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

Nested Classes

Modifier and Type	Class and Description
static class	OboFileParser.SOPair

Field Summary

Fields

Modifier and Type	Field and Description
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

Constructors

Constructor and Description
OboFileParser()

Method Summary

Modifier and Type	Method and Description
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