Class GuessTableTypes

java.lang.Object
org.snpeff.fileIterator.GuessTableTypes

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

    • debug

      public static boolean debug
    • MIN_LINES

      public static int MIN_LINES
  • Constructor Details

    • GuessTableTypes

      public GuessTableTypes(String fileName)
  • Method Details

    • foundAllTypes

      public boolean foundAllTypes()
    • getFieldNames

      public String[] getFieldNames()
    • getFileName

      public String getFileName()
    • getMultipleValues

      public boolean[] getMultipleValues()
    • getNames2index

      public HashMap<String,Integer> getNames2index()
    • getType

      public VcfInfoType getType(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(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 Boolean isMultipleValues(String fieldName)
      Has this field multiple values
      Parameters:
      fieldName -
      Returns:
    • parsedHeader

      public boolean parsedHeader()
    • setColumnSeparator

      public void setColumnSeparator(String columnSeparator)
    • setSubfieldSeparator

      public void setSubfieldSeparator(String subfieldSeparator)
    • toString

      public String toString()
      Overrides:
      toString in class Object