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