owltools.idmap
Class AbstractMappingParser
java.lang.Object
owltools.idmap.AbstractMappingParser
- Direct Known Subclasses:
- IDMappingPIRParser, UniProtIDMapParser
public abstract class AbstractMappingParser
- extends Object
Parses the IDMapping file available here:
ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz
- Author:
- cjm
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
reader
protected BufferedReader reader
currentRow
protected String currentRow
currentCols
protected String[] currentCols
expectedNumCols
protected int expectedNumCols
lineNumber
protected int lineNumber
AbstractMappingParser
public AbstractMappingParser()
parse
public void parse(String file)
throws IOException,
URISyntaxException
- Parameters:
file
- is the location of the mapping file. The location
could be http url, absolute path and uri.
- Throws:
IOException
URISyntaxException
parse
public abstract void parse(Reader reader)
throws IOException
- Throws:
IOException
parse
public void parse(File file)
throws IOException
- Throws:
IOException
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