Package org.snpeff.outputFormatter
Class OutputFormatter
- java.lang.Object
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- org.snpeff.outputFormatter.OutputFormatter
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- Direct Known Subclasses:
BedOutputFormatter
,VcfOutputFormatter
public abstract class OutputFormatter extends java.lang.Object
Formats output How is this used: - newSection(); // Create a new 'section' on the output format (e.g. a new Marker) - add(); // Add all changes related to this section (i.e. all changes related to this marker) - endSection(); // Output all changes related to this section (output header if needed), clean up list of changes- Author:
- pcingola
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Constructor Summary
Constructors Constructor Description OutputFormatter()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description void
add(VariantEffect variantEffect)
Add effects to listOutputFormatter
clone()
void
close()
CLose output files, if anyjava.lang.String
endSection(Marker marker)
Finish up sectionvoid
print(java.lang.String outStr)
Print a "raw" string to a filevoid
printSection(Marker marker)
End this section and print resultsvoid
setChrStr(java.lang.String chrStr)
void
setCommandLineStr(java.lang.String commandLineStr)
void
setConfig(Config config)
void
setOutOffset(int outOffset)
void
setOutputFile(java.lang.String outputFile)
void
setShowHeader(boolean showHeader)
void
setSupressOutput(boolean supressOutput)
void
setUseGeneId(boolean useGeneId)
void
setUseHgvs(boolean useHgvs)
void
setUseOicr(boolean useOicr)
void
setUseSequenceOntology(boolean useSequenceOntology)
void
setVariantEffectResutFilter(VariantEffectFilter changeEffectResutFilter)
void
setVersion(java.lang.String version)
void
startSection(Marker marker)
Starts a new sectionjava.lang.String
toString()
protected abstract java.lang.String
toStringHeader()
Show header
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Method Detail
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add
public void add(VariantEffect variantEffect)
Add effects to list
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clone
public OutputFormatter clone()
- Overrides:
clone
in classjava.lang.Object
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close
public void close()
CLose output files, if any
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endSection
public java.lang.String endSection(Marker marker)
Finish up section
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print
public void print(java.lang.String outStr)
Print a "raw" string to a file
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printSection
public void printSection(Marker marker)
End this section and print results
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setChrStr
public void setChrStr(java.lang.String chrStr)
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setCommandLineStr
public void setCommandLineStr(java.lang.String commandLineStr)
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setConfig
public void setConfig(Config config)
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setOutOffset
public void setOutOffset(int outOffset)
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setOutputFile
public void setOutputFile(java.lang.String outputFile)
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setShowHeader
public void setShowHeader(boolean showHeader)
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setSupressOutput
public void setSupressOutput(boolean supressOutput)
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setUseGeneId
public void setUseGeneId(boolean useGeneId)
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setUseHgvs
public void setUseHgvs(boolean useHgvs)
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setUseOicr
public void setUseOicr(boolean useOicr)
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setUseSequenceOntology
public void setUseSequenceOntology(boolean useSequenceOntology)
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setVariantEffectResutFilter
public void setVariantEffectResutFilter(VariantEffectFilter changeEffectResutFilter)
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setVersion
public void setVersion(java.lang.String version)
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startSection
public void startSection(Marker marker)
Starts a new section
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toStringHeader
protected abstract java.lang.String toStringHeader()
Show header
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