Package de.unijena.cheminf.deglycosylation.tools

Class DynamicSMILESFileFormat

java.lang.Object
de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat
public class DynamicSMILESFileFormat extends Object
Data wrapper for defining the outline of a SMILES file or CSV file containing SMILES codes.
Version:
1.0.0.0
Author:
Jonas Schaub

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    DEFAULT_SMILES_COLUMN_POSITION
    Default SMILES column position for files with only one column.
    static final int
    PLACEHOLDER_ID_COLUMN_POSITION
    Placeholder ID column position for files without an ID column.
    static final Character
    PLACEHOLDER_SEPARATOR_CHAR
    Placeholder separator char for files that have only one column.

  • Constructor Summary

    Constructors
    Constructor
    Description
    DynamicSMILESFileFormat(boolean aHasHeaderLine)
    Defines the format as a file that has only one column of SMILES codes and nothing else, so no ID column and no separator character.
    DynamicSMILESFileFormat(boolean aHasHeaderLine, Character aSeparatorChar, int aSMILESCodeColumnPosition, int anIDColumnPosition)
    Defines the format as a file that has at least two columns, defines the character that separates the columns, the position of the SMILES code column and the ID/name column, and whether the first line in the file is a header or contains a valid SMILES code as well.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    getIDColumnPosition()
    Position of the ID/name column in the file.
    Character
    getSeparatorChar()
    Character that separates the columns.
    int
    getSMILESCodeColumnPosition()
    Position of the SMILES column in the file.
    boolean
    hasHeaderLine()
    Whether the first line in the file is a header or contains a valid SMILES code as well.
    boolean
    hasIDColumn()
    Whether the file has an additional column containing names/IDs of the structures.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • PLACEHOLDER_SEPARATOR_CHAR

      public static final Character PLACEHOLDER_SEPARATOR_CHAR
      Placeholder separator char for files that have only one column.

    • PLACEHOLDER_ID_COLUMN_POSITION

      public static final int PLACEHOLDER_ID_COLUMN_POSITION
      Placeholder ID column position for files without an ID column.
      See Also:

    • DEFAULT_SMILES_COLUMN_POSITION

      public static final int DEFAULT_SMILES_COLUMN_POSITION
      Default SMILES column position for files with only one column.
      See Also:

  • Constructor Details

    • DynamicSMILESFileFormat

      public DynamicSMILESFileFormat(boolean aHasHeaderLine)
      Defines the format as a file that has only one column of SMILES codes and nothing else, so no ID column and no separator character. All other fields will be set to their placeholder values.
      Parameters:
      aHasHeaderLine - whether the first line in the file is a header or contains a valid SMILES code as well

    • DynamicSMILESFileFormat

      public DynamicSMILESFileFormat(boolean aHasHeaderLine, Character aSeparatorChar, int aSMILESCodeColumnPosition, int anIDColumnPosition)
      Defines the format as a file that has at least two columns, defines the character that separates the columns, the position of the SMILES code column and the ID/name column, and whether the first line in the file is a header or contains a valid SMILES code as well.
      No parameter checks to keep this data container flexible and be able to use the placeholder values here as well, so be careful!
      Parameters:
      aHasHeaderLine - whether the first line in the file is a header or contains a valid SMILES code as well
      aSeparatorChar - character that separates the columns
      aSMILESCodeColumnPosition - position of the SMILES code column
      anIDColumnPosition - position of the ID/name column

  • Method Details

    • hasHeaderLine

      public boolean hasHeaderLine()
      Whether the first line in the file is a header or contains a valid SMILES code as well.
      Returns:
      whether the first line of the file should be parsed as well or skipped

    • getSeparatorChar

      public Character getSeparatorChar()
      Character that separates the columns. If the file has only one column, this field will be set to its placeholder value (check whether the file has an ID/name column).
      Returns:
      character separating the columns

    • getSMILESCodeColumnPosition

      public int getSMILESCodeColumnPosition()
      Position of the SMILES column in the file.
      Returns:
      position of SMILES column

    • hasIDColumn

      public boolean hasIDColumn()
      Whether the file has an additional column containing names/IDs of the structures. If false, it can be assumed that the files has only one column, the SMILES column. The separator character and the ID column position will be set to their placeholder values.
      Returns:
      whether the file has an additional column containing names/IDs of the structures

    • getIDColumnPosition

      public int getIDColumnPosition()
      Position of the ID/name column in the file. If the file has only one column, this field will be set to its placeholder value (check whether the file has an ID/name column).
      Returns:
      position of ID/name column