Package org.snpeff.fileIterator

Class GuessTableTypes

  • public class GuessTableTypes
extends java.lang.Object
    Given a table in a TXT file, try to guess the value types for each column
    Author:
    pcingola

    • Field Detail

      • debug

        public static boolean debug

      • MIN_LINES

        public static int MIN_LINES

    • Constructor Detail

      • GuessTableTypes

        public GuessTableTypes​(java.lang.String fileName)

    • Method Detail

      • foundAllTypes

        public boolean foundAllTypes()

      • getFieldNames

        public java.lang.String[] getFieldNames()

      • getFileName

        public java.lang.String getFileName()

      • getMultipleValues

        public boolean[] getMultipleValues()

      • getNames2index

        public java.util.HashMap<java.lang.String,​java.lang.Integer> getNames2index()

      • getType

        public VcfInfoType getType​(java.lang.String fieldName)
        Get field type
        Parameters:
        fieldName -
        Returns:

      • getTypes

        public VcfInfoType[] getTypes()
        Get an array of types (ordered by column)
        Returns:

      • guessType

        public VcfInfoType guessType​(java.lang.String value)
        Guess data type for this value
        Parameters:
        value -
        Returns:

      • guessTypes

        public boolean guessTypes()
        Find column names form header and guess data types from values
        Returns:
        true of OK, false if there was an error parsing header or data

      • isMultipleValues

        public java.lang.Boolean isMultipleValues​(java.lang.String fieldName)
        Has this field multiple values
        Parameters:
        fieldName -
        Returns:

      • parsedHeader

        public boolean parsedHeader()

      • setColumnSeparator

        public void setColumnSeparator​(java.lang.String columnSeparator)

      • setSubfieldSeparator

        public void setSubfieldSeparator​(java.lang.String subfieldSeparator)

      • toString

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