Class OboParser


  • public class OboParser
    extends java.lang.Object
    Parses an OBO file.
    Since:
    1.7

    Example

     OboParser parser = new OboParser();
                    InputStream inStream = this.getClass().getResourceAsStream("/files/ontology/biosapiens.obo");
                    
                    BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );
                    try {
                            Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");
                                                    
                            Set keys = ontology.getTerms();
                            Iterator iter = keys.iterator();
                            while (iter.hasNext()){
                                    System.out.println(iter.next());
                            }
                            
                    } catch (Exception e){
                            e.printStackTrace();
                    }
     
    Author:
    Andreas Prlic
    • Constructor Summary

      Constructors 
      Constructor Description
      OboParser()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Ontology parseOBO​(java.io.BufferedReader oboFile, java.lang.String ontoName, java.lang.String ontoDescription)
      Parse a OBO file and return its content as a BioJava Ontology object
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • OboParser

        public OboParser()
    • Method Detail

      • parseOBO

        public Ontology parseOBO​(java.io.BufferedReader oboFile,
                                 java.lang.String ontoName,
                                 java.lang.String ontoDescription)
                          throws ParseException,
                                 java.io.IOException
        Parse a OBO file and return its content as a BioJava Ontology object
        Parameters:
        oboFile - the file to be parsed
        ontoName -
        ontoDescription -
        Returns:
        the ontology represented as a BioJava ontology file
        Throws:
        ParseException
        java.io.IOException