Index (Sugar Removal Utility 1.6.0.0 API)

C D E G H I M N P R S V W
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C

close() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
compareVersions(String, String) - Static method in class de.unijena.cheminf.deglycosylation.Main: Compares two version strings of the form "x.y.z" of variable length position by position after splitting at each "." and parsing to integers.

D

de.unijena.cheminf.deglycosylation - package de.unijena.cheminf.deglycosylation
de.unijena.cheminf.deglycosylation.tools - package de.unijena.cheminf.deglycosylation.tools
DEFAULT_SMILES_COLUMN_POSITION - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Default SMILES column position for files with only one column.
detectFormat(File) - Static method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Checking the first few lines of the SMILES file for parsable SMILES codes and saving the determined separator character and SMILES code and ID column positions.
detectFormat(List<String>) - Static method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Checking the first few lines of a SMILES file for parsable SMILES codes and saving the determined separator character and SMILES code and ID column positions.
DynamicSMILESFileFormat - Class in de.unijena.cheminf.deglycosylation.tools: Data wrapper for defining the outline of a SMILES file or CSV file containing SMILES codes.
DynamicSMILESFileFormat(boolean) - Constructor for class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: 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, Character, int, int) - Constructor for class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: 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.
DynamicSMILESFileReader - Class in de.unijena.cheminf.deglycosylation.tools: File reader for different kinds of files with a SMILES code column.
DynamicSMILESFileReader(File, DynamicSMILESFileFormat) - Constructor for class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Constructs a new DynamicSMILESFileReader that can read molecules from a given file.
DynamicSMILESFileReader(InputStream, DynamicSMILESFileFormat) - Constructor for class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Constructs a new DynamicSMILESFileReader that can read molecules from a given a InputStream.
DynamicSMILESFileReader(Reader, DynamicSMILESFileFormat) - Constructor for class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Constructs a new DynamicSMILESFileReader that can read molecules from a given a Reader.

E

execute() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Executes the application.

G

getFileExtension(String) - Static method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Returns the extension of the file represented by the given pathname.
getFormat() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
getIDColumnPosition() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Position of the ID/name column in the file.
getSeparatorChar() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Character that separates the columns.
getSkippedLinesCounter() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Returns the number of lines that were skipped (empty or erroneous SMILES codes etc.) in the last file import of this instance (reset at each new import), headline not counted.
getSMILESCodeColumnPosition() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Position of the SMILES column in the file.

H

hasHeaderLine() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Whether the first line in the file is a header or contains a valid SMILES code as well.
hasIDColumn() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Whether the file has an additional column containing names/IDs of the structures.
hasNext() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader

I

isLegalTypeOfMoietiesToRemove(int) - Static method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Checks whether the given integer number is mapped to a type of moieties to remove, i.e.

M

main(String[]) - Static method in class de.unijena.cheminf.deglycosylation.Main: Instantiates the SugarRemovalUtilityCmdApplication class and calls its execute() method.
Main - Class in de.unijena.cheminf.deglycosylation: Main entry point for the Sugar Removal Utility command-line application.
Main() - Constructor for class de.unijena.cheminf.deglycosylation.Main
MAXIMUM_LINE_NUMBER_TO_CHECK_IN_SMILES_FILES - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Maximum number of lines starting from the first one to check for valid SMILES strings in a SMILES file when trying to determine the SMILES code column and separator.

N

next() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader

P

PARSABLE_SMILES_EXCEPTIONS - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Strings that can be parsed by CDK SmilesParser as SMILES codes but should be ignored when detecting the file structure, e.g.
PLACEHOLDER_ID_COLUMN_POSITION - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Placeholder ID column position for files without an ID column.
PLACEHOLDER_SEPARATOR_CHAR - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat: Placeholder separator char for files that have only one column.
POSSIBLE_SMILES_FILE_SEPARATORS - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Possible SMILES file separators used to separate SMILES code from ID.

R

readToSet() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader: Reads SMILES file according to the given format.

S

setReader(InputStream) - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
setReader(Reader) - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
setSMILESFileFormat(DynamicSMILESFileFormat) - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
SugarRemovalUtilityCmdApplication - Class in de.unijena.cheminf.deglycosylation: Controller of the Sugar Removal/Detection Utility command-line application.
SugarRemovalUtilityCmdApplication(String[]) - Constructor for class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Constructor that parses the command-line arguments and instantiates this class and the SugarRemovalUtility with the given settings.

V

VERSION - Static variable in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Version string of this class to print out if -v --version is queried from the command-line.

W

wasHelpOrVersionQueried() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication: Returns true if the -h --help or -v --version options were used at the command-line.

C D E G H I M N P R S V W
All Classes and Interfaces|All Packages|Constant Field Values