Index
All Classes and Interfaces|All Packages|Constant Field Values
C
- close() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
- compareVersions(String, String) - Static method in class de.unijena.cheminf.deglycosylation.Main
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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
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Default SMILES column position for files with only one column.
- detectFormat(File) - Static method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
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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
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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
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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
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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
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Constructs a new DynamicSMILESFileReader that can read molecules from a given file.
- DynamicSMILESFileReader(InputStream, DynamicSMILESFileFormat) - Constructor for class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
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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
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Constructs a new DynamicSMILESFileReader that can read molecules from a given a Reader.
E
- execute() - Method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication
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Executes the application.
G
- getFileExtension(String) - Static method in class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication
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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
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Position of the ID/name column in the file.
- getSeparatorChar() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat
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Character that separates the columns.
- getSkippedLinesCounter() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
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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
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Position of the SMILES column in the file.
H
- hasHeaderLine() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat
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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
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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
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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
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Instantiates the SugarRemovalUtilityCmdApplication class and calls its execute() method.
- Main - Class in de.unijena.cheminf.deglycosylation
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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
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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
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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
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Placeholder ID column position for files without an ID column.
- PLACEHOLDER_SEPARATOR_CHAR - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileFormat
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Placeholder separator char for files that have only one column.
- POSSIBLE_SMILES_FILE_SEPARATORS - Static variable in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
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Possible SMILES file separators used to separate SMILES code from ID.
R
- readToSet() - Method in class de.unijena.cheminf.deglycosylation.tools.DynamicSMILESFileReader
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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
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Controller of the Sugar Removal/Detection Utility command-line application.
- SugarRemovalUtilityCmdApplication(String[]) - Constructor for class de.unijena.cheminf.deglycosylation.SugarRemovalUtilityCmdApplication
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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
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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
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Returns true if the -h --help or -v --version options were used at the command-line.
All Classes and Interfaces|All Packages|Constant Field Values