Class ODEFileParser

    • Constructor Detail

      • ODEFileParser

        public ODEFileParser​(java.lang.String fileName)
      • ODEFileParser

        public ODEFileParser​(java.io.File file)
      • ODEFileParser

        public ODEFileParser​(java.io.Reader reader)
    • Method Detail

      • getFieldNames

        public java.lang.String[] getFieldNames()
        Description copied from class: CompoundFileParser
        Compiles all column names that contain alpha-numerical information. Columns containing chemistry objects, coordinates or descriptors don't appear in the list.
        Specified by:
        getFieldNames in class CompoundFileParser
        Returns:
        columns name array in the order of appearance
      • advanceToNext

        protected boolean advanceToNext()
        Description copied from class: CompoundFileParser
        Dont't call this method directly. Use next() instead.
        Specified by:
        advanceToNext in class CompoundFileParser
        Returns:
        false if there is no next row
      • getMoleculeName

        public java.lang.String getMoleculeName()
        Specified by:
        getMoleculeName in class CompoundFileParser
        Returns:
        name/id of (primary) chemical structure of the current row
      • getRowCount

        public int getRowCount()
        Description copied from class: CompoundFileParser
        Depending on data source returns the total row count or -1 if unknown
        Specified by:
        getRowCount in class CompoundFileParser
        Returns:
        number of rows or -1
      • moreRecordsAvailable

        public boolean moreRecordsAvailable()
      • getIDCode

        public java.lang.String getIDCode()
        Description copied from class: CompoundFileParser
        Either this method and getCoordinates() or getMolecule() must be overwritten!!!
        Overrides:
        getIDCode in class CompoundFileParser
        Returns:
        idcode of first chemical structure column of the current row
      • getCoordinates

        public java.lang.String getCoordinates()
        Description copied from class: CompoundFileParser
        Either getIDCode and this method or getMolecule() must be overwritten!!!
        Overrides:
        getCoordinates in class CompoundFileParser
        Returns:
        idcoords of first chemical structure column of the current row
      • getIndex

        public java.lang.String getIndex()
      • getFieldData

        public java.lang.String getFieldData​(int no)
        Description copied from class: CompoundFileParser
        Returns the cell content of the current row. Multi-line cell entries are separated by a '\n' character.
        Specified by:
        getFieldData in class CompoundFileParser
        Parameters:
        no - refers to alpha-numerical columns only, as getFieldNames()
        Returns:
      • extractValue

        public static java.lang.String extractValue​(java.lang.String theLine)