owltools.gaf.parser
Class GpadParser
java.lang.Object
owltools.gaf.parser.GpadParser
- All Implemented Interfaces:
- Closeable
public class GpadParser
- 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
GpadParser
public GpadParser()
getColumn
public String getColumn(owltools.gaf.parser.GpadParser.GpadColumns col)
getDB
public String getDB()
getDB_Object_ID
public String getDB_Object_ID()
getQualifier
public String getQualifier()
getGO_ID
public String getGO_ID()
getDB_Reference
public String getDB_Reference()
getEvidence_Code
public String getEvidence_Code()
getWith
public String getWith()
getInteracting_Taxon_ID
public String getInteracting_Taxon_ID()
getDate
public String getDate()
getAssigned_by
public String getAssigned_by()
getAnnotation_Extension
public String getAnnotation_Extension()
getAnnotation_Properties
public String getAnnotation_Properties()
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
handleComment
protected void handleComment(String line)
- Parameters:
line
-
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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