org.biojava.ontology.obo
Class OboFileParser
java.lang.Object
org.biojava.ontology.obo.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
Field Summary |
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
|
Method Summary |
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 |
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
OboFileParser
public OboFileParser()
addOboFileEventListener
public void addOboFileEventListener(OboFileEventListener listener)
getOboFileEventListener
public java.util.List<OboFileEventListener> getOboFileEventListener()
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)
unescape
public java.lang.String unescape(java.lang.String str)
throws ParseException
- Throws:
ParseException
unescape
public OboFileParser.SOPair unescape(java.lang.String str,
char toChar,
int startindex,
boolean mustFindChar)
throws ParseException
- Throws:
ParseException
unescape
public OboFileParser.SOPair unescape(java.lang.String str,
char toChar,
int startindex,
int endindex,
boolean mustFindChar)
throws ParseException
- Throws:
ParseException
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