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## org.biojava.ontology.obo
Class OboFileParser

    java.lang.Object
      org.biojava.ontology.obo.OboFileParser

    public class OboFileParser

extends 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
`static class` | `OboFileParser.SOPair`

Field Summary
`protected int` | `bytesRead`
`protected SimpleDateFormat` | `dateFormat`
`protected static Map<Character,Character>` | `escapeChars`
`protected String` | `line`
`protected int` | `linenum`
`protected StringBuffer` | `tempBuffer`
`protected int` | `totalSize`
`protected static Map<Character,Character>` | `unescapeChars`

Constructor Summary
`OboFileParser()`

Method Summary
`void` | `addOboFileEventListener(OboFileEventListener listener)`
`static String` | `escape(String str, boolean escapespaces)`
`static int` | `findUnescaped(String str, char toChar)`
`static int` | `findUnescaped(String str, char toChar, int startIndex, int endIndex)`
`static int` | `findUnescaped(String str, char toChar, int startindex, int endindex, boolean honorQuotes)`
`protected Map<String,Object>[]` | `getDbxrefList(String line, int startoffset, int endoffset)`
`protected int` | `getNestedValue(org.biojava.ontology.obo.NestedValue nv, String str, int startIndex)`
`List<OboFileEventListener>` | `getOboFileEventListener()`
`protected StringBuffer` | `getTempBuffer()`
`static boolean` | `isEscapeStarter(char c)`
`static boolean` | `isQuote(char c)`
`void` | `parseOBO(BufferedReader oboFile)` parse an ontology file
`protected Map<String,Object>` | `parseXref(String line, int startoffset, int endoffset)`
`protected OboFileParser.SOPair` | `readQuotedString(String value, int startIndex, int stopIndex, char terminatingChar, boolean requireQuotes, boolean legalEndOfLine)`
`String` | `unescape(String str)`
`OboFileParser.SOPair` | `unescape(String str, char toChar, int startindex, boolean mustFindChar)`
`OboFileParser.SOPair` | `unescape(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 String line

### linenum

    protected int linenum

### totalSize

    protected int totalSize

### bytesRead

    protected int bytesRead

### tempBuffer

    protected StringBuffer tempBuffer

### dateFormat

    protected SimpleDateFormat dateFormat

### escapeChars

    protected static final Map<Character,Character> escapeChars

### unescapeChars

    protected static final Map<Character,Character> unescapeChars

Constructor Detail

### OboFileParser

    public OboFileParser()

Method Detail

### addOboFileEventListener

    public void addOboFileEventListener(OboFileEventListener listener)

### getOboFileEventListener

    public List<OboFileEventListener> getOboFileEventListener()

### parseOBO

    public void parseOBO(BufferedReader oboFile)
                  throws IOException,
                         ParseException

  parse an ontology file

  Parameters:
    `oboFile` -
  Throws:
    `IOException`
    `ParseException`

### getDbxrefList

    protected Map<String,Object>[] getDbxrefList(String line,
                                                 int startoffset,
                                                 int endoffset)
                                          throws ParseException

  Throws:
    `ParseException`

### parseXref

    protected Map<String,Object> parseXref(String line,
                                           int startoffset,
                                           int endoffset)
                                    throws ParseException

  Throws:
    `ParseException`

### escape

    public static String escape(String str,
                                boolean escapespaces)

### unescape

    public String unescape(String str)
                    throws ParseException

  Throws:
    `ParseException`

### unescape

    public OboFileParser.SOPair unescape(String str,
                                         char toChar,
                                         int startindex,
                                         boolean mustFindChar)
                                  throws ParseException

  Throws:
    `ParseException`

### unescape

    public OboFileParser.SOPair unescape(String str,
                                         char toChar,
                                         int startindex,
                                         int endindex,
                                         boolean mustFindChar)
                                  throws ParseException

  Throws:
    `ParseException`

### findUnescaped

    public static int findUnescaped(String str,
                                    char toChar)

### findUnescaped

    public static int findUnescaped(String str,
                                    char toChar,
                                    int startIndex,
                                    int endIndex)

### findUnescaped

    public static int findUnescaped(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 StringBuffer getTempBuffer()

### readQuotedString

    protected OboFileParser.SOPair readQuotedString(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,
                                 String str,
                                 int startIndex)
                          throws ParseException

  Throws:
    `ParseException`

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