Package org.snpeff.outputFormatter

Class OutputFormatter

  • 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

    • Constructor Detail

      • OutputFormatter

        public OutputFormatter()

    • Method Detail

      • add

        public void add​(VariantEffect variantEffect)
        Add effects to list

      • clone

        public OutputFormatter clone()
        Overrides:
        clone in class java.lang.Object

      • close

        public void close()
        CLose output files, if any

      • endSection

        public java.lang.String endSection​(Marker marker)
        Finish up section

      • print

        public void print​(java.lang.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​(java.lang.String chrStr)

      • setCommandLineStr

        public void setCommandLineStr​(java.lang.String commandLineStr)

      • setConfig

        public void setConfig​(Config config)

      • setOutOffset

        public void setOutOffset​(int outOffset)

      • setOutputFile

        public void setOutputFile​(java.lang.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​(java.lang.String version)

      • startSection

        public void startSection​(Marker marker)
        Starts a new section

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toStringHeader

        protected abstract java.lang.String toStringHeader()
        Show header