Package org.snpeff.outputFormatter

Class OutputFormatter

java.lang.Object
org.snpeff.outputFormatter.OutputFormatter
Direct Known Subclasses:
BedOutputFormatter, VcfOutputFormatter
public abstract class OutputFormatter extends 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

  • Constructor Details

    • OutputFormatter

      public OutputFormatter()

  • Method Details

    • add

      public void add(VariantEffect variantEffect)
      Add effects to list

    • clone

      public OutputFormatter clone()
      Overrides:
      clone in class Object

    • close

      public void close()
      CLose output files, if any

    • endSection

      public String endSection(Marker marker)
      Finish up section

    • print

      public void print(String outStr)
      Print a "raw" string to a file

    • printSection

      public void printSection(Marker marker)
      End this section and print results

    • setChrStr

      public void setChrStr(String chrStr)

    • setCommandLineStr

      public void setCommandLineStr(String commandLineStr)

    • setConfig

      public void setConfig(Config config)

    • setOutOffset

      public void setOutOffset(int outOffset)

    • setOutputFile

      public void setOutputFile(String outputFile)

    • setShowHeader

      public void setShowHeader(boolean showHeader)

    • setSupressOutput

      public void setSupressOutput(boolean supressOutput)

    • setUseGeneId

      public void setUseGeneId(boolean useGeneId)

    • setUseHgvs

      public void setUseHgvs(boolean useHgvs)

    • setUseOicr

      public void setUseOicr(boolean useOicr)

    • setUseSequenceOntology

      public void setUseSequenceOntology(boolean useSequenceOntology)

    • setVariantEffectResutFilter

      public void setVariantEffectResutFilter(VariantEffectFilter changeEffectResutFilter)

    • setVersion

      public void setVersion(String version)

    • startSection

      public void startSection(Marker marker)
      Starts a new section

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • toStringHeader

      protected abstract String toStringHeader()
      Show header