javax.annotation.Nullable -> org.jetbrains.annotations.Nullable

Author: labkey-adam

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/SVAnnotateStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
@@ -16,7 +17,6 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java

@@ -7,6 +7,7 @@
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
@@ -35,7 +36,6 @@
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
 
-import javax.annotation.Nullable;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SNPEffStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
@@ -18,7 +19,6 @@
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SampleRenameStep.java

@@ -10,6 +10,7 @@
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
@@ -23,7 +24,6 @@
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
 import org.labkey.api.sequenceanalysis.run.VariantFiltrationWrapper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SelectSNVsStep.java

@@ -3,6 +3,7 @@
 import htsjdk.samtools.util.Interval;
 import htsjdk.variant.variantcontext.VariantContext;
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
@@ -17,7 +18,6 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SelectSamplesStep.java

@@ -1,6 +1,7 @@
 package org.labkey.sequenceanalysis.run.variant;
 
 import htsjdk.samtools.util.Interval;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam;
@@ -15,7 +16,6 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SelectVariantsStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.exp.api.ExpData;
@@ -21,7 +22,6 @@
 import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantAnnotatorStep.java

@@ -1,6 +1,7 @@
 package org.labkey.sequenceanalysis.run.variant;
 
 import htsjdk.samtools.util.Interval;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
@@ -17,7 +18,6 @@
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 import org.labkey.sequenceanalysis.run.util.VariantAnnotatorWrapper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantEvalStep.java

@@ -1,6 +1,7 @@
 package org.labkey.sequenceanalysis.run.variant;
 
 import htsjdk.samtools.util.Interval;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
@@ -12,7 +13,6 @@
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 import org.labkey.sequenceanalysis.run.util.VariantEvalWrapper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.List;
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantFiltrationStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
@@ -23,7 +24,6 @@
 import org.labkey.api.sequenceanalysis.run.VariantFiltrationWrapper;
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;