public class OboFileParser
extends java.lang.Object
Modifier and Type | Class | Description |
---|---|---|
static class |
OboFileParser.SOPair |
Modifier and Type | Field | 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 | Description |
---|---|
OboFileParser() |
Modifier and Type | Method | 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.nbio.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
oboFile
- java.io.IOException
java.io.IOException
protected java.util.Map<java.lang.String,java.lang.Object>[] getDbxrefList(java.lang.String line, int startoffset, int endoffset) throws java.io.IOException
java.io.IOException
protected java.util.Map<java.lang.String,java.lang.Object> parseXref(java.lang.String line, int startoffset, int endoffset) throws java.io.IOException
java.io.IOException
public static java.lang.String escape(java.lang.String str, boolean escapespaces)
public java.lang.String unescape(java.lang.String str) throws java.io.IOException
java.io.IOException
public OboFileParser.SOPair unescape(java.lang.String str, char toChar, int startindex, boolean mustFindChar) throws java.io.IOException
java.io.IOException
public OboFileParser.SOPair unescape(java.lang.String str, char toChar, int startindex, int endindex, boolean mustFindChar) throws java.io.IOException
java.io.IOException
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 java.io.IOException
java.io.IOException
protected int getNestedValue(org.biojava.nbio.ontology.obo.NestedValue nv, java.lang.String str, int startIndex) throws java.io.IOException
java.io.IOException