diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReport.java b/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReport.java rename to java/src/org/broadinstitute/sting/gatk/report/GATKReport.java index 0df025e86..92252c39e 100755 --- a/java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReport.java +++ b/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.GATKReport; +package org.broadinstitute.sting.gatk.report; import java.io.PrintStream; import java.util.TreeMap; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportColumn.java b/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportColumn.java rename to java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java index 0883091c1..e9c6d0218 100755 --- a/java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportColumn.java +++ b/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.GATKReport; +package org.broadinstitute.sting.gatk.report; import java.util.TreeMap; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportTable.java b/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportTable.java rename to java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java index 7c848254c..cde8052f4 100755 --- a/java/src/org/broadinstitute/sting/playground/utils/report/GATKReport/GATKReportTable.java +++ b/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.GATKReport; +package org.broadinstitute.sting.gatk.report; import java.io.PrintStream; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CompOverlap.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CompOverlap.java index 64d91bc7b..6edb5c06d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CompOverlap.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CompOverlap.java @@ -5,8 +5,8 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.*; -import org.broadinstitute.sting.playground.utils.report.tags.Analysis; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; /** * The Broad Institute diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java index 63ea4062e..4cd502a00 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountFunctionalClasses.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; import org.broad.tribble.util.variantcontext.VariantContext; -import org.broadinstitute.sting.playground.utils.report.tags.Analysis; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java index 86e99e514..f040b2e62 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java @@ -5,8 +5,8 @@ import org.broad.tribble.util.variantcontext.VariantContext; 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.playground.utils.report.tags.Analysis; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java index 208504588..a85198ac8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java @@ -5,9 +5,9 @@ import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.*; -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.utils.TableType; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java index bff5af37a..8384890e9 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java @@ -5,9 +5,9 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.playground.gatk.walkers.phasing.*; -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.utils.TableType; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.GenomeLoc; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.MathUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java index 007a2c70a..9cad48f95 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java @@ -4,9 +4,9 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -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.utils.TableType; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java index e400297f3..36995a070 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java @@ -6,8 +6,8 @@ import org.broad.tribble.util.variantcontext.VariantContext; 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.playground.utils.report.tags.Analysis; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java index 961121849..6f279635b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java @@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -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.utils.TableType; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ThetaVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ThetaVariantEvaluator.java index 4ce203de9..3f6a776de 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ThetaVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ThetaVariantEvaluator.java @@ -6,8 +6,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.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.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; import java.util.concurrent.ConcurrentMap; import java.util.concurrent.ConcurrentHashMap; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java index 6716a4f35..307f253c7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TiTvVariantEvaluator.java @@ -5,8 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils 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.playground.utils.report.tags.Analysis; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; @Analysis(name = "Ti/Tv Variant Evaluator", description = "Ti/Tv Variant Evaluator") public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 84f905e42..aa546a4da 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -41,10 +41,10 @@ import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.ApplyVariantCuts; -import org.broadinstitute.sting.playground.utils.report.ReportMarshaller; -import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory; -import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat; -import org.broadinstitute.sting.playground.utils.report.utils.Node; +import org.broadinstitute.sting.utils.report.ReportMarshaller; +import org.broadinstitute.sting.utils.report.VE2ReportFactory; +import org.broadinstitute.sting.utils.report.templates.ReportFormat; +import org.broadinstitute.sting.utils.report.utils.Node; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.classloader.PackageUtils; import org.broadinstitute.sting.utils.Utils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java index 9b595ae3a..ccebaac76 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantQualityScore.java @@ -31,9 +31,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -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.utils.TableType; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.collections.Pair; import java.util.ArrayList; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java index edd2d40b1..82053559a 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java @@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -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.utils.TableType; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.utils.TableType; import org.broadinstitute.sting.utils.analysis.AminoAcid; import org.broadinstitute.sting.utils.analysis.AminoAcidTable; import org.broadinstitute.sting.utils.analysis.AminoAcidUtils; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java index ef56da715..e29dc7d7f 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/FunctionalClassBySample.java @@ -6,11 +6,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample; -import org.broadinstitute.sting.playground.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample; -import org.broadinstitute.sting.playground.utils.report.tags.Analysis; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; import java.util.ArrayList; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java index 14ad75aa3..473a56577 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/SimpleMetricsBySample.java @@ -8,8 +8,8 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.SampleDataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluatorBySample; -import org.broadinstitute.sting.playground.utils.report.tags.Analysis; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; import java.util.ArrayList; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java index 273603f8e..989654c3c 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/VariantEvaluatorBySample.java @@ -5,8 +5,8 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; -import org.broadinstitute.sting.playground.utils.report.utils.TableType; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.utils.TableType; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java index 1e12e9af6..af69c4cef 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ErrorRatePerCycle.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.playground.utils.report.GATKReport.GATKReport; +import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.utils.BaseUtils; import java.io.PrintStream; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java b/java/src/org/broadinstitute/sting/utils/report/AnalysisModuleScanner.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java rename to java/src/org/broadinstitute/sting/utils/report/AnalysisModuleScanner.java index 46b23719d..17da36b25 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java +++ b/java/src/org/broadinstitute/sting/utils/report/AnalysisModuleScanner.java @@ -21,11 +21,11 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.utils.report; +package org.broadinstitute.sting.utils.report; -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.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Param; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.annotation.Annotation; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java b/java/src/org/broadinstitute/sting/utils/report/ReportMarshaller.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java rename to java/src/org/broadinstitute/sting/utils/report/ReportMarshaller.java index 1dc360797..e51b8466c 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java +++ b/java/src/org/broadinstitute/sting/utils/report/ReportMarshaller.java @@ -21,12 +21,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.utils.report; +package org.broadinstitute.sting.utils.report; -import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat; -import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils; -import org.broadinstitute.sting.playground.utils.report.utils.Node; +import org.broadinstitute.sting.utils.report.templates.ReportFormat; +import org.broadinstitute.sting.utils.report.utils.ComplexDataUtils; +import org.broadinstitute.sting.utils.report.utils.Node; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.*; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java b/java/src/org/broadinstitute/sting/utils/report/VE2ReportFactory.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java rename to java/src/org/broadinstitute/sting/utils/report/VE2ReportFactory.java index b77ca24be..673bcc3ab 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java +++ b/java/src/org/broadinstitute/sting/utils/report/VE2ReportFactory.java @@ -1,7 +1,7 @@ -package org.broadinstitute.sting.playground.utils.report; +package org.broadinstitute.sting.utils.report; -import org.broadinstitute.sting.playground.utils.report.templates.*; -import org.broadinstitute.sting.playground.utils.report.utils.Node; +import org.broadinstitute.sting.utils.report.templates.*; +import org.broadinstitute.sting.utils.report.utils.Node; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import java.io.*; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/tags/Analysis.java b/java/src/org/broadinstitute/sting/utils/report/tags/Analysis.java similarity index 89% rename from java/src/org/broadinstitute/sting/playground/utils/report/tags/Analysis.java rename to java/src/org/broadinstitute/sting/utils/report/tags/Analysis.java index 584831aa8..260d06c57 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/tags/Analysis.java +++ b/java/src/org/broadinstitute/sting/utils/report/tags/Analysis.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.tags; +package org.broadinstitute.sting.utils.report.tags; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/tags/DataPoint.java b/java/src/org/broadinstitute/sting/utils/report/tags/DataPoint.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/utils/report/tags/DataPoint.java rename to java/src/org/broadinstitute/sting/utils/report/tags/DataPoint.java index c19b6d620..828812aaf 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/tags/DataPoint.java +++ b/java/src/org/broadinstitute/sting/utils/report/tags/DataPoint.java @@ -21,7 +21,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.utils.report.tags; +package org.broadinstitute.sting.utils.report.tags; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/tags/Param.java b/java/src/org/broadinstitute/sting/utils/report/tags/Param.java similarity index 90% rename from java/src/org/broadinstitute/sting/playground/utils/report/tags/Param.java rename to java/src/org/broadinstitute/sting/utils/report/tags/Param.java index 79530d215..fb99757cf 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/tags/Param.java +++ b/java/src/org/broadinstitute/sting/utils/report/tags/Param.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.tags; +package org.broadinstitute.sting.utils.report.tags; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/CSVFormat.java b/java/src/org/broadinstitute/sting/utils/report/templates/CSVFormat.java similarity index 94% rename from java/src/org/broadinstitute/sting/playground/utils/report/templates/CSVFormat.java rename to java/src/org/broadinstitute/sting/utils/report/templates/CSVFormat.java index f732c5b6f..f8b9375b6 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/CSVFormat.java +++ b/java/src/org/broadinstitute/sting/utils/report/templates/CSVFormat.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; /** * the basic comma separated value format diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/GrepFormat.java b/java/src/org/broadinstitute/sting/utils/report/templates/GrepFormat.java similarity index 95% rename from java/src/org/broadinstitute/sting/playground/utils/report/templates/GrepFormat.java rename to java/src/org/broadinstitute/sting/utils/report/templates/GrepFormat.java index 4735dfa6f..11ae1cc78 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/GrepFormat.java +++ b/java/src/org/broadinstitute/sting/utils/report/templates/GrepFormat.java @@ -1,6 +1,6 @@ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; -import org.broadinstitute.sting.playground.utils.report.utils.Node; +import org.broadinstitute.sting.utils.report.utils.Node; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/RFormat.java b/java/src/org/broadinstitute/sting/utils/report/templates/RFormat.java similarity index 91% rename from java/src/org/broadinstitute/sting/playground/utils/report/templates/RFormat.java rename to java/src/org/broadinstitute/sting/utils/report/templates/RFormat.java index 99129a19c..781550e76 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/RFormat.java +++ b/java/src/org/broadinstitute/sting/utils/report/templates/RFormat.java @@ -1,6 +1,6 @@ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; -import org.broadinstitute.sting.playground.utils.report.utils.Node; +import org.broadinstitute.sting.utils.report.utils.Node; import java.io.PrintWriter; import java.io.Writer; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/ReportFormat.java b/java/src/org/broadinstitute/sting/utils/report/templates/ReportFormat.java similarity index 78% rename from java/src/org/broadinstitute/sting/playground/utils/report/templates/ReportFormat.java rename to java/src/org/broadinstitute/sting/utils/report/templates/ReportFormat.java index 6427a349b..93c0e6f2c 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/ReportFormat.java +++ b/java/src/org/broadinstitute/sting/utils/report/templates/ReportFormat.java @@ -1,6 +1,6 @@ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; -import org.broadinstitute.sting.playground.utils.report.utils.Node; +import org.broadinstitute.sting.utils.report.utils.Node; import java.io.File; import java.io.Writer; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableBasedFormat.java b/java/src/org/broadinstitute/sting/utils/report/templates/TableBasedFormat.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/utils/report/templates/TableBasedFormat.java rename to java/src/org/broadinstitute/sting/utils/report/templates/TableBasedFormat.java index 75cc72122..1446ec0d7 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableBasedFormat.java +++ b/java/src/org/broadinstitute/sting/utils/report/templates/TableBasedFormat.java @@ -1,6 +1,6 @@ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; -import org.broadinstitute.sting.playground.utils.report.utils.Node; +import org.broadinstitute.sting.utils.report.utils.Node; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.*; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java b/java/src/org/broadinstitute/sting/utils/report/templates/TableFormat.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java rename to java/src/org/broadinstitute/sting/utils/report/templates/TableFormat.java index 1067058f9..7ce40179e 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java +++ b/java/src/org/broadinstitute/sting/utils/report/templates/TableFormat.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; /** diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TextTable.java b/java/src/org/broadinstitute/sting/utils/report/templates/TextTable.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/utils/report/templates/TextTable.java rename to java/src/org/broadinstitute/sting/utils/report/templates/TextTable.java index eb332b7b4..765fa0555 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/templates/TextTable.java +++ b/java/src/org/broadinstitute/sting/utils/report/templates/TextTable.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/utils/ComplexDataUtils.java b/java/src/org/broadinstitute/sting/utils/report/utils/ComplexDataUtils.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/utils/report/utils/ComplexDataUtils.java rename to java/src/org/broadinstitute/sting/utils/report/utils/ComplexDataUtils.java index aa6f87938..20660d110 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/utils/ComplexDataUtils.java +++ b/java/src/org/broadinstitute/sting/utils/report/utils/ComplexDataUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.utils; +package org.broadinstitute.sting.utils.report.utils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java b/java/src/org/broadinstitute/sting/utils/report/utils/Node.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java rename to java/src/org/broadinstitute/sting/utils/report/utils/Node.java index e597300fb..3ebdc45bb 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java +++ b/java/src/org/broadinstitute/sting/utils/report/utils/Node.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.utils; +package org.broadinstitute.sting.utils.report.utils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/utils/NodeUtils.java b/java/src/org/broadinstitute/sting/utils/report/utils/NodeUtils.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/utils/report/utils/NodeUtils.java rename to java/src/org/broadinstitute/sting/utils/report/utils/NodeUtils.java index 1ffb66d67..2d11c88d6 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/utils/NodeUtils.java +++ b/java/src/org/broadinstitute/sting/utils/report/utils/NodeUtils.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.utils; +package org.broadinstitute.sting.utils.report.utils; import java.util.ArrayList; import java.util.List; diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/utils/TableType.java b/java/src/org/broadinstitute/sting/utils/report/utils/TableType.java similarity index 81% rename from java/src/org/broadinstitute/sting/playground/utils/report/utils/TableType.java rename to java/src/org/broadinstitute/sting/utils/report/utils/TableType.java index 3ae51bdcc..d6be5cf59 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/utils/TableType.java +++ b/java/src/org/broadinstitute/sting/utils/report/utils/TableType.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.utils; +package org.broadinstitute.sting.utils.report.utils; /** diff --git a/java/test/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScannerUnitTest.java b/java/test/org/broadinstitute/sting/utils/report/AnalysisModuleScannerUnitTest.java similarity index 87% rename from java/test/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScannerUnitTest.java rename to java/test/org/broadinstitute/sting/utils/report/AnalysisModuleScannerUnitTest.java index 96ef334a0..b2b64fa97 100644 --- a/java/test/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScannerUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/report/AnalysisModuleScannerUnitTest.java @@ -1,9 +1,9 @@ -package org.broadinstitute.sting.playground.utils.report; +package org.broadinstitute.sting.utils.report; import org.broadinstitute.sting.BaseTest; -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.utils.report.tags.Analysis; +import org.broadinstitute.sting.utils.report.tags.DataPoint; +import org.broadinstitute.sting.utils.report.tags.Param; import org.junit.Assert; import org.junit.Test; diff --git a/java/test/org/broadinstitute/sting/playground/utils/report/ReportMarshallerUnitTest.java b/java/test/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java similarity index 97% rename from java/test/org/broadinstitute/sting/playground/utils/report/ReportMarshallerUnitTest.java rename to java/test/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java index 8ab0b37b1..6cd329c1c 100644 --- a/java/test/org/broadinstitute/sting/playground/utils/report/ReportMarshallerUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java @@ -21,7 +21,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.playground.utils.report; +package org.broadinstitute.sting.utils.report; import org.broadinstitute.sting.BaseTest; import org.junit.Test; diff --git a/java/test/org/broadinstitute/sting/playground/utils/report/templates/TextTableUnitTest.java b/java/test/org/broadinstitute/sting/utils/report/templates/TextTableUnitTest.java similarity index 95% rename from java/test/org/broadinstitute/sting/playground/utils/report/templates/TextTableUnitTest.java rename to java/test/org/broadinstitute/sting/utils/report/templates/TextTableUnitTest.java index b77438b27..f31781e21 100644 --- a/java/test/org/broadinstitute/sting/playground/utils/report/templates/TextTableUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/report/templates/TextTableUnitTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.utils.report.templates; +package org.broadinstitute.sting.utils.report.templates; import org.junit.Assert; import org.junit.Test;