owltools.gaf.parser
Class GpiParser
java.lang.Object
owltools.gaf.parser.GpiParser
- All Implemented Interfaces:
- Closeable
public class GpiParser
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
version
protected double version
currentRow
protected String currentRow
currentCols
protected String[] currentCols
lineNumber
protected int lineNumber
GpiParser
public GpiParser()
getColumn
public String getColumn(owltools.gaf.parser.GpiParser.GpiColumns col)
getDB_Object_ID
public String getDB_Object_ID()
getDB_Object_Symbol
public String getDB_Object_Symbol()
getDB_Object_Name
public String getDB_Object_Name()
getDB_Object_Synonym
public String getDB_Object_Synonym()
getDB_Object_Type
public String getDB_Object_Type()
getTaxon
public String getTaxon()
getParent_Object_ID
public String getParent_Object_ID()
getDB_Xref
public String getDB_Xref()
getGene_Product_Properties
public String getGene_Product_Properties()
getNamespace
public String getNamespace()
handleComment
protected void handleComment(String line)
isFormatDeclaration
protected boolean isFormatDeclaration(String line)
parseVersion
protected double parseVersion(String line)
getExpectedColumnCount
protected int getExpectedColumnCount()
next
public boolean next()
throws IOException
- Try to parse a next line, may skip lines until a line is parsed successfully or the file ends.
- Returns:
- true, if there is a next line.
- Throws:
IOException
validateLine
protected owltools.gaf.parser.AbstractAnnotationFileParser.ReadState validateLine(String[] currentCols)
- Parameters:
currentCols
-
- Returns:
- readstate
fireParsingError
protected void fireParsingError(String message)
fireParsingWarning
protected void fireParsingWarning(String message)
createReader
public void createReader(InputStream inputStream)
setReader
public void setReader(BufferedReader reader)
getCurrentRow
public String getCurrentRow()
getLineNumber
public int getLineNumber()
addParserListener
public void addParserListener(ParserListener listener)
remoteParserListener
public void remoteParserListener(ParserListener listener)
addCommentListener
public void addCommentListener(CommentListener listener)
removeCommentListener
public void removeCommentListener(CommentListener listener)
addViolation
protected void addViolation(Object violation)
getViolations
public List<Object> getViolations()
close
public void close()
throws IOException
- Specified by:
close
in interface Closeable
- Throws:
IOException
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