ch.epfl.bbp.uima

Class BlueCasUtil

java.lang.Object

ch.epfl.bbp.uima.BlueCasUtil

public class BlueCasUtil
extends Object

Utility class to work with JCases

Author:

renaud.richardet@epfl.ch

See Also:

JCasUtil

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BlueCasUtil.Position

Constructor Summary

Constructors

Constructor and Description
BlueCasUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static ArrayList<org.apache.uima.jcas.JCas>	asList(org.apache.uima.collection.CollectionReader cr)
static <T extends org.apache.uima.jcas.cas.TOP> List<T>	asList(Iterable<T> select) (Potentially) Slow, but convenient
static int	distance(org.apache.uima.jcas.tcas.Annotation a1, org.apache.uima.jcas.tcas.Annotation a2)
static <T> Collection<T>	filterStrict(Iterable<T> raw, Class<?> strictClass)
static List<org.apache.uima.jcas.tcas.Annotation>	findOverlapping(org.apache.uima.jcas.JCas jcas, org.apache.uima.jcas.tcas.Annotation annotIn)
static void	fixNoSentences(org.apache.uima.jcas.JCas jCas) If this cas has no Sentence annotation, creates one with the whole cas text
static void	fixNoText(org.apache.uima.jcas.JCas jCas) If this cas has no text, set it to ""
static String	getHeaderDocId(org.apache.uima.jcas.JCas jCas)
static int	getHeaderIntDocId(org.apache.uima.jcas.JCas jCas)
static String	getHeaderSource(org.apache.uima.jcas.JCas jCas)
static String	getSinglePosTag(Token t)
static String	getTitle(org.apache.uima.jcas.JCas jCas)
static boolean	haveSameBeginEnd(org.apache.uima.jcas.tcas.Annotation a, org.apache.uima.jcas.tcas.Annotation b)
static String	inspect(org.apache.uima.jcas.tcas.Annotation a) Util to print an annotation for inspection.Prints some text before and after this annotation, and add '{', '}' around the annotation text.
static String	inspect(org.apache.uima.jcas.JCas jcas, int begin, int end)
static BlueCasUtil.Position	isBefore(org.apache.uima.jcas.tcas.Annotation a1, org.apache.uima.jcas.tcas.Annotation a2)
static boolean	isContained(org.apache.uima.jcas.tcas.Annotation a1, org.apache.uima.jcas.tcas.Annotation a2)
static boolean	isDocAnnot(org.apache.uima.cas.text.AnnotationFS a)
static boolean	isEmptyText(org.apache.uima.jcas.JCas jCas)
static Iterator<org.apache.uima.jcas.JCas>	iterator(org.apache.uima.collection.CollectionReader cr)
static boolean	keepDoc(org.apache.uima.jcas.JCas jCas) Whether this document should be kept for analysis, based on: language == en OOV < 0.4 (see TooMuchOOVFilterAnnotator) Enough tokens per page (see TooFewTokensFilterAnnotator)
static int	maxEnd(org.apache.uima.jcas.tcas.Annotation a1, org.apache.uima.jcas.tcas.Annotation a2)
static int	minBegin(org.apache.uima.jcas.tcas.Annotation a1, org.apache.uima.jcas.tcas.Annotation a2)
static List<org.apache.uima.jcas.tcas.Annotation>	selectCovered(org.apache.uima.cas.CAS cas, org.apache.uima.cas.text.AnnotationFS coveringAnnotation) REM: modified from CasUtils..
static <T extends org.apache.uima.jcas.cas.TOP> Collection<T>	selectStrict(org.apache.uima.jcas.JCas jcas, Class<T> clasz, Class<?> strictClass)
static org.apache.uima.jcas.JCas	setDocId(org.apache.uima.jcas.JCas jCas, int docId)
static List<String>	toList(org.apache.uima.jcas.cas.StringArray tokens)

Methods inherited from class java.lang.Object

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

Constructor Detail

BlueCasUtil

public BlueCasUtil()

Method Detail

selectStrict

public static <T extends org.apache.uima.jcas.cas.TOP> Collection<T> selectStrict(org.apache.uima.jcas.JCas jcas,
                                                                  Class<T> clasz,
                                                                  Class<?> strictClass)

Parameters:

jcas -

clasz -

strictClass -

Returns:

the annotations of this jcas that are strictly equal to strictClass

isEmptyText

public static boolean isEmptyText(org.apache.uima.jcas.JCas jCas)

findOverlapping

public static List<org.apache.uima.jcas.tcas.Annotation> findOverlapping(org.apache.uima.jcas.JCas jcas,
                                                         org.apache.uima.jcas.tcas.Annotation annotIn)

Returns:

all annotations of this jcas that start and end at the same char as annotIn

filterStrict

public static <T> Collection<T> filterStrict(Iterable<T> raw,
                             Class<?> strictClass)

getHeaderIntDocId

public static int getHeaderIntDocId(org.apache.uima.jcas.JCas jCas)

Returns:

the value of the Header.getDocId() for this jCas as an int, if set; -1 otherwise

getHeaderDocId

public static String getHeaderDocId(org.apache.uima.jcas.JCas jCas)

Returns:

the value of the Header.getDocId() for this jCas, if set; null otherwise

getHeaderSource

public static String getHeaderSource(org.apache.uima.jcas.JCas jCas)

Returns:

the value of the Header.getSource() for this jCas, if set; null otherwise

fixNoSentences

public static void fixNoSentences(org.apache.uima.jcas.JCas jCas)

If this cas has no Sentence annotation, creates one with the whole cas text

fixNoText

public static void fixNoText(org.apache.uima.jcas.JCas jCas)

If this cas has no text, set it to ""

getSinglePosTag

public static String getSinglePosTag(Token t)

iterator

public static Iterator<org.apache.uima.jcas.JCas> iterator(org.apache.uima.collection.CollectionReader cr)

asList

public static ArrayList<org.apache.uima.jcas.JCas> asList(org.apache.uima.collection.CollectionReader cr)

inspect

public static String inspect(org.apache.uima.jcas.JCas jcas,
             int begin,
             int end)

inspect

public static String inspect(org.apache.uima.jcas.tcas.Annotation a)

Util to print an annotation for inspection.Prints some text before and after this annotation, and add '{', '}' around the annotation text.

Returns:

setDocId

public static org.apache.uima.jcas.JCas setDocId(org.apache.uima.jcas.JCas jCas,
                                 int docId)

haveSameBeginEnd

public static boolean haveSameBeginEnd(org.apache.uima.jcas.tcas.Annotation a,
                       org.apache.uima.jcas.tcas.Annotation b)

getTitle

public static String getTitle(org.apache.uima.jcas.JCas jCas)

Returns:

the value of the Header.getTitle() for this jCas, if set; empty string otherwise

selectCovered

public static List<org.apache.uima.jcas.tcas.Annotation> selectCovered(org.apache.uima.cas.CAS cas,
                                                       org.apache.uima.cas.text.AnnotationFS coveringAnnotation)

REM: modified from CasUtils.. Get a list of annotations constraint by a certain annotation. Iterates over all annotations to find the covered annotations. Does not use subiterators and does not respect type prioritites. Was adapted from Subiterator. Uses the same approach except that type priorities are ignored.

Parameters:

cas - a CAS.

coveringAnnotation - the covering annotation.

See Also:

Subiterator

keepDoc

public static boolean keepDoc(org.apache.uima.jcas.JCas jCas)

Whether this document should be kept for analysis, based on:

• language == en
• OOV < 0.4 (see TooMuchOOVFilterAnnotator)
• Enough tokens per page (see TooFewTokensFilterAnnotator)

asList

public static <T extends org.apache.uima.jcas.cas.TOP> List<T> asList(Iterable<T> select)

(Potentially) Slow, but convenient

Parameters:

select - comes from JCasUtil select.

isDocAnnot

public static boolean isDocAnnot(org.apache.uima.cas.text.AnnotationFS a)

distance

public static int distance(org.apache.uima.jcas.tcas.Annotation a1,
           org.apache.uima.jcas.tcas.Annotation a2)

Parameters:

annot1 -

annot2 -

Returns:

the distance (gap) between these two annotation, or -1 if they overlap

maxEnd

public static int maxEnd(org.apache.uima.jcas.tcas.Annotation a1,
         org.apache.uima.jcas.tcas.Annotation a2)

minBegin

public static int minBegin(org.apache.uima.jcas.tcas.Annotation a1,
           org.apache.uima.jcas.tcas.Annotation a2)

isBefore

public static BlueCasUtil.Position isBefore(org.apache.uima.jcas.tcas.Annotation a1,
                            org.apache.uima.jcas.tcas.Annotation a2)

Parameters:

annot1 -

annot2 -

Returns:

whether annot1 is before annot2

isContained

public static boolean isContained(org.apache.uima.jcas.tcas.Annotation a1,
                  org.apache.uima.jcas.tcas.Annotation a2)

Parameters:

annot1 -

annot2 -

Returns:

whether annot1 is contained in annot2. true if has same begin-end

toList

public static List<String> toList(org.apache.uima.jcas.cas.StringArray tokens)