<commit_before>package fi.csc.microarray.description;

import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;

import org.apache.log4j.Logger;

import fi.csc.microarray.description.SADLDescription.Input;
import fi.csc.microarray.description.SADLDescription.Name;
import fi.csc.microarray.description.SADLDescription.Output;
import fi.csc.microarray.description.SADLDescription.Parameter;
import fi.csc.microarray.description.SADLSyntax.InputType;
import fi.csc.microarray.description.SADLSyntax.ParameterType;
import fi.csc.microarray.description.SADLTokeniser.TokenType;
import fi.csc.microarray.description.vvsadl.CompatibilityVVSADLParser;
import fi.csc.microarray.exception.MicroarrayException;



/**
 * <p>Parses SADL analysis descriptions. SADL stands for  
 * Simple Analysis Description Language. It is used to manage analysis 
 * description data inside the Chipster system. Parsing is event based (cf. SAX).</p>
 *  
 * @see fi.csc.microarray.description.SADLSyntax
 * 
 * @author <NAME>
 */
public class SADLParser {
		
	/**
	 * Logger for this class (debugging).
	 */
	private static final Logger logger = Logger.getLogger(SADLParser.class);

	
	/**
	 * Parse failure caused by illegal input data (bad SADL).
	 */
	public static class ParseException extends MicroarrayException {
		public ParseException(String msg) {
			super(msg);
		}
		
		public ParseException(String msg, String filename) {
			super(msg + (filename != null ? (" (in " + filename + ")") : ""));
		}
	}
	
	private String unitName;
	private HashMap<String, InputType> inputTypeMap = new HashMap<String, InputType>();
	
	public static String generateOperationIdentifier(String category, String name) {
		return "\"" + category + "\"/\"" + name + "\"";
	}
	
	public SADLParser() {
		this(null);<commit_msg>Add @SuppressWarnings("serial")<commit_after>package fi.csc.microarray.description;

import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;

import org.apache.log4j.Logger;

import fi.csc.microarray.description.SADLDescription.Input;
import fi.csc.microarray.description.SADLDescription.Name;
import fi.csc.microarray.description.SADLDescription.Output;
import fi.csc.microarray.description.SADLDescription.Parameter;
import fi.csc.microarray.description.SADLSyntax.InputType;
import fi.csc.microarray.description.SADLSyntax.ParameterType;
import fi.csc.microarray.description.SADLTokeniser.TokenType;
import fi.csc.microarray.description.vvsadl.CompatibilityVVSADLParser;
import fi.csc.microarray.exception.MicroarrayException;



/**
 * <p>Parses SADL analysis descriptions. SADL stands for  
 * Simple Analysis Description Language. It is used to manage analysis 
 * description data inside the Chipster system. Parsing is event based (cf. SAX).</p>
 *  
 * @see fi.csc.microarray.description.SADLSyntax
 * 
 * @author <NAME>
 */
public class SADLParser {
		
	/**
	 * Logger for this class (debugging).
	 */
	private static final Logger logger = Logger.getLogger(SADLParser.class);

	
	/**
	 * Parse failure caused by illegal input data (bad SADL).
	 */
	@SuppressWarnings("serial")
	public static class ParseException extends MicroarrayException {
		public ParseException(String msg) {
			super(msg);
		}
		
		public ParseException(String msg, String filename) {
			super(msg + (filename != null ? (" (in " + filename + ")") : ""));
		}
	}
	
	private String unitName;
	private HashMap<String, InputType> inputTypeMap = new HashMap<String, InputType>();
	
	public static String generateOperationIdentifier(String category, String name) {
		return "\"" + category + "\"/\"" + name + "\"";
	}
	
	public SADLParser() {
		this(null);
{'fraction_non_alphanumeric': 0.1162981162981163, 'fraction_numerical': 0.000546000546000546, 'mean_word_length': 4.654320987654321, 'pattern_counts': {'":': 0, '<': 13, '<?xml version=': 0, '>': 13, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6539019', 'n_tokens_mistral': 1203, 'n_tokens_neox': 1120, 'n_words': 255}