public class GpadParser extends Object
Modifier and Type | Field and Description |
---|---|
protected String |
commentPrefix |
protected String[] |
currentCols |
protected String |
currentRow |
protected int |
lineNumber |
protected double |
version |
Constructor and Description |
---|
GpadParser() |
protected double version
protected String currentRow
protected String[] currentCols
protected int lineNumber
protected final String commentPrefix
public String getColumn(owltools.gaf.parser.GpadParser.GpadColumns col)
public String getDB()
public String getDB_Object_ID()
public String getQualifier()
public String getGO_ID()
public String getDB_Reference()
public String getEvidence_Code()
public String getWith()
public String getInteracting_Taxon_ID()
public String getDate()
public String getAssigned_by()
public String getAnnotation_Extension()
public String getAnnotation_Properties()
protected boolean isFormatDeclaration(String line)
protected boolean isHeaderMetaData(String line)
protected double parseVersion(String line)
protected int getExpectedColumnCount()
public boolean next() throws IOException
IOException
protected owltools.gaf.parser.AbstractAnnotationFileParser.ReadState validateLine(String[] currentCols)
currentCols
- protected void handleHeaderMetaData(String line)
line
- protected void fireParsingError(String message)
protected void fireParsingWarning(String message)
public void createReader(InputStream inputStream)
public void setReader(BufferedReader reader)
public String getCurrentRow()
public int getLineNumber()
public void addParserListener(ParserListener listener)
public void remoteParserListener(ParserListener listener)
public void addCommentListener(CommentListener listener)
public void removeCommentListener(CommentListener listener)
protected void addViolation(Object violation)
public void close() throws IOException
close
in interface Closeable
close
in interface AutoCloseable
IOException
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