public class OboFileParser
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
OboFileParser.SOPair |
Modifier and Type | Field and 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 and Description |
---|
OboFileParser() |
Modifier and Type | Method and 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) |
protected java.lang.String line
protected int linenum
protected int totalSize
protected int bytesRead
protected java.lang.StringBuffer tempBuffer
protected java.text.SimpleDateFormat dateFormat
protected static final java.util.Map<java.lang.Character,java.lang.Character> escapeChars
protected static final java.util.Map<java.lang.Character,java.lang.Character> unescapeChars
public void addOboFileEventListener(OboFileEventListener listener)
public java.util.List<OboFileEventListener> getOboFileEventListener()
public void parseOBO(java.io.BufferedReader oboFile) throws java.io.IOException, ParseException
oboFile
- java.io.IOException
ParseException
protected java.util.Map<java.lang.String,java.lang.Object>[] getDbxrefList(java.lang.String line, int startoffset, int endoffset) throws ParseException
ParseException
protected java.util.Map<java.lang.String,java.lang.Object> parseXref(java.lang.String line, int startoffset, int endoffset) throws ParseException
ParseException
public static java.lang.String escape(java.lang.String str, boolean escapespaces)
public java.lang.String unescape(java.lang.String str) throws ParseException
ParseException
public OboFileParser.SOPair unescape(java.lang.String str, char toChar, int startindex, boolean mustFindChar) throws ParseException
ParseException
public OboFileParser.SOPair unescape(java.lang.String str, char toChar, int startindex, int endindex, boolean mustFindChar) throws ParseException
ParseException
public static int findUnescaped(java.lang.String str, char toChar)
public static int findUnescaped(java.lang.String str, char toChar, int startIndex, int endIndex)
public static int findUnescaped(java.lang.String str, char toChar, int startindex, int endindex, boolean honorQuotes)
public static boolean isEscapeStarter(char c)
public static boolean isQuote(char c)
protected java.lang.StringBuffer getTempBuffer()
protected OboFileParser.SOPair readQuotedString(java.lang.String value, int startIndex, int stopIndex, char terminatingChar, boolean requireQuotes, boolean legalEndOfLine) throws ParseException
ParseException
protected int getNestedValue(org.biojava.ontology.obo.NestedValue nv, java.lang.String str, int startIndex) throws ParseException
ParseException