Package chemaxon.marvin.io

Class MRecord

java.lang.Object
chemaxon.marvin.io.MRecord
@PublicApi public class MRecord extends Object
Record in a multi-molecule file.
Since:
Marvin 5.0, 04/06/2006

  • Field Details

    • F_MOL_MISSING

      public static final int F_MOL_MISSING
      Molecule (or reaction) is missing from the record. This record descriptor flag is set if the molecule part of the record contains only a registry number ("MIREG", "MEREG", "RIREG" or "REREG") in case of an RDfile.
      Since:
      Marvin 5.0.3, 03/20/2008
      See Also:

    • fileStartPosition

      protected long fileStartPosition

    • fileEndPosition

      protected long fileEndPosition

    • properties

      protected MPropertyContainer properties

  • Constructor Details

    • MRecord

      public MRecord()
      Default constructor.
      Since:
      Marvin 5.2

    • MRecord

      public MRecord(long start, long end, int lineno, String s, MPropertyContainer p, int[] lmap)
      Creates a record.
      Parameters:
      start - the start position in input file
      end - the end position in input file
      lineno - the line number at the starting point
      s - the record string
      p - the properties
      lmap - original line numbers

    • MRecord

      public MRecord(long start, long end, int lineno, String s, MPropertyContainer p, int[] lmap, int descflags)
      Creates a record.
      Parameters:
      start - the start position in input file
      end - the end position in input file
      lineno - the line number at the starting point
      s - the record string
      p - the properties
      lmap - original line numbers
      descflags - extra record descriptor flags

    • MRecord

      public MRecord(long start, long end, int lineno, String s, MPropertyContainer p, int[] lmap, int descflags, String moleculeName)
      Creates a record.
      Parameters:
      start - the start position in input file
      end - the end position in input file
      lineno - the line number at the starting point
      s - the record string
      p - the properties
      lmap - original line numbers
      descflags - extra record descriptor flags
      moleculeName - name of the molecule
      Since:
      Marvin 5.0.3, 03/20/2008

  • Method Details

    • getEncoding

      public String getEncoding()
      Gets the encoding.
      Returns:
      the encoding
      Since:
      Marvin 5.3

    • setMolString

      public void setMolString(String molstr)

    • getMolString

      public String getMolString()
      Gets the molecule string, with preprended header and appended footer if appropriate. This string can be imported to get a valid molecule.
      Returns:
      the molecule string
      Since:
      Marvin 5.3

    • setMolBytes

      public void setMolBytes(byte[] molBytes)
      Sets the molecule bytes. Used for binary formats, otherwise setMolString(java.lang.String) is called to set the mol string.
      Parameters:
      molBytes - the molecule bytes

    • getMolBytes

      public byte[] getMolBytes()
      Gets the molecule bytes, with preprended header and appended footer if appropriate. This byte array can be imported to get a valid molecule. Only used for binary formats, otherwise call getMolString().
      Returns:
      the molecule string
      Since:
      Marvin 5.4

    • getHeaderNewLineCount

      public int getHeaderNewLineCount()
      Gets the number of new lines in the molecule header part.
      Returns:
      the number of new lines in the molecule header part
      Since:
      Marvin 5.3

    • getFormat

      public String getFormat()
      Gets the full format string of the record. E.g. for a gzipped mrv it returns "gzip:mrv".
      Returns:
      the format of the record as a string.

    • getInputFormat

      public String getInputFormat()
      Gets the input format. This the format of the file. E.g for a gzipped mrv it returns "mrv"
      Returns:
      the input format
      Since:
      Marvin 5.3

    • getString

      public String getString()
      Gets the record text as string. Note that the returned string is not guaranteed to be a valid molecule file. Prepend the molecule file header and append the footer to get an importable file.
      Returns:
      the text
      See Also:

    • getPropertyContainer

      public MPropertyContainer getPropertyContainer()
      Gets the properties.
      Returns:
      the properties

    • getLineNumberMap

      public int[] getLineNumberMap()
      Gets the line number to original line number mapping.
      Returns:
      the mapping

    • getStartPosition

      public long getStartPosition()
      Gets the start position in the input file.
      Returns:
      the position

    • getEndPosition

      public long getEndPosition()
      Gets the end position in the input file.
      Returns:
      the position

    • getStartLineCount

      public int getStartLineCount()
      Gets the line number at the starting point.
      Returns:
      the line number

    • getEndLineCount

      public int getEndLineCount()
      Gets the line number at the ending point.
      Returns:
      the line number
      Since:
      Marvin 5.3

    • getFlags

      public int getFlags()
      Gets the record descriptor flags.
      Returns:
      the record descriptor flags
      Since:
      Marvin 5.0.3, 03/20/2008
      See Also:

    • getMoleculeName

      public String getMoleculeName()
      Returns the name of the molecule in the record.
      Returns:
      the name or an empty string if it's not specified
      Since:
      Marvin 6.3