public class GpiParser 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 |
---|
GpiParser() |
protected double version
protected String currentRow
protected String[] currentCols
protected int lineNumber
protected final String commentPrefix
public String getColumn(owltools.gaf.parser.GpiParser.GpiColumns col)
public String getDB_Object_ID()
public String getDB_Object_Symbol()
public String getDB_Object_Name()
public String getDB_Object_Synonym()
public String getDB_Object_Type()
public String getTaxon()
public String getParent_Object_ID()
public String getDB_Xref()
public String getGene_Product_Properties()
public String getNamespace()
protected void handleHeaderMetaData(String line)
protected boolean isHeaderMetaData(String line)
protected boolean isFormatDeclaration(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 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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