Package com.actelion.research.chem.io

Class CompoundFileParser

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected java.io.BufferedReader mReader  

    • Method Summary

      All Methods Static Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      protected abstract boolean advanceToNext()
      Dont't call this method directly.
      void close()
      Closes the underlying reader.
      static CompoundFileParser createParser​(java.lang.String fileName)
      Creates the proper parser for the given type of compound file (currently SD or DWAR).
      java.lang.String getCoordinates()
      Either getIDCode and this method or getMolecule() must be overwritten!!!
      java.lang.Object getDescriptor​(java.lang.String shortName)
      If the file source contains encoded descriptors, then overwrite this method to save the calculation time.
      DescriptorHandlerFactory getDescriptorHandlerFactory()  
      abstract java.lang.String getFieldData​(int column)
      Returns the cell content of the current row.
      int getFieldIndex​(java.lang.String fieldName)  
      abstract java.lang.String[] getFieldNames()
      Compiles all column names that contain alpha-numerical information.
      java.lang.String getIDCode()
      Either this method and getCoordinates() or getMolecule() must be overwritten!!!
      StereoMolecule getMolecule()
      Either this method or getIDCode() and getCoordinates() must be overwritten!!!
      abstract java.lang.String getMoleculeName()  
      abstract int getRowCount()
      Depending on data source returns the total row count or -1 if unknown
      boolean isOpen()  
      boolean next()
      Advances the row counter to the next row
      void setDescriptorHandlerFactory​(DescriptorHandlerFactory factory)
      If a requested descriptor is not available in a particuar compound record, the parser can create one itself, provided its DescriptorHandlerFactory knows the descriptor name.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • mReader

        protected java.io.BufferedReader mReader

    • Constructor Detail

      • CompoundFileParser

        public CompoundFileParser()

    • Method Detail

      • createParser

        public static CompoundFileParser createParser​(java.lang.String fileName)
        Creates the proper parser for the given type of compound file (currently SD or DWAR).
        Parameters:
        fileName -
        Returns:
        parser or null, if the file doesn't exist or cannot be accessed

      • getFieldNames

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

      • getFieldData

        public abstract java.lang.String getFieldData​(int column)
        Returns the cell content of the current row. Multi-line cell entries are separated by a '\n' character.
        Parameters:
        column - refers to alpha-numerical columns only, as getFieldNames()
        Returns:

      • getRowCount

        public abstract int getRowCount()
        Depending on data source returns the total row count or -1 if unknown
        Returns:
        number of rows or -1

      • advanceToNext

        protected abstract boolean advanceToNext()
        Dont't call this method directly. Use next() instead.
        Returns:
        false if there is no next row

      • isOpen

        public boolean isOpen()
        Returns:
        whether the file was found and open to accept next() calls

      • next

        public boolean next()
        Advances the row counter to the next row
        Returns:
        false if there is no next row

      • close

        public final void close()
        Closes the underlying reader. Call this, if you don't read all records of the file. The reader is closed automatically after the last record has been read.

      • getIDCode

        public java.lang.String getIDCode()
        Either this method and getCoordinates() or getMolecule() must be overwritten!!!
        Returns:
        idcode of first chemical structure column of the current row

      • getCoordinates

        public java.lang.String getCoordinates()
        Either getIDCode and this method or getMolecule() must be overwritten!!!
        Returns:
        idcoords of first chemical structure column of the current row

      • getMoleculeName

        public abstract java.lang.String getMoleculeName()
        Returns:
        name/id of (primary) chemical structure of the current row

      • setDescriptorHandlerFactory

        public void setDescriptorHandlerFactory​(DescriptorHandlerFactory factory)
        If a requested descriptor is not available in a particuar compound record, the parser can create one itself, provided its DescriptorHandlerFactory knows the descriptor name. The default DescriptorHandlerFactory is null, thus one needs to set one in order to allow the parser to create descriptors.
        Parameters:
        factory -

      • getDescriptorHandlerFactory

        public DescriptorHandlerFactory getDescriptorHandlerFactory()
        Returns:
        currently used DescriptorHandlerFactory

      • getFieldIndex

        public int getFieldIndex​(java.lang.String fieldName)
        Parameters:
        fieldName -
        Returns:
        index of the field with the given name, -1 if fieldName doesn't exist

      • getDescriptor

        public java.lang.Object getDescriptor​(java.lang.String shortName)
        If the file source contains encoded descriptors, then overwrite this method to save the calculation time.
        Parameters:
        shortName -
        Returns:
        descriptor as int[] or whatever is the descriptors binary format

      • getMolecule

        public StereoMolecule getMolecule()
        Either this method or getIDCode() and getCoordinates() must be overwritten!!!
        Returns:
        the structure of the records (primary) molecule or null