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csn_trainjava_testjs

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public void setHighLevelMeta ( int i ) { String meta = "<Table>\n" ; meta = meta + "<pageNumInDoc>" + ( i + 1 ) + "</pageNumInDoc>\n" ; m_caption = replaceAllSpecialChracters ( m_caption ) ; meta = meta + "<TableCaption>" + m_caption + "</TableCaption>\n" ; String location = "" ; if ( m_topCaptionLocation ) location = "top" ; else location = "below" ; location = replaceAllSpecialChracters ( location ) ; meta = meta + "<CaptionLocation>" + location + "</CaptionLocation>\n" ; m_metadata_HighLevel = replaceAllSpecialChracters ( m_metadata_HighLevel ) ; meta = meta + "<dataHighLevel>" + m_metadata_HighLevel + "</dataHighLevel>\n" ; this . setMetadataHighLevel ( meta ) ; }
Sets the high - level table metadata
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public void setEmptyMetadataStructureLevel ( int YNum , int cc , List < TextPiece > wordsOfAPage , DocInfo m_docInfo ) { String meta = "" ; meta = "<TableColumnHeading>\n" + "</TableColumnHeading>" + "\n" ; meta = meta + "<TableContent>\n" ; meta = meta + "</TableContent>" + "\n" ; meta = meta + "<TableRowHeading>" + "</TableRowHeading>" + "\n" ; meta = meta + "<TableFootnote>" ; meta = meta + "... </TableFootnote>" + "\n" ; meta = meta + "<ColumnNum>" + "</ColumnNum>" + "\n" ; meta = meta + "<RowNum>" + "</RowNum>" + "\n" ; meta = meta + "<ColumnCoordinates>" + "</ColumnCoordinates>" + "\n" ; meta = meta + "<TableHeight>" + "</TableHeight>" + "\n" ; meta = meta + "<TableWidth>" + "</TableWidth>" + "\n" ; meta = meta + "<isWideTable>" + m_WideTable + "</isWideTable>\n" ; m_referenceText = replaceAllSpecialChracters ( m_referenceText ) ; meta = meta + "<TableReferenceText>" + m_referenceText + "</TableReferenceText>" + "\n" ; meta = meta + "</Table>" + "\n" ; setMetadataStructureLevel ( meta ) ; int tableNum = m_docInfo . getTableNum ( ) ; }
Sets an empty metadata file
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public static String replaceAllSpecialChracters ( String toBeReplaced ) { toBeReplaced = toBeReplaced . replaceAll ( "&" , "&amp;" ) ; toBeReplaced = toBeReplaced . replaceAll ( "<" , "&lt;" ) ; toBeReplaced = toBeReplaced . replaceAll ( ">" , "&gt;" ) ; toBeReplaced = toBeReplaced . replaceAll ( "\"" , "&quot;" ) ; toBeReplaced = toBeReplaced . replaceAll ( "'" , "&apos;" ) ; int len = toBeReplaced . length ( ) ; char [ ] temp = toBeReplaced . toCharArray ( ) ; for ( int i = 0 ; i < len ; i ++ ) { char xCode = temp [ i ] ; if ( ( xCode > '\u0000' && xCode <= '\u0020' ) || ( xCode == '\u0026' ) || ( xCode == '\u0022' ) || ( xCode == '\u02C6' ) || ( xCode == '\u201C' ) || ( xCode == '\u201D' ) || ( xCode == '\u201E' ) ) { String sub1 = toBeReplaced . substring ( 0 , i ) ; String sub2 = toBeReplaced . substring ( i + 1 , len ) ; String replacement = "" ; if ( ( xCode > '\u0000' && xCode <= '\u0020' ) ) replacement = " " ; if ( xCode == '\u0026' ) replacement = " " ; if ( xCode == '\u0022' ) replacement = " " ; if ( xCode == '\u02C6' ) replacement = " " ; if ( xCode == '\u201C' ) replacement = " " ; if ( xCode == '\u201D' ) replacement = " " ; if ( xCode == '\u201E' ) replacement = " " ; toBeReplaced = sub1 + replacement + sub2 ; } len = toBeReplaced . length ( ) ; temp = toBeReplaced . toCharArray ( ) ; } return ( toBeReplaced ) ; }
Replaces all special characters in a given string
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public void addPreviousPunctuation ( Parse punct ) { if ( this . prevPunctSet == null ) { this . prevPunctSet = new LinkedHashSet ( ) ; } prevPunctSet . add ( punct ) ; }
Designates that the specifed punctuation should is prior to this parse .
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public void addNextPunctuation ( Parse punct ) { if ( this . nextPunctSet == null ) { this . nextPunctSet = new LinkedHashSet ( ) ; } nextPunctSet . add ( punct ) ; }
Designates that the specifed punctuation follows this parse .
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public void insert ( final Parse constituent ) { Span ic = constituent . span ; if ( span . contains ( ic ) ) { int pi = 0 ; int pn = parts . size ( ) ; for ( ; pi < pn ; pi ++ ) { Parse subPart = ( Parse ) parts . get ( pi ) ; Span sp = subPart . span ; if ( sp . getStart ( ) >= ic . getEnd ( ) ) { break ; } else if ( ic . contains ( sp ) ) { parts . remove ( pi ) ; pi -- ; constituent . parts . add ( subPart ) ; subPart . setParent ( constituent ) ; pn = parts . size ( ) ; } else if ( sp . contains ( ic ) ) { subPart . insert ( constituent ) ; return ; } } parts . add ( pi , constituent ) ; constituent . setParent ( this ) ; } else { throw ( new InternalError ( "Inserting constituent not contained in the sentence!" ) ) ; } }
Inserts the specified constituent into this parse based on its text span . This method assumes that the specified constituent can be inserted into this parse .
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public double getTagSequenceProb ( ) { if ( parts . size ( ) == 1 && ( ( Parse ) parts . get ( 0 ) ) . type . equals ( ParserME . TOK_NODE ) ) { return ( Math . log ( prob ) ) ; } else if ( parts . size ( ) == 0 ) { System . err . println ( "Parse.getTagSequenceProb: Wrong base case!" ) ; return ( 0.0 ) ; } else { double sum = 0.0 ; for ( Iterator pi = parts . iterator ( ) ; pi . hasNext ( ) ; ) { sum += ( ( Parse ) pi . next ( ) ) . getTagSequenceProb ( ) ; } return ( sum ) ; } }
Returns the probability associed with the pos - tag sequence assigned to this parse .
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public void updateHeads ( HeadRules rules ) { if ( parts != null && parts . size ( ) != 0 ) { for ( int pi = 0 , pn = parts . size ( ) ; pi < pn ; pi ++ ) { Parse c = ( Parse ) parts . get ( pi ) ; c . updateHeads ( rules ) ; } this . head = rules . getHead ( ( Parse [ ] ) parts . toArray ( new Parse [ parts . size ( ) ] ) , type ) ; if ( head == null ) { head = this ; } } else { this . head = this ; } }
Computes the head parses for this parse and its sub - parses and stores this information in the parse data structure .
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public boolean isPosTag ( ) { return ( parts . size ( ) == 1 && ( ( Parse ) parts . get ( 0 ) ) . getType ( ) . equals ( ParserME . TOK_NODE ) ) ; }
Indicates wether this parse node is a pos - tag .
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public Parse getCommonParent ( Parse node ) { if ( this == node ) { return parent ; } Set parents = new HashSet ( ) ; Parse cparent = this ; while ( cparent != null ) { parents . add ( cparent ) ; cparent = cparent . getParent ( ) ; } while ( node != null ) { if ( parents . contains ( node ) ) { return node ; } node = node . getParent ( ) ; } return null ; }
Returns the deepest shared parent of this node and the specified node . If the nodes are identical then their parent is returned . If one node is the parent of the other then the parent node is returned .
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protected int countCorrectPairs ( MatchData data ) { Map counter = new HashMap ( ) ; for ( int i = 0 ; i < data . numSources ( ) ; i ++ ) { String src = data . getSource ( i ) ; for ( int j = 0 ; j < data . numInstances ( src ) ; j ++ ) { String id = data . getInstance ( src , j ) . getId ( ) ; if ( id != null ) { IdKey key = new IdKey ( id , src ) ; Integer c = ( Integer ) counter . get ( key ) ; counter . put ( key , ( c == null ? new Integer ( 1 ) : new Integer ( c . intValue ( ) + 1 ) ) ) ; } } } int numCorrectPairs = 0 ; Set idsInSrc1 = new HashSet ( ) ; for ( int i = 0 ; i < data . numSources ( ) ; i ++ ) { String src1 = data . getSource ( i ) ; idsInSrc1 . clear ( ) ; for ( int j = 0 ; j < data . numInstances ( src1 ) ; j ++ ) { String id = data . getInstance ( src1 , j ) . getId ( ) ; idsInSrc1 . add ( id ) ; for ( int k = i + 1 ; k < data . numSources ( ) ; k ++ ) { String src2 = data . getSource ( k ) ; Integer cInteger = ( Integer ) counter . get ( new IdKey ( id , src2 ) ) ; if ( cInteger != null ) { numCorrectPairs += cInteger . intValue ( ) ; } } } if ( clusterMode ) { for ( Iterator j = idsInSrc1 . iterator ( ) ; j . hasNext ( ) ; ) { String id = ( String ) j . next ( ) ; Integer cInteger = ( Integer ) counter . get ( new IdKey ( id , src1 ) ) ; int c = cInteger . intValue ( ) ; numCorrectPairs += c * ( c - 1 ) / 2 ; } } } return numCorrectPairs ; }
Compute number of correct pairs betwn src1 and src2 where src2 > src1
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protected void loadGrams ( DataInputStream input ) throws IOException { gramSet = new HashSet ( ) ; try { while ( true ) { int gramLength = input . readInt ( ) ; int [ ] words = new int [ gramLength ] ; for ( int wi = 0 ; wi < gramLength ; wi ++ ) { words [ wi ] = input . readInt ( ) ; } gramSet . add ( new NGram ( words ) ) ; } } catch ( EOFException e ) { } }
Loads the contents of the specified input stream into this dictionary .
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public boolean contains ( String [ ] words ) { if ( words . length == 1 ) { return wordMap . contains ( words [ 0 ] ) ; } else { NGram ngram = nGramFactory . createNGram ( words ) ; if ( ngram == null ) { return false ; } else { return gramSet . contains ( ngram ) ; } } }
Returns true if this dictionary contains the n - gram consisting of the specified words .
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public static void main ( String [ ] args ) throws IOException { if ( args . length == 0 ) { System . err . println ( "Usage: Dictionary dictionary_file" ) ; System . exit ( 0 ) ; } Dictionary dict = new Dictionary ( args [ 0 ] ) ; BufferedReader in = new BufferedReader ( new InputStreamReader ( System . in ) ) ; String line ; while ( null != ( line = in . readLine ( ) ) ) { String [ ] words = line . split ( " " ) ; if ( dict . contains ( words ) ) { System . out . println ( "Dictionary contains: " + line ) ; } else { System . out . println ( "Dictionary does not contain: " + line ) ; } } }
Allows a dictionery to be queried for specific n - grams from the command - line from statndard in using space delimited n - grams on a single line .
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public Title getSectionHeading ( ) { if ( Section_Type . featOkTst && ( ( Section_Type ) jcasType ) . casFeat_sectionHeading == null ) jcasType . jcas . throwFeatMissing ( "sectionHeading" , "de.julielab.jules.types.Section" ) ; return ( Title ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Section_Type ) jcasType ) . casFeatCode_sectionHeading ) ) ) ; }
getter for sectionHeading - gets the title of the section
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public void setSectionHeading ( Title v ) { if ( Section_Type . featOkTst && ( ( Section_Type ) jcasType ) . casFeat_sectionHeading == null ) jcasType . jcas . throwFeatMissing ( "sectionHeading" , "de.julielab.jules.types.Section" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( Section_Type ) jcasType ) . casFeatCode_sectionHeading , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for sectionHeading - sets the title of the section
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public String getSectionId ( ) { if ( Section_Type . featOkTst && ( ( Section_Type ) jcasType ) . casFeat_sectionId == null ) jcasType . jcas . throwFeatMissing ( "sectionId" , "de.julielab.jules.types.Section" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Section_Type ) jcasType ) . casFeatCode_sectionId ) ; }
getter for sectionId - gets the id of the section for example as mentioned in the original file or level of the section
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public void setSectionId ( String v ) { if ( Section_Type . featOkTst && ( ( Section_Type ) jcasType ) . casFeat_sectionId == null ) jcasType . jcas . throwFeatMissing ( "sectionId" , "de.julielab.jules.types.Section" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Section_Type ) jcasType ) . casFeatCode_sectionId , v ) ; }
setter for sectionId - sets the id of the section for example as mentioned in the original file or level of the section
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final public void train ( StringWrapperIterator i ) { Set seenTokens = new HashSet ( ) ; while ( i . hasNext ( ) ) { StringWrapper s = ( StringWrapper ) i . next ( ) ; BagOfTokens bag = asBagOfTokens ( i . nextStringWrapper ( ) ) ; for ( Iterator j = bag . tokenIterator ( ) ; j . hasNext ( ) ; ) { Token tokj = ( Token ) j . next ( ) ; totalTokens ++ ; Integer freq = ( Integer ) backgroundFrequency . get ( tokj ) ; if ( freq == null ) backgroundFrequency . put ( tokj , ONE ) ; else if ( freq == ONE ) backgroundFrequency . put ( tokj , TWO ) ; else if ( freq == TWO ) backgroundFrequency . put ( tokj , THREE ) ; else backgroundFrequency . put ( tokj , new Integer ( freq . intValue ( ) + 1 ) ) ; } } }
Accumulate statistics on how often each token occurs .
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final public StringWrapper prepare ( String s ) { BagOfTokens bag = new BagOfTokens ( s , tokenizer . tokenize ( s ) ) ; double totalWeight = bag . getTotalWeight ( ) ; for ( Iterator i = bag . tokenIterator ( ) ; i . hasNext ( ) ; ) { Token tok = ( Token ) i . next ( ) ; double freq = bag . getWeight ( tok ) ; bag . setWeight ( tok , smoothedProbability ( tok , freq , totalWeight ) ) ; } return bag ; }
Preprocess a string by finding tokens and giving them weights W such that W is the smoothed probability of the token appearing in the document .
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protected double backgroundProb ( Token tok ) { Integer freqInteger = ( Integer ) backgroundFrequency . get ( tok ) ; double freq = freqInteger == null ? 0 : freqInteger . intValue ( ) ; return freq / totalTokens ; }
Probability of token in the background language model
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final public double score ( StringWrapper s , StringWrapper t ) { BagOfTokens sBag = ( BagOfTokens ) s ; BagOfTokens tBag = ( BagOfTokens ) t ; double sum = 0 ; for ( Iterator i = sBag . tokenIterator ( ) ; i . hasNext ( ) ; ) { Token tok = ( Token ) i . next ( ) ; if ( tBag . contains ( tok ) ) { double ps = sBag . getWeight ( tok ) ; double pt = tBag . getWeight ( tok ) ; sum -= h ( ps + pt ) - h ( ps ) - h ( pt ) ; } } return 0.5 * sum / Math . log ( 2 ) ; }
Jensen - Shannon distance between distributions .
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public void prepare ( StringDistance [ ] innerDistances ) { if ( ! fieldsPrepared ) { for ( int i = 0 ; i < size ( ) ; i ++ ) { StringDistance d = innerDistances [ getDistanceLearnerIndex ( i ) ] ; set ( i , d . prepare ( get ( i ) . unwrap ( ) ) ) ; } } }
Prepare each field with the appropriate distance
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public String getMod ( ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_mod == null ) jcasType . jcas . throwFeatMissing ( "mod" , "de.julielab.jules.types.ace.Timex2" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_mod ) ; }
getter for mod - gets
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public void setMod ( String v ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_mod == null ) jcasType . jcas . throwFeatMissing ( "mod" , "de.julielab.jules.types.ace.Timex2" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_mod , v ) ; }
setter for mod - sets
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public String getComment ( ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_comment == null ) jcasType . jcas . throwFeatMissing ( "comment" , "de.julielab.jules.types.ace.Timex2" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_comment ) ; }
getter for comment - gets
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public void setComment ( String v ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_comment == null ) jcasType . jcas . throwFeatMissing ( "comment" , "de.julielab.jules.types.ace.Timex2" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_comment , v ) ; }
setter for comment - sets
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public String getAnchor_val ( ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_anchor_val == null ) jcasType . jcas . throwFeatMissing ( "anchor_val" , "de.julielab.jules.types.ace.Timex2" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_anchor_val ) ; }
getter for anchor_val - gets
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public void setAnchor_val ( String v ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_anchor_val == null ) jcasType . jcas . throwFeatMissing ( "anchor_val" , "de.julielab.jules.types.ace.Timex2" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_anchor_val , v ) ; }
setter for anchor_val - sets
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public String getVal ( ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_val == null ) jcasType . jcas . throwFeatMissing ( "val" , "de.julielab.jules.types.ace.Timex2" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_val ) ; }
getter for val - gets
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public void setVal ( String v ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_val == null ) jcasType . jcas . throwFeatMissing ( "val" , "de.julielab.jules.types.ace.Timex2" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_val , v ) ; }
setter for val - sets
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public String getSet ( ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_set == null ) jcasType . jcas . throwFeatMissing ( "set" , "de.julielab.jules.types.ace.Timex2" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_set ) ; }
getter for set - gets
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public void setSet ( String v ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_set == null ) jcasType . jcas . throwFeatMissing ( "set" , "de.julielab.jules.types.ace.Timex2" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_set , v ) ; }
setter for set - sets
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public String getNon_specific ( ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_non_specific == null ) jcasType . jcas . throwFeatMissing ( "non_specific" , "de.julielab.jules.types.ace.Timex2" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_non_specific ) ; }
getter for non_specific - gets
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public void setNon_specific ( String v ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_non_specific == null ) jcasType . jcas . throwFeatMissing ( "non_specific" , "de.julielab.jules.types.ace.Timex2" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_non_specific , v ) ; }
setter for non_specific - sets
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public String getAnchor_dir ( ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_anchor_dir == null ) jcasType . jcas . throwFeatMissing ( "anchor_dir" , "de.julielab.jules.types.ace.Timex2" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_anchor_dir ) ; }
getter for anchor_dir - gets
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public void setAnchor_dir ( String v ) { if ( Timex2_Type . featOkTst && ( ( Timex2_Type ) jcasType ) . casFeat_anchor_dir == null ) jcasType . jcas . throwFeatMissing ( "anchor_dir" , "de.julielab.jules.types.ace.Timex2" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Timex2_Type ) jcasType ) . casFeatCode_anchor_dir , v ) ; }
setter for anchor_dir - sets
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public String getEvent_type ( ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_event_type == null ) jcasType . jcas . throwFeatMissing ( "event_type" , "ch.epfl.bbp.uima.genia.Event" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_event_type ) ; }
getter for event_type - gets
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public void setEvent_type ( String v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_event_type == null ) jcasType . jcas . throwFeatMissing ( "event_type" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_event_type , v ) ; }
setter for event_type - sets
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public FSArray getThemes_protein ( ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_protein == null ) jcasType . jcas . throwFeatMissing ( "themes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; return ( FSArray ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_protein ) ) ) ; }
getter for themes_protein - gets
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public void setThemes_protein ( FSArray v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_protein == null ) jcasType . jcas . throwFeatMissing ( "themes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_protein , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for themes_protein - sets
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public Protein getThemes_protein ( int i ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_protein == null ) jcasType . jcas . throwFeatMissing ( "themes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_protein ) , i ) ; return ( Protein ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_protein ) , i ) ) ) ; }
indexed getter for themes_protein - gets an indexed value -
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public void setThemes_protein ( int i , Protein v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_protein == null ) jcasType . jcas . throwFeatMissing ( "themes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_protein ) , i ) ; jcasType . ll_cas . ll_setRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_protein ) , i , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
indexed setter for themes_protein - sets an indexed value -
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public FSArray getCauses_protein ( ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_protein == null ) jcasType . jcas . throwFeatMissing ( "causes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; return ( FSArray ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_protein ) ) ) ; }
getter for causes_protein - gets
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public void setCauses_protein ( FSArray v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_protein == null ) jcasType . jcas . throwFeatMissing ( "causes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_protein , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for causes_protein - sets
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public Protein getCauses_protein ( int i ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_protein == null ) jcasType . jcas . throwFeatMissing ( "causes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_protein ) , i ) ; return ( Protein ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_protein ) , i ) ) ) ; }
indexed getter for causes_protein - gets an indexed value -
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public void setCauses_protein ( int i , Protein v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_protein == null ) jcasType . jcas . throwFeatMissing ( "causes_protein" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_protein ) , i ) ; jcasType . ll_cas . ll_setRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_protein ) , i , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
indexed setter for causes_protein - sets an indexed value -
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public String getSite ( ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_site == null ) jcasType . jcas . throwFeatMissing ( "site" , "ch.epfl.bbp.uima.genia.Event" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_site ) ; }
getter for site - gets
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public void setSite ( String v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_site == null ) jcasType . jcas . throwFeatMissing ( "site" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_site , v ) ; }
setter for site - sets
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public FSArray getThemes_event ( ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_event == null ) jcasType . jcas . throwFeatMissing ( "themes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; return ( FSArray ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_event ) ) ) ; }
getter for themes_event - gets
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public void setThemes_event ( FSArray v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_event == null ) jcasType . jcas . throwFeatMissing ( "themes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_event , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for themes_event - sets
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public Event getThemes_event ( int i ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_event == null ) jcasType . jcas . throwFeatMissing ( "themes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_event ) , i ) ; return ( Event ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_event ) , i ) ) ) ; }
indexed getter for themes_event - gets an indexed value -
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public void setThemes_event ( int i , Event v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_themes_event == null ) jcasType . jcas . throwFeatMissing ( "themes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_event ) , i ) ; jcasType . ll_cas . ll_setRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_themes_event ) , i , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
indexed setter for themes_event - sets an indexed value -
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public FSArray getCauses_event ( ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_event == null ) jcasType . jcas . throwFeatMissing ( "causes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; return ( FSArray ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_event ) ) ) ; }
getter for causes_event - gets
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public void setCauses_event ( FSArray v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_event == null ) jcasType . jcas . throwFeatMissing ( "causes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_event , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for causes_event - sets
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public Event getCauses_event ( int i ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_event == null ) jcasType . jcas . throwFeatMissing ( "causes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_event ) , i ) ; return ( Event ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_event ) , i ) ) ) ; }
indexed getter for causes_event - gets an indexed value -
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public void setCauses_event ( int i , Event v ) { if ( Event_Type . featOkTst && ( ( Event_Type ) jcasType ) . casFeat_causes_event == null ) jcasType . jcas . throwFeatMissing ( "causes_event" , "ch.epfl.bbp.uima.genia.Event" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_event ) , i ) ; jcasType . ll_cas . ll_setRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( Event_Type ) jcasType ) . casFeatCode_causes_event ) , i , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
indexed setter for causes_event - sets an indexed value -
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private String punct ( Parse punct , int i ) { StringBuffer feat = new StringBuffer ( 5 ) ; feat . append ( i ) . append ( "=" ) ; feat . append ( punct . getType ( ) ) ; return ( feat . toString ( ) ) ; }
Creates punctuation feature for the specified punctuation at the specfied index .
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public String getGender ( ) { if ( NounFeats_Type . featOkTst && ( ( NounFeats_Type ) jcasType ) . casFeat_gender == null ) jcasType . jcas . throwFeatMissing ( "gender" , "de.julielab.jules.types.NounFeats" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( NounFeats_Type ) jcasType ) . casFeatCode_gender ) ; }
getter for gender - gets Gender C
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public String getLdcatr ( ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_ldcatr == null ) jcasType . jcas . throwFeatMissing ( "ldcatr" , "de.julielab.jules.types.ace.EntityMention" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_ldcatr ) ; }
getter for ldcatr - gets
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public void setLdcatr ( String v ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_ldcatr == null ) jcasType . jcas . throwFeatMissing ( "ldcatr" , "de.julielab.jules.types.ace.EntityMention" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_ldcatr , v ) ; }
setter for ldcatr - sets
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public String getRole ( ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_role == null ) jcasType . jcas . throwFeatMissing ( "role" , "de.julielab.jules.types.ace.EntityMention" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_role ) ; }
getter for role - gets
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public String getMetonymy_mention ( ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_metonymy_mention == null ) jcasType . jcas . throwFeatMissing ( "metonymy_mention" , "de.julielab.jules.types.ace.EntityMention" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_metonymy_mention ) ; }
getter for metonymy_mention - gets
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public void setMetonymy_mention ( String v ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_metonymy_mention == null ) jcasType . jcas . throwFeatMissing ( "metonymy_mention" , "de.julielab.jules.types.ace.EntityMention" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_metonymy_mention , v ) ; }
setter for metonymy_mention - sets
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public String getMention_type ( ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_mention_type == null ) jcasType . jcas . throwFeatMissing ( "mention_type" , "de.julielab.jules.types.ace.EntityMention" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_mention_type ) ; }
getter for mention_type - gets
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public void setMention_type ( String v ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_mention_type == null ) jcasType . jcas . throwFeatMissing ( "mention_type" , "de.julielab.jules.types.ace.EntityMention" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_mention_type , v ) ; }
setter for mention_type - sets
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public String getMention_ldctype ( ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_mention_ldctype == null ) jcasType . jcas . throwFeatMissing ( "mention_ldctype" , "de.julielab.jules.types.ace.EntityMention" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_mention_ldctype ) ; }
getter for mention_ldctype - gets
20,367
public void setMention_ldctype ( String v ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_mention_ldctype == null ) jcasType . jcas . throwFeatMissing ( "mention_ldctype" , "de.julielab.jules.types.ace.EntityMention" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_mention_ldctype , v ) ; }
setter for mention_ldctype - sets
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public Entity getEntity_ref ( ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_entity_ref == null ) jcasType . jcas . throwFeatMissing ( "entity_ref" , "de.julielab.jules.types.ace.EntityMention" ) ; return ( Entity ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_entity_ref ) ) ) ; }
getter for entity_ref - gets
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public void setEntity_ref ( Entity v ) { if ( EntityMention_Type . featOkTst && ( ( EntityMention_Type ) jcasType ) . casFeat_entity_ref == null ) jcasType . jcas . throwFeatMissing ( "entity_ref" , "de.julielab.jules.types.ace.EntityMention" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( EntityMention_Type ) jcasType ) . casFeatCode_entity_ref , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for entity_ref - sets
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public String getSpecificType ( ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_specificType == null ) jcasType . jcas . throwFeatMissing ( "specificType" , "de.julielab.jules.types.ConceptMention" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_specificType ) ; }
getter for specificType - gets
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public void setSpecificType ( String v ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_specificType == null ) jcasType . jcas . throwFeatMissing ( "specificType" , "de.julielab.jules.types.ConceptMention" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_specificType , v ) ; }
setter for specificType - sets
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public TOP getRef ( ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_ref == null ) jcasType . jcas . throwFeatMissing ( "ref" , "de.julielab.jules.types.ConceptMention" ) ; return ( TOP ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_ref ) ) ) ; }
getter for ref - gets The reference to the Concept we use here the super type TOP in order to avoid the recursive dependencies between type systems
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public void setRef ( TOP v ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_ref == null ) jcasType . jcas . throwFeatMissing ( "ref" , "de.julielab.jules.types.ConceptMention" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_ref , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for ref - sets The reference to the Concept we use here the super type TOP in order to avoid the recursive dependencies between type systems
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public FSArray getResourceEntryList ( ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_resourceEntryList == null ) jcasType . jcas . throwFeatMissing ( "resourceEntryList" , "de.julielab.jules.types.ConceptMention" ) ; return ( FSArray ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_resourceEntryList ) ) ) ; }
getter for resourceEntryList - gets
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public void setResourceEntryList ( FSArray v ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_resourceEntryList == null ) jcasType . jcas . throwFeatMissing ( "resourceEntryList" , "de.julielab.jules.types.ConceptMention" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_resourceEntryList , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for resourceEntryList - sets
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public ResourceEntry getResourceEntryList ( int i ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_resourceEntryList == null ) jcasType . jcas . throwFeatMissing ( "resourceEntryList" , "de.julielab.jules.types.ConceptMention" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_resourceEntryList ) , i ) ; return ( ResourceEntry ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_resourceEntryList ) , i ) ) ) ; }
indexed getter for resourceEntryList - gets an indexed value -
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public void setResourceEntryList ( int i , ResourceEntry v ) { if ( ConceptMention_Type . featOkTst && ( ( ConceptMention_Type ) jcasType ) . casFeat_resourceEntryList == null ) jcasType . jcas . throwFeatMissing ( "resourceEntryList" , "de.julielab.jules.types.ConceptMention" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_resourceEntryList ) , i ) ; jcasType . ll_cas . ll_setRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( ConceptMention_Type ) jcasType ) . casFeatCode_resourceEntryList ) , i , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
indexed setter for resourceEntryList - sets an indexed value -
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@ SuppressWarnings ( "unchecked" ) public ArrayList < ArrayList < TextPiece > > getTextPiecesByPage ( File pdfFile ) { assert ( pdfFile . exists ( ) ) : "pdfFile does not exist" ; m_wordsByPage = new ArrayList < ArrayList < TextPiece > > ( ) ; PDDocument document = null ; try { document = PDDocument . load ( pdfFile ) ; resetEngine ( ) ; m_currentPageNo = 0 ; if ( document . isEncrypted ( ) ) { } else { ArrayList < PDPage > pages = ( ArrayList < PDPage > ) document . getDocumentCatalog ( ) . getAllPages ( ) ; for ( PDPage page : pages ) { m_currentPageNo ++ ; PDStream contentStream = page . getContents ( ) ; if ( contentStream != null ) { COSStream contents = contentStream . getStream ( ) ; processPage ( page , contents ) ; } } } } catch ( Exception e ) { System . out . printf ( "[Error] Fail to extract words\n" ) ; m_wordsByPage = null ; } catch ( OutOfMemoryError e ) { System . out . printf ( "[Error] Out Of Memory\n" ) ; m_wordsByPage = null ; } finally { if ( document != null ) { try { document . close ( ) ; } catch ( IOException e ) { } } } return m_wordsByPage ; }
Get text pieces from a PDF document
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public String stem ( String token ) { if ( token != null && token . length ( ) > 3 && token . endsWith ( "s" ) ) { return token . substring ( 0 , token . length ( ) - 1 ) ; } return token ; }
Removes ending s of words longer than 3 chars
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private static File materializeDescriptor ( ResourceSpecifier resource ) throws IOException , SAXException { File tempDesc = File . createTempFile ( "desc" , ".xml" ) ; BufferedWriter out = new BufferedWriter ( new OutputStreamWriter ( new FileOutputStream ( tempDesc ) , "UTF-8" ) ) ; resource . toXML ( out ) ; out . close ( ) ; return tempDesc ; }
Writes a temporary file containing a xml descriptor of the given resource . Returns the file .
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public String getCat ( ) { if ( CoordinationElement_Type . featOkTst && ( ( CoordinationElement_Type ) jcasType ) . casFeat_cat == null ) jcasType . jcas . throwFeatMissing ( "cat" , "de.julielab.jules.types.CoordinationElement" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( CoordinationElement_Type ) jcasType ) . casFeatCode_cat ) ; }
getter for cat - gets
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public void setCat ( String v ) { if ( CoordinationElement_Type . featOkTst && ( ( CoordinationElement_Type ) jcasType ) . casFeat_cat == null ) jcasType . jcas . throwFeatMissing ( "cat" , "de.julielab.jules.types.CoordinationElement" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( CoordinationElement_Type ) jcasType ) . casFeatCode_cat , v ) ; }
setter for cat - sets
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public Set < String > getSynonyms ( final String canonical ) { Set < String > syn = Sets . newHashSet ( ) ; for ( Map < String , Concept > lexica : lexicon ) { for ( String lexCanonical : lexica . keySet ( ) ) { Set < String > variants = lexica . get ( lexCanonical ) . getVariants ( ) ; for ( String variant : variants ) { if ( canonical . equals ( variant ) ) { for ( String v : variants ) { syn . add ( v . toLowerCase ( ) ) ; } } } } } return syn ; }
given a canonical form ( found with a lex - NER return all variants if any
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public int codePointConversion ( String fontName , int codePoint ) { NonStandardFontFamily nonStandardFontFamily = get ( fontName ) ; if ( nonStandardFontFamily == null ) return codePoint ; CodePointSet codePointSet = nonStandardFontFamily . getCodePointSet ( ) ; if ( codePointSet == null ) return codePoint ; CodePoint decimalCodePoint = codePointSet . getByDecimal ( codePoint ) ; if ( decimalCodePoint != null ) return decimalCodePoint . getUnicodeDecimal ( ) ; CodePoint nameCodePoint = codePointSet . getByName ( charNameByCodePoint . get ( codePoint ) ) ; if ( nameCodePoint != null ) return nameCodePoint . getUnicodeDecimal ( ) ; return codePoint ; }
Takes in argument a codepoint . If for the given police the codepoint doesn t correspond to what the font actually displays the conversion is made . Otherwise the old codepoint is return .
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public String getPerson ( ) { if ( VerbFeats_Type . featOkTst && ( ( VerbFeats_Type ) jcasType ) . casFeat_person == null ) jcasType . jcas . throwFeatMissing ( "person" , "de.julielab.jules.types.VerbFeats" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( VerbFeats_Type ) jcasType ) . casFeatCode_person ) ; }
getter for person - gets Person
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public void setPerson ( String v ) { if ( VerbFeats_Type . featOkTst && ( ( VerbFeats_Type ) jcasType ) . casFeat_person == null ) jcasType . jcas . throwFeatMissing ( "person" , "de.julielab.jules.types.VerbFeats" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( VerbFeats_Type ) jcasType ) . casFeatCode_person , v ) ; }
setter for person - sets Person
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public String getVoice ( ) { if ( VerbFeats_Type . featOkTst && ( ( VerbFeats_Type ) jcasType ) . casFeat_voice == null ) jcasType . jcas . throwFeatMissing ( "voice" , "de.julielab.jules.types.VerbFeats" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( VerbFeats_Type ) jcasType ) . casFeatCode_voice ) ; }
getter for voice - gets Voice
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public void setVoice ( String v ) { if ( VerbFeats_Type . featOkTst && ( ( VerbFeats_Type ) jcasType ) . casFeat_voice == null ) jcasType . jcas . throwFeatMissing ( "voice" , "de.julielab.jules.types.VerbFeats" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( VerbFeats_Type ) jcasType ) . casFeatCode_voice , v ) ; }
setter for voice - sets Voice
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public String getAspect ( ) { if ( VerbFeats_Type . featOkTst && ( ( VerbFeats_Type ) jcasType ) . casFeat_aspect == null ) jcasType . jcas . throwFeatMissing ( "aspect" , "de.julielab.jules.types.VerbFeats" ) ; return jcasType . ll_cas . ll_getStringValue ( addr , ( ( VerbFeats_Type ) jcasType ) . casFeatCode_aspect ) ; }
getter for aspect - gets Aspect
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public void setAspect ( String v ) { if ( VerbFeats_Type . featOkTst && ( ( VerbFeats_Type ) jcasType ) . casFeat_aspect == null ) jcasType . jcas . throwFeatMissing ( "aspect" , "de.julielab.jules.types.VerbFeats" ) ; jcasType . ll_cas . ll_setStringValue ( addr , ( ( VerbFeats_Type ) jcasType ) . casFeatCode_aspect , v ) ; }
setter for aspect - sets Aspect
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public FSArray getFullTextLinks ( ) { if ( FullTextLinkList_Type . featOkTst && ( ( FullTextLinkList_Type ) jcasType ) . casFeat_fullTextLinks == null ) jcasType . jcas . throwFeatMissing ( "fullTextLinks" , "de.julielab.jules.types.FullTextLinkList" ) ; return ( FSArray ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( FullTextLinkList_Type ) jcasType ) . casFeatCode_fullTextLinks ) ) ) ; }
getter for fullTextLinks - gets
20,392
public void setFullTextLinks ( FSArray v ) { if ( FullTextLinkList_Type . featOkTst && ( ( FullTextLinkList_Type ) jcasType ) . casFeat_fullTextLinks == null ) jcasType . jcas . throwFeatMissing ( "fullTextLinks" , "de.julielab.jules.types.FullTextLinkList" ) ; jcasType . ll_cas . ll_setRefValue ( addr , ( ( FullTextLinkList_Type ) jcasType ) . casFeatCode_fullTextLinks , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
setter for fullTextLinks - sets
20,393
public FullTextLink getFullTextLinks ( int i ) { if ( FullTextLinkList_Type . featOkTst && ( ( FullTextLinkList_Type ) jcasType ) . casFeat_fullTextLinks == null ) jcasType . jcas . throwFeatMissing ( "fullTextLinks" , "de.julielab.jules.types.FullTextLinkList" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( FullTextLinkList_Type ) jcasType ) . casFeatCode_fullTextLinks ) , i ) ; return ( FullTextLink ) ( jcasType . ll_cas . ll_getFSForRef ( jcasType . ll_cas . ll_getRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( FullTextLinkList_Type ) jcasType ) . casFeatCode_fullTextLinks ) , i ) ) ) ; }
indexed getter for fullTextLinks - gets an indexed value -
20,394
public void setFullTextLinks ( int i , FullTextLink v ) { if ( FullTextLinkList_Type . featOkTst && ( ( FullTextLinkList_Type ) jcasType ) . casFeat_fullTextLinks == null ) jcasType . jcas . throwFeatMissing ( "fullTextLinks" , "de.julielab.jules.types.FullTextLinkList" ) ; jcasType . jcas . checkArrayBounds ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( FullTextLinkList_Type ) jcasType ) . casFeatCode_fullTextLinks ) , i ) ; jcasType . ll_cas . ll_setRefArrayValue ( jcasType . ll_cas . ll_getRefValue ( addr , ( ( FullTextLinkList_Type ) jcasType ) . casFeatCode_fullTextLinks ) , i , jcasType . ll_cas . ll_getFSRef ( v ) ) ; }
indexed setter for fullTextLinks - sets an indexed value -
20,395
public void read ( File f ) throws IOException { FileInputStream fis = new FileInputStream ( f ) ; try { read ( new BufferedReader ( new InputStreamReader ( fis , "UTF-8" ) ) ) ; } finally { IOUtils . closeQuietly ( fis ) ; } }
Read a . obo file
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public void addTerm ( OntologyTerm term ) { terms . put ( term . getId ( ) , term ) ; indexTerm ( term ) ; isTypeOfIsBuilt = false ; }
Add a single OntologyTerm to the ontology .
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public void addOntology ( OBOOntology ont ) { for ( String id : ont . terms . keySet ( ) ) { addTerm ( ont . terms . get ( id ) ) ; } }
Merge a whole ontology into the current one .
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public void writeOntTxt ( PrintWriter pw ) { for ( String id : terms . keySet ( ) ) { OntologyTerm term = terms . get ( id ) ; Set < String > synSet = new HashSet < String > ( ) ; synSet . add ( term . getName ( ) ) ; for ( Synonym s : term . getSynonyms ( ) ) { String st = s . getType ( ) ; if ( id . startsWith ( "PTCO" ) || ( st != null && ! st . matches ( ".*(InChI|SMILES|FORMULA).*" ) ) ) { String synonym = s . getSyn ( ) ; if ( ! synonym . matches ( "\\S" ) ) { synSet . add ( synonym ) ; } } } pw . println ( "[" + id + "]" ) ; for ( String syn : synSet ) pw . println ( syn ) ; pw . println ( ) ; } pw . flush ( ) ; }
Writes a file suitable for use as onotology . txt .
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public Set < String > getIdsForIdsWithAncestors ( Collection < String > termIds ) { Stack < String > idsToConsider = new Stack < String > ( ) ; idsToConsider . addAll ( termIds ) ; Set < String > resultIds = new HashSet < String > ( ) ; while ( ! idsToConsider . isEmpty ( ) ) { String id = idsToConsider . pop ( ) ; if ( ! resultIds . contains ( id ) ) { resultIds . add ( id ) ; if ( terms . containsKey ( id ) ) idsToConsider . addAll ( terms . get ( id ) . getIsA ( ) ) ; } } return resultIds ; }
Given a set of IDs return a set that contains all of the IDs the parents of those IDs the grandparents etc .