From 497bcbcbb7e833ff5b85216e81854da71082e37b Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 24 Sep 2010 22:09:12 +0000 Subject: [PATCH] Recent changes to the build system make the build system complain loudly about pieces of core that depend on playground. Most of these have been eliminated by (temporarily) promoting Aaron's report system to core in this checkin. I'll follow up with other changes in separately. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a --- .../report/GATKReport => gatk/report}/GATKReport.java | 2 +- .../GATKReport => gatk/report}/GATKReportColumn.java | 2 +- .../GATKReport => gatk/report}/GATKReportTable.java | 2 +- .../sting/gatk/walkers/varianteval/CompOverlap.java | 4 ++-- .../gatk/walkers/varianteval/CountFunctionalClasses.java | 4 ++-- .../sting/gatk/walkers/varianteval/CountVariants.java | 4 ++-- .../gatk/walkers/varianteval/GenotypeConcordance.java | 6 +++--- .../walkers/varianteval/GenotypePhasingEvaluator.java | 6 +++--- .../gatk/walkers/varianteval/IndelLengthHistogram.java | 6 +++--- .../walkers/varianteval/MendelianViolationEvaluator.java | 4 ++-- .../sting/gatk/walkers/varianteval/SimpleMetricsByAC.java | 6 +++--- .../gatk/walkers/varianteval/ThetaVariantEvaluator.java | 4 ++-- .../gatk/walkers/varianteval/TiTvVariantEvaluator.java | 4 ++-- .../sting/gatk/walkers/varianteval/VariantEvalWalker.java | 8 ++++---- .../gatk/walkers/varianteval/VariantQualityScore.java | 6 +++--- .../walkers/varianteval/AminoAcidTransition.java | 6 +++--- .../walkers/varianteval/FunctionalClassBySample.java | 6 +++--- .../walkers/varianteval/SimpleMetricsBySample.java | 4 ++-- .../walkers/varianteval/VariantEvaluatorBySample.java | 4 ++-- .../gatk/walkers/diagnostics/ErrorRatePerCycle.java | 2 +- .../utils/report/AnalysisModuleScanner.java | 8 ++++---- .../{playground => }/utils/report/ReportMarshaller.java | 8 ++++---- .../{playground => }/utils/report/VE2ReportFactory.java | 6 +++--- .../{playground => }/utils/report/tags/Analysis.java | 2 +- .../{playground => }/utils/report/tags/DataPoint.java | 2 +- .../sting/{playground => }/utils/report/tags/Param.java | 2 +- .../utils/report/templates/CSVFormat.java | 2 +- .../utils/report/templates/GrepFormat.java | 4 ++-- .../{playground => }/utils/report/templates/RFormat.java | 4 ++-- .../utils/report/templates/ReportFormat.java | 4 ++-- .../utils/report/templates/TableBasedFormat.java | 4 ++-- .../utils/report/templates/TableFormat.java | 2 +- .../utils/report/templates/TextTable.java | 2 +- .../utils/report/utils/ComplexDataUtils.java | 2 +- .../sting/{playground => }/utils/report/utils/Node.java | 2 +- .../{playground => }/utils/report/utils/NodeUtils.java | 2 +- .../{playground => }/utils/report/utils/TableType.java | 2 +- .../utils/report/AnalysisModuleScannerUnitTest.java | 8 ++++---- .../utils/report/ReportMarshallerUnitTest.java | 2 +- .../utils/report/templates/TextTableUnitTest.java | 2 +- 40 files changed, 80 insertions(+), 80 deletions(-) rename java/src/org/broadinstitute/sting/{playground/utils/report/GATKReport => gatk/report}/GATKReport.java (94%) rename java/src/org/broadinstitute/sting/{playground/utils/report/GATKReport => gatk/report}/GATKReportColumn.java (97%) rename java/src/org/broadinstitute/sting/{playground/utils/report/GATKReport => gatk/report}/GATKReportTable.java (99%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/AnalysisModuleScanner.java (94%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/ReportMarshaller.java (96%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/VE2ReportFactory.java (94%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/tags/Analysis.java (89%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/tags/DataPoint.java (96%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/tags/Param.java (90%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/templates/CSVFormat.java (94%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/templates/GrepFormat.java (95%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/templates/RFormat.java (91%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/templates/ReportFormat.java (78%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/templates/TableBasedFormat.java (98%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/templates/TableFormat.java (97%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/templates/TextTable.java (98%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/utils/ComplexDataUtils.java (98%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/utils/Node.java (97%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/utils/NodeUtils.java (98%) rename java/src/org/broadinstitute/sting/{playground => }/utils/report/utils/TableType.java (81%) rename java/test/org/broadinstitute/sting/{playground => }/utils/report/AnalysisModuleScannerUnitTest.java (87%) rename java/test/org/broadinstitute/sting/{playground => }/utils/report/ReportMarshallerUnitTest.java (97%) rename java/test/org/broadinstitute/sting/{playground => }/utils/report/templates/TextTableUnitTest.java (95%) 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;