/**
 * 
 */
package oboannotator.ontology;

import java.util.regex.Matcher;
import java.util.regex.Pattern;


/**
 * @author ahmedabdeenhamed
 *
 */
public class OntoUtil {
	
	private static Pattern quotedTextPattern = Pattern.compile("\\.owl$", Pattern.CASE_INSENSITIVE );
	public static final String OBO = "OBO";
	public static final String OWL = "OWL";
	public static final String NOT_SUPPORTED = "NOT_SUPPORTED";
	
	public static String extractAnnotationNameFromURI(String uri){
		int index = uri.indexOf('#');
		return uri.substring(index+1);
	}

	public static String extractSynonymFromOwlComment(String owlComment){
		String synonym = null;
		
		//int length = owlComment.length();
		
		String cleanString = cleanupAnnotationFromCarretString(owlComment);
		//System.out.println("Matched Result is 1: "  + cleanString);
		if(!cleanString.contains("synonym")){
			return synonym;
		}
		//System.out.println("Matched Result is 2: "  + cleanString);
		int index = cleanString.indexOf(":");
		if(index>0){
			synonym = cleanString.substring(cleanString.indexOf("synonym"));
			synonym = synonym.substring(synonym.indexOf(':')+1);
			//System.out.println("Extacted synonym:" + synonym.trim());
			return synonym.trim();
		}		
		return synonym;
	}
	
	public static String cleanupAnnotationFromCarretString(String annotation){
		String cleanString = null;
		if(annotation.contains("^^string")){
			cleanString = annotation.replace("^^string", "");
			return cleanString.trim();
		}
		//System.out.println("Matched Result is: "  + cleanString);
		return annotation;
	}
	
	public static String extractTextFromQuotedText(String text){
		String matchedResult = null;
		if (text.contains("\"")){
			matchedResult = text.replace("\"",	"");
			//System.out.println("Matched Result is: "  + matchedResult);
			return matchedResult.trim();
			
		}
		return text;
	}
	
	public static String[] tokenizeOwlTerm(String term){
		String[] listOfTokens = null;
		listOfTokens = term.split("_");	
		return listOfTokens;
	}
	
	public static String oboOrOwl(String ontologyUri){
		Pattern owlPattern = Pattern.compile("\\.owl$", Pattern.CASE_INSENSITIVE);
		Pattern oboPattern = Pattern.compile("\\.obo$", Pattern.CASE_INSENSITIVE);
		Matcher matchOwl = owlPattern.matcher(ontologyUri);
		Matcher matchObo = oboPattern.matcher(ontologyUri);
		if(matchOwl.find()){
			//System.out.println("OWL");
			return OWL;
		}
		if(matchObo.find()){
			//System.out.println("OBO");
			return OBO;
		}
		//System.out.println("NOT_SUPPORTED");
		return NOT_SUPPORTED;
	}
	
	
	/**
	 * @param args
	 */
	public static void main(String[] args) {
		// TODO Auto-generated method stub
		//System.out.println("CURRENT ANNOTATION: " + extractAnnotationNameFromURI("http://www.geneontology.org/go#def"));
		//System.out.println("CURRENT ANNOTATION: " + extractAnnotationNameFromURI("http://www.geneontology.org/go#synonym"));
//		System.out.println("CURRENT ANNOTATION: " + extractAnnotationFromURI("http://www.geneontology.org/go#xdef"));
//		System.out.println("CURRENT ANNOTATION: " + extractAnnotationFromURI("http://www.geneontology.org/go#namespace"));
//		System.out.println("CURRENT ANNOTATION: " + extractAnnotationFromURI("http://www.geneontology.org/go#label"));
		
		//extractSynonymFromOwlComment("defprov: Bruker website synonym: Bruker Efficient Sample Transfer NMR\"^^string");
		//extractTextFromQuotedText("\"defprov: Bruker website synonym: Bruker Efficient Sample Transfer NMR\"^^string");
		//extractSynonymFromOwlComment("tempdef: An improved water-suppression technique called WET (water suppression enhanced through T1 effects), developed from a Bloch equation analysis of the longitudinal magnetization over the T1 and B1 ranges of interest, achieves T1- and B1-insensitive suppression with four RF pulses, each having a numerically optimized flip angle. Once flip angles have been optimized for a given sequence, time-consuming flip-angle adjustments during clinical examinations are eliminated. defprov: Daniel Schober synonym: WET");
		//		String[] list = tokenizeOwlTerm("Ahmed_abdeen_hamed_is_married_to_lindsay_and_has_laila");
		//		for(String token: list){
		//			System.out.print(token + " ");
		//			
		//		}
		
		String ontoType = oboOrOwl("https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl");
		ontoType = oboOrOwl("http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/worm_phenotype.obo");
		ontoType = oboOrOwl("http://obi.svn.sourceforge.net/svnroot/obi/tags/releases/2008-06-27/merged/OBI.owl");
		ontoType = oboOrOwl("");
		
		
		
		
	}
}