textractor.tools.lookup
Class AbstractLookupProteinname

java.lang.Object
  textractor.tools.lookup.AbstractLookupProteinname

Direct Known Subclasses:

LookupProteinname, LookupProteinnameStandalone

public abstract class AbstractLookupProteinname
extends Object

Provides basic functionality for looking up protein names.

Field Summary

protected boolean	checkAndRemoveRedundancy
protected Dictionary	dictionary Dictionary used to lookup terms.
static String	DICTIONARY_DIRECTORY Default directory name for the dictionary.
protected DocumentIndexManager	docManager Document manager used to lookup terms.
protected String	indexBasename
static String	LOOKUP_RESULTS_DIRECTORY Directory name for results of a lookup.
protected PaiceHuskStemmer	stemmer
protected boolean	stemming Indicates that stemming is enabled.
protected String	subLookupResultsDirectory

Constructor Summary

AbstractLookupProteinname()

AbstractLookupProteinname(String[] args)

Method Summary

protected Map<Integer,DocumentTermPositions>	lookupAllTermsByDocument(String basename)
Collection<LookupResult>	lookupAllTermsByTerm(String basename)
void	setDictionary(String filename)

Methods inherited from class java.lang.Object

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

Field Detail

indexBasename

protected String indexBasename

dictionary

protected Dictionary dictionary

Dictionary used to lookup terms.

docManager

protected DocumentIndexManager docManager

Document manager used to lookup terms.

stemming

protected boolean stemming

Indicates that stemming is enabled.

stemmer

protected PaiceHuskStemmer stemmer

checkAndRemoveRedundancy

protected boolean checkAndRemoveRedundancy

subLookupResultsDirectory

protected String subLookupResultsDirectory

DICTIONARY_DIRECTORY

public static final String DICTIONARY_DIRECTORY

Default directory name for the dictionary.

See Also:

Constant Field Values

LOOKUP_RESULTS_DIRECTORY

public static final String LOOKUP_RESULTS_DIRECTORY

Directory name for results of a lookup.

See Also:

Constant Field Values

Constructor Detail

AbstractLookupProteinname

public AbstractLookupProteinname()
                          throws IOException

Throws:

IOException

AbstractLookupProteinname

public AbstractLookupProteinname(String[] args)
                          throws IOException

Throws:

IOException

Method Detail

setDictionary

public void setDictionary(String filename)
                   throws IOException

Throws:

IOException

lookupAllTermsByTerm

public Collection<LookupResult> lookupAllTermsByTerm(String basename)
                                              throws NoSuchMethodException,
                                                     IllegalAccessException,
                                                     ConfigurationException,
                                                     IOException,
                                                     InvocationTargetException,
                                                     InstantiationException,
                                                     ClassNotFoundException,
                                                     URISyntaxException

Throws:

NoSuchMethodException

IllegalAccessException

ConfigurationException

IOException

InvocationTargetException

InstantiationException

ClassNotFoundException

URISyntaxException

lookupAllTermsByDocument

protected final Map<Integer,DocumentTermPositions> lookupAllTermsByDocument(String basename)
                                                                     throws IOException,
                                                                            ConfigurationException,
                                                                            NoSuchMethodException,
                                                                            IllegalAccessException,
                                                                            InvocationTargetException,
                                                                            InstantiationException,
                                                                            ClassNotFoundException,
                                                                            URISyntaxException

Throws:

IOException

ConfigurationException

NoSuchMethodException

IllegalAccessException

InvocationTargetException

InstantiationException

ClassNotFoundException

URISyntaxException