutValidationData = true;
|
||||
}
|
||||
|
|
@ -154,26 +200,26 @@ public class GenotypeConcordance extends VariantEvaluator {
|
|||
}
|
||||
|
||||
determineStats(eval, validation);
|
||||
|
||||
|
||||
return interesting; // we don't capture any interesting sites
|
||||
}
|
||||
|
||||
private void determineStats(VariantContext eval, VariantContext validation) {
|
||||
|
||||
// determine concordance for eval data
|
||||
if ( eval != null ) {
|
||||
if (eval != null) {
|
||||
|
||||
for ( String sample : eval.getSampleNames() ) {
|
||||
for (String sample : eval.getSampleNames()) {
|
||||
Genotype.Type called = eval.getGenotype(sample).getType();
|
||||
Genotype.Type truth;
|
||||
|
||||
if ( !isValidVC(validation) || !validation.hasGenotype(sample) )
|
||||
if (!isValidVC(validation) || !validation.hasGenotype(sample))
|
||||
truth = Genotype.Type.NO_CALL;
|
||||
else
|
||||
truth = validation.getGenotype(sample).getType();
|
||||
|
||||
SampleStats stats = concordanceStats.get(sample);
|
||||
if ( stats == null )
|
||||
if (stats == null)
|
||||
throw new StingException("Sample " + sample + " has not been seen in a previous eval; this analysis module assumes that all samples are present in each variant context");
|
||||
stats.concordance[truth.ordinal()][called.ordinal()]++;
|
||||
}
|
||||
|
|
@ -183,9 +229,9 @@ public class GenotypeConcordance extends VariantEvaluator {
|
|||
|
||||
Genotype.Type called = Genotype.Type.NO_CALL;
|
||||
|
||||
for ( String sample : validation.getSampleNames() ) {
|
||||
for (String sample : validation.getSampleNames()) {
|
||||
SampleStats stats = concordanceStats.get(sample);
|
||||
if ( stats == null )
|
||||
if (stats == null)
|
||||
continue;
|
||||
|
||||
Genotype.Type truth = validation.getGenotype(sample).getType();
|
||||
|
|
@ -194,15 +240,15 @@ public class GenotypeConcordance extends VariantEvaluator {
|
|||
}
|
||||
|
||||
// determine allele count concordance ()
|
||||
if ( isValidVC(validation) && validation.isPolymorphic() ) {
|
||||
if (isValidVC(validation) && validation.isPolymorphic()) {
|
||||
int trueAlleleCount = 0;
|
||||
for ( Allele a : validation.getAlternateAlleles() )
|
||||
for (Allele a : validation.getAlternateAlleles())
|
||||
trueAlleleCount += validation.getChromosomeCount(a);
|
||||
|
||||
if ( !alleleCountStats.containsKey(trueAlleleCount) )
|
||||
if (!alleleCountStats.containsKey(trueAlleleCount))
|
||||
alleleCountStats.put(trueAlleleCount, new FrequencyStats());
|
||||
FrequencyStats stats = alleleCountStats.get(trueAlleleCount);
|
||||
if ( eval != null )
|
||||
if (eval != null)
|
||||
stats.nFound++;
|
||||
else
|
||||
stats.nMissed++;
|
||||
|
|
@ -215,7 +261,7 @@ public class GenotypeConcordance extends VariantEvaluator {
|
|||
|
||||
private void createConcordanceTable(VariantContext vc) {
|
||||
concordanceStats = new HashMap<String, SampleStats>();
|
||||
for ( String sample : vc.getSampleNames() )
|
||||
for (String sample : vc.getSampleNames())
|
||||
concordanceStats.put(sample, new SampleStats());
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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("(.*)\\+(.*)=(.*)");
|
||||
|
||||
|
|
@ -54,7 +71,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
|
|||
|
||||
public static TrioStructure parseTrioDescription(String family) {
|
||||
Matcher m = FAMILY_PATTERN.matcher(family);
|
||||
if ( m.matches() ) {
|
||||
if (m.matches()) {
|
||||
TrioStructure trio = new TrioStructure();
|
||||
//System.out.printf("Found a family pattern: %s%n", parent.FAMILY_STRUCTURE);
|
||||
trio.mom = m.group(1);
|
||||
|
|
@ -69,7 +86,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
|
|||
public MendelianViolationEvaluator(VariantEval2Walker parent) {
|
||||
this.parent = parent;
|
||||
|
||||
if ( enabled() ) {
|
||||
if (enabled()) {
|
||||
trio = parseTrioDescription(parent.FAMILY_STRUCTURE);
|
||||
parent.getLogger().debug(String.format("Found a family pattern: %s mom=%s dad=%s child=%s",
|
||||
parent.FAMILY_STRUCTURE, trio.mom, trio.dad, trio.child));
|
||||
|
|
@ -93,30 +110,30 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
|
|||
}
|
||||
|
||||
public String update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
if ( vc.isBiallelic() && vc.hasGenotypes() ) { // todo -- currently limited to biallelic loci
|
||||
Genotype momG = vc.getGenotype(trio.mom);
|
||||
Genotype dadG = vc.getGenotype(trio.dad);
|
||||
if (vc.isBiallelic() && vc.hasGenotypes()) { // todo -- currently limited to biallelic loci
|
||||
Genotype momG = vc.getGenotype(trio.mom);
|
||||
Genotype dadG = vc.getGenotype(trio.dad);
|
||||
Genotype childG = vc.getGenotype(trio.child);
|
||||
|
||||
if ( includeGenotype(momG) && includeGenotype(dadG) && includeGenotype(childG) ) {
|
||||
if (includeGenotype(momG) && includeGenotype(dadG) && includeGenotype(childG)) {
|
||||
nVariants++;
|
||||
|
||||
if ( momG == null || dadG == null || childG == null )
|
||||
if (momG == null || dadG == null || childG == null)
|
||||
throw new IllegalArgumentException(String.format("VariantContext didn't contain genotypes for expected trio members: mom=%s dad=%s child=%s", trio.mom, trio.dad, trio.child));
|
||||
|
||||
// all genotypes are good, so let's see if child is a violation
|
||||
|
||||
if ( isViolation(vc, momG, dadG, childG) ) {
|
||||
if (isViolation(vc, momG, dadG, childG)) {
|
||||
nViolations++;
|
||||
|
||||
String label;
|
||||
if ( childG.isHomRef() && (momG.isHomVar() || dadG.isHomVar() )) {
|
||||
if (childG.isHomRef() && (momG.isHomVar() || dadG.isHomVar())) {
|
||||
label = "KidHomRef_ParentHomVar";
|
||||
KidHomRef_ParentHomVar++;
|
||||
} else if (childG.isHet() && (momG.isHomRef() && dadG.isHomRef()) ) {
|
||||
} else if (childG.isHet() && (momG.isHomRef() && dadG.isHomRef())) {
|
||||
label = "KidHet_ParentsHomRef";
|
||||
KidHet_ParentsHomRef++;
|
||||
} else if (childG.isHet() && (momG.isHomVar() && dadG.isHomVar()) ) {
|
||||
} else if (childG.isHet() && (momG.isHomVar() && dadG.isHomVar())) {
|
||||
label = "KidHet_ParentsHomVar";
|
||||
KidHet_ParentsHomVar++;
|
||||
} else if (childG.isHomVar() && (momG.isHomRef() || dadG.isHomRef())) {
|
||||
|
|
@ -138,20 +155,20 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
|
|||
return g.getNegLog10PError() > getQThreshold() && g.isCalled();
|
||||
}
|
||||
|
||||
public static boolean isViolation(VariantContext vc, Genotype momG, Genotype dadG, Genotype childG ) {
|
||||
public static boolean isViolation(VariantContext vc, Genotype momG, Genotype dadG, Genotype childG) {
|
||||
return isViolation(vc, momG.getAlleles(), dadG.getAlleles(), childG.getAlleles());
|
||||
}
|
||||
|
||||
public static boolean isViolation(VariantContext vc, List<Allele> momA, List<Allele> dadA, List<Allele> childA ) {
|
||||
public static boolean isViolation(VariantContext vc, List<Allele> momA, List<Allele> dadA, List<Allele> childA) {
|
||||
//VariantContext momVC = vc.subContextFromGenotypes(momG);
|
||||
//VariantContext dadVC = vc.subContextFromGenotypes(dadG);
|
||||
int i = 0;
|
||||
Genotype childG = new Genotype("kidG", childA);
|
||||
for ( Allele momAllele : momA ) {
|
||||
for ( Allele dadAllele : dadA ) {
|
||||
if ( momAllele.isCalled() && dadAllele.isCalled() ) {
|
||||
for (Allele momAllele : momA) {
|
||||
for (Allele dadAllele : dadA) {
|
||||
if (momAllele.isCalled() && dadAllele.isCalled()) {
|
||||
Genotype possibleChild = new Genotype("possibleGenotype" + i, Arrays.asList(momAllele, dadAllele));
|
||||
if ( childG.sameGenotype(possibleChild, false) ) {
|
||||
if (childG.sameGenotype(possibleChild, false)) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,20 +4,32 @@ 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";
|
||||
}
|
||||
|
|
@ -27,18 +39,20 @@ 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 (vc != null && vc.isSNP() && vc.isBiallelic()) {
|
||||
if (vc.isTransition()) {
|
||||
if (updateStandard) nTiInStd++;
|
||||
else nTi++;
|
||||
} else {
|
||||
if ( updateStandard ) nTvInStd++; else nTv++;
|
||||
if (updateStandard) nTvInStd++;
|
||||
else nTv++;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public String update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
if ( vc1 != null ) updateTiTv(vc1, false);
|
||||
if ( vc2 != null ) updateTiTv(vc2, true);
|
||||
if (vc1 != null) updateTiTv(vc1, false);
|
||||
if (vc2 != null) updateTiTv(vc2, true);
|
||||
|
||||
//if ( vc1 == null && vc2 != null && vc2.isSNP() && vc2.isBiallelic() )
|
||||
// System.out.printf("VC2 = %s%n", vc2);
|
||||
|
|
|
|||
|
|
@ -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(" ")));
|
||||
|
|
@ -81,26 +88,25 @@ public class ValidationRate extends VariantEvaluator {
|
|||
public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
String interesting = null;
|
||||
|
||||
if ( validation != null && validation.hasGenotypes() && validation.isNotFiltered() ) {
|
||||
if (validation != null && validation.hasGenotypes() && validation.isNotFiltered()) {
|
||||
SiteStats overlap;
|
||||
|
||||
if ( validation.isPolymorphic() ) {
|
||||
if (validation.isPolymorphic()) {
|
||||
validationStats.nPoly++;
|
||||
overlap = evalOverlapAtPoly;
|
||||
if ( eval == null || eval.isMonomorphic() )
|
||||
if (eval == null || eval.isMonomorphic())
|
||||
interesting = "ValidationStatus=FN";
|
||||
}
|
||||
else {
|
||||
} else {
|
||||
validationStats.nMono++;
|
||||
overlap = evalOverlapAtMono;
|
||||
|
||||
if ( eval != null && eval.isPolymorphic() )
|
||||
if (eval != null && eval.isPolymorphic())
|
||||
interesting = "ValidationStatus=FP";
|
||||
}
|
||||
|
||||
if ( eval == null )
|
||||
if (eval == null)
|
||||
overlap.nNoCall++;
|
||||
else if ( eval.isPolymorphic() )
|
||||
else if (eval.isPolymorphic())
|
||||
overlap.nPoly++;
|
||||
else
|
||||
overlap.nMono++;
|
||||
|
|
|
|||
|
|
@ -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.Collection;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
import java.util.*;
|
||||
|
||||
|
||||
/**
|
||||
|
|
@ -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);
|
||||
Node title= new Node("title");
|
||||
title.addChild(new Node(reportName));
|
||||
root.addChild(title);
|
||||
root = new Node("report", reportName, "the overarching report object");
|
||||
root.addChild(new Node("title", reportName, "title of the report"));
|
||||
this.writeLocation = filename;
|
||||
}
|
||||
|
||||
|
|
@ -77,7 +73,7 @@ public class ReportMarshaller {
|
|||
* @param reportName the report name
|
||||
*/
|
||||
public ReportMarshaller(String reportName, File filename) {
|
||||
init(reportName,filename);
|
||||
init(reportName, filename);
|
||||
temp = createTemplate();
|
||||
}
|
||||
|
||||
|
|
@ -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());
|
||||
Node description = new Node("description");
|
||||
description.createSubNode(moduleScanner.getAnalysis().description());
|
||||
analysis.addChild(description);
|
||||
return analysis;
|
||||
return new Node("analysis", moduleScanner.getAnalysis().name(), moduleScanner.getAnalysis().description());
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -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 {
|
||||
|
|
@ -154,7 +184,7 @@ public class ReportMarshaller {
|
|||
try {
|
||||
// add the data to a map
|
||||
Map map = new HashMap();
|
||||
map.put("root",root);
|
||||
map.put("root", root);
|
||||
temp.process(map, out);
|
||||
out.flush();
|
||||
} catch (TemplateException e) {
|
||||
|
|
@ -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();
|
||||
}
|
||||
|
|
@ -183,9 +213,10 @@ 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
|
||||
* @param f the field
|
||||
* @param node the node to add a child node to
|
||||
*/
|
||||
private static void addChildNodeFromField(Object toMarshall, Field f, Node node) {
|
||||
f.setAccessible(true);
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,20 +1,22 @@
|
|||
package org.broadinstitute.sting.playground.utils.report.utils;
|
||||
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
|
||||
/**
|
||||
*
|
||||
* @author aaron
|
||||
*
|
||||
* Class ComplexDataUtils
|
||||
*
|
||||
* This class contains methods and techniques for breaking down complex data in the output system
|
||||
* @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
|
||||
*/
|
||||
|
|
@ -22,41 +24,50 @@ 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()));
|
||||
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());
|
||||
for (Object key : ((Map) obj).keySet()) {
|
||||
Node keyNode = new Node("key", key.toString(), "map key");
|
||||
nodes.add(keyNode);
|
||||
keyNode.addAllChildren(resolveObjects(((Map)obj).get(key)));
|
||||
keyNode.addAllChildren(resolveObjects(((Map) obj).get(key)));
|
||||
}
|
||||
} else if (obj instanceof Collection)
|
||||
nodes.addAll(listToNode((Collection)obj, "collection"));
|
||||
nodes.addAll(listToNode((Collection) obj, "collection"));
|
||||
else if (obj.getClass().isArray())
|
||||
nodes.addAll(listToNode(Arrays.asList(obj),"array"));
|
||||
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++) {
|
||||
Node col = new Node(cols[y].toString());
|
||||
for (int y = 0; y < table.getColumnKeys().length; y++) {
|
||||
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));
|
||||
value.addChild(new Node(iter.next().toString()));
|
||||
Node value = new Node("column " + x, String.valueOf(x), "column");
|
||||
value.addChild(new Node("value " + x, iter.next().toString(), "value"));
|
||||
nodes.add(value);
|
||||
}
|
||||
return nodes;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,15 +4,27 @@ import java.util.Collection;
|
|||
import java.util.LinkedHashSet;
|
||||
|
||||
/**
|
||||
* a node, extracted using the new report output system.
|
||||
*/
|
||||
* a node, extracted using the new report output system.
|
||||
*/
|
||||
public class Node {
|
||||
public String value;
|
||||
public String description; // if one is available
|
||||
public final String name;
|
||||
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) {
|
||||
addChild(new Node(value));
|
||||
public void createSubNode(String name, String value, String description) {
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue