apollo.util
Class OBOParser

java.lang.Object
  apollo.util.OBOParser

public class OBOParser
extends java.lang.Object

This class will parse OBO files and generate indexes on different identifiers (e.g. id, name, etc)

Author:

elee

Constructor Summary

OBOParser(java.util.Collection<java.lang.String> fnames)
Build an OBOParser from a collection of filenames (defaults to non-case sensitive)

OBOParser(java.util.Collection<java.lang.String> fnames, boolean isCaseSensitive)
Build an OBOParser from a collection of filenames and a flag for whether the indexing should be case sensitive

OBOParser(java.lang.String fname)
Build an OBOParser from a filename (defaults to non-case sensitive)

OBOParser(java.lang.String fname, boolean isCaseSensitive)
Build an OBOParser from a filename and a flag for whether the indexing should be case sensitive

Method Summary

org.obo.datamodel.IdentifiedObject	getTermById(java.lang.String id) Get a term IdentifiedObject by ID
Pair<org.obo.datamodel.IdentifiedObject,java.lang.String>	getTermByName(java.lang.String name) Get a term IdentifiedObject by name
boolean	hasTermWithId(java.lang.String id) Check to see if a term with the given ID exists
boolean	hasTermWithName(java.lang.String name) Check to see if a term with the given name exists

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OBOParser

public OBOParser(java.lang.String fname)
          throws java.io.IOException,
                 org.obo.dataadapter.OBOParseException

Build an OBOParser from a filename (defaults to non-case sensitive)

Parameters:

fname - - OBO filename to parse

Throws:

java.io.IOException

org.obo.dataadapter.OBOParseException

OBOParser

public OBOParser(java.util.Collection<java.lang.String> fnames)
          throws java.io.IOException,
                 org.obo.dataadapter.OBOParseException

Build an OBOParser from a collection of filenames (defaults to non-case sensitive)

Parameters:

fnames - - OBO filenames to parse

Throws:

java.io.IOException

org.obo.dataadapter.OBOParseException

OBOParser

public OBOParser(java.lang.String fname,
                 boolean isCaseSensitive)
          throws java.io.IOException,
                 org.obo.dataadapter.OBOParseException

Build an OBOParser from a filename and a flag for whether the indexing should be case sensitive

Parameters:

fname - - OBO filename to parse

isCaseSensitive - - whether the indexing should be case sensitive

Throws:

java.io.IOException

org.obo.dataadapter.OBOParseException

OBOParser

public OBOParser(java.util.Collection<java.lang.String> fnames,
                 boolean isCaseSensitive)
          throws java.io.IOException,
                 org.obo.dataadapter.OBOParseException

Build an OBOParser from a collection of filenames and a flag for whether the indexing should be case sensitive

Parameters:

fname - - OBO filenames to parse

isCaseSensitive - - whether the indexing should be case sensitive

Throws:

java.io.IOException

org.obo.dataadapter.OBOParseException

Method Detail

getTermById

public org.obo.datamodel.IdentifiedObject getTermById(java.lang.String id)

Get a term IdentifiedObject by ID

Parameters:

id - - ID of the term object

Returns:

IdentifiedObject for the ID (null if not found)

getTermByName

public Pair<org.obo.datamodel.IdentifiedObject,java.lang.String> getTermByName(java.lang.String name)

Get a term IdentifiedObject by name

Parameters:

name - - name of the term object

Returns:

IdentifiedObject for the name (null if not found)

hasTermWithId

public boolean hasTermWithId(java.lang.String id)

Check to see if a term with the given ID exists

Parameters:

id - - ID to search against

Returns:

whether a term exists with the given ID

hasTermWithName

public boolean hasTermWithName(java.lang.String name)

Check to see if a term with the given name exists

Parameters:

name - - name to search against

Returns:

whether a term exists with the given name