org.biojava.nbio.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

Description

static class

OboFileParser.SOPair
Field Summary

Fields

Modifier and Type

Field

Description

protected int

bytesRead

protected SimpleDateFormat

dateFormat

protected static final Map<Character,Character>

escapeChars

protected String

line

protected int

linenum

protected StringBuffer

tempBuffer

protected int

totalSize

protected static final Map<Character,Character>

unescapeChars
Constructor Summary

Constructors

Constructor

Description

OboFileParser()
Method Summary

Modifier and Type

Method

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.nbio.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 Details
- 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 Details
- OboFileParser
  
  public OboFileParser()
Method Details
- addOboFileEventListener
  
  public void addOboFileEventListener(OboFileEventListener listener)
- getOboFileEventListener
  
  public List<OboFileEventListener> getOboFileEventListener()
- parseOBO
  
  public void parseOBO(BufferedReader oboFile) throws IOException
  
  parse an ontology file
  
  Parameters:
  
  oboFile -
  
  Throws:
  
  IOException
  
  IOException
- getDbxrefList
  
  protected Map<String,Object>[] getDbxrefList(String line, int startoffset, int endoffset) throws IOException
  
  Throws:
  
  IOException
- parseXref
  
  protected Map<String,Object> parseXref(String line, int startoffset, int endoffset) throws IOException
  
  Throws:
  
  IOException
- escape
  
  public static String escape(String str, boolean escapespaces)
- unescape
  
  public String unescape(String str) throws IOException
  
  Throws:
  
  IOException
- unescape
  
  public OboFileParser.SOPair unescape(String str, char toChar, int startindex, boolean mustFindChar) throws IOException
  
  Throws:
  
  IOException
- unescape
  
  public OboFileParser.SOPair unescape(String str, char toChar, int startindex, int endindex, boolean mustFindChar) throws IOException
  
  Throws:
  
  IOException
- 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 IOException
  
  Throws:
  
  IOException
- getNestedValue
  
  protected int getNestedValue(org.biojava.nbio.ontology.obo.NestedValue nv, String str, int startIndex) throws IOException
  
  Throws:
  
  IOException

Class OboFileParser

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

line

linenum

totalSize

bytesRead

tempBuffer

dateFormat

escapeChars

unescapeChars

Constructor Details

OboFileParser

Method Details

addOboFileEventListener

getOboFileEventListener

parseOBO

getDbxrefList

parseXref

escape

unescape

unescape

unescape

findUnescaped

findUnescaped

findUnescaped

isEscapeStarter

isQuote

getTempBuffer

readQuotedString

getNestedValue