Package org.biojava.ontology.obo

Class OboFileParser

  • public class OboFileParser
extends java.lang.Object
    A class to parse the content of an OBO file. It delegates handling of the content to the OBOFileEventListener implementation. This file contains parts of the OBO-Edit file OBOParseEngine, (particularly the encoding and decoding part) http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup Thanks to the OboEdit developers for giving permission to release this in BioJava.
    Since:
    1.6
    Author:
    Andreas Prlic, John Day Richter

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      static class  OboFileParser.SOPair  

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int bytesRead  
      protected java.text.SimpleDateFormat dateFormat  
      protected static java.util.Map<java.lang.Character,​java.lang.Character> escapeChars  
      protected java.lang.String line  
      protected int linenum  
      protected java.lang.StringBuffer tempBuffer  
      protected int totalSize  
      protected static java.util.Map<java.lang.Character,​java.lang.Character> unescapeChars  

    • Constructor Summary

      Constructors 
      Constructor Description
      OboFileParser()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addOboFileEventListener​(OboFileEventListener listener)  
      static java.lang.String escape​(java.lang.String str, boolean escapespaces)  
      static int findUnescaped​(java.lang.String str, char toChar)  
      static int findUnescaped​(java.lang.String str, char toChar, int startIndex, int endIndex)  
      static int findUnescaped​(java.lang.String str, char toChar, int startindex, int endindex, boolean honorQuotes)  
      protected java.util.Map<java.lang.String,​java.lang.Object>[] getDbxrefList​(java.lang.String line, int startoffset, int endoffset)  
      protected int getNestedValue​(org.biojava.ontology.obo.NestedValue nv, java.lang.String str, int startIndex)  
      java.util.List<OboFileEventListener> getOboFileEventListener()  
      protected java.lang.StringBuffer getTempBuffer()  
      static boolean isEscapeStarter​(char c)  
      static boolean isQuote​(char c)  
      void parseOBO​(java.io.BufferedReader oboFile)
      parse an ontology file
      protected java.util.Map<java.lang.String,​java.lang.Object> parseXref​(java.lang.String line, int startoffset, int endoffset)  
      protected OboFileParser.SOPair readQuotedString​(java.lang.String value, int startIndex, int stopIndex, char terminatingChar, boolean requireQuotes, boolean legalEndOfLine)  
      java.lang.String unescape​(java.lang.String str)  
      OboFileParser.SOPair unescape​(java.lang.String str, char toChar, int startindex, boolean mustFindChar)  
      OboFileParser.SOPair unescape​(java.lang.String str, char toChar, int startindex, int endindex, boolean mustFindChar)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • line

        protected java.lang.String line

      • linenum

        protected int linenum

      • totalSize

        protected int totalSize

      • bytesRead

        protected int bytesRead

      • tempBuffer

        protected java.lang.StringBuffer tempBuffer

      • dateFormat

        protected java.text.SimpleDateFormat dateFormat

      • escapeChars

        protected static final java.util.Map<java.lang.Character,​java.lang.Character> escapeChars

      • unescapeChars

        protected static final java.util.Map<java.lang.Character,​java.lang.Character> unescapeChars

    • Constructor Detail

      • OboFileParser

        public OboFileParser()

    • Method Detail

      • parseOBO

        public void parseOBO​(java.io.BufferedReader oboFile)
              throws java.io.IOException,
                     ParseException
        parse an ontology file
        Parameters:
        oboFile -
        Throws:
        java.io.IOException
        ParseException

      • getDbxrefList

        protected java.util.Map<java.lang.String,​java.lang.Object>[] getDbxrefList​(java.lang.String line,
                                                                                 int startoffset,
                                                                                 int endoffset)
                                                                          throws ParseException
        Throws:
        ParseException

      • parseXref

        protected java.util.Map<java.lang.String,​java.lang.Object> parseXref​(java.lang.String line,
                                                                           int startoffset,
                                                                           int endoffset)
                                                                    throws ParseException
        Throws:
        ParseException

      • escape

        public static java.lang.String escape​(java.lang.String str,
                                      boolean escapespaces)

      • findUnescaped

        public static int findUnescaped​(java.lang.String str,
                                char toChar)

      • findUnescaped

        public static int findUnescaped​(java.lang.String str,
                                char toChar,
                                int startIndex,
                                int endIndex)

      • findUnescaped

        public static int findUnescaped​(java.lang.String str,
                                char toChar,
                                int startindex,
                                int endindex,
                                boolean honorQuotes)

      • isEscapeStarter

        public static boolean isEscapeStarter​(char c)

      • isQuote

        public static boolean isQuote​(char c)

      • getTempBuffer

        protected java.lang.StringBuffer getTempBuffer()

      • readQuotedString

        protected OboFileParser.SOPair readQuotedString​(java.lang.String value,
                                                int startIndex,
                                                int stopIndex,
                                                char terminatingChar,
                                                boolean requireQuotes,
                                                boolean legalEndOfLine)
                                         throws ParseException
        Throws:
        ParseException

      • getNestedValue

        protected int getNestedValue​(org.biojava.ontology.obo.NestedValue nv,
                             java.lang.String str,
                             int startIndex)
                      throws ParseException
        Throws:
        ParseException