docstring stringlengths 3 2.38k | code stringlengths 9 99.4k |
|---|---|
emit annotation | Annotation . getName StringBuilder . append Annotation . getName String . substring StringBuilder . append |
get the canonical names for the whole annotation | Annotation . getNames HashSet . <init> HashSet . add Set . iterator Iterator . hasNext Iterator . next Map < String , Set < String > > . get Set . iterator Iterator . hasNext Iterator . next HashSet . remove HashSet . add |
get the canonical names for the whole annotation | Annotation . getNames HashSet . <init> HashSet . add Set . iterator Iterator . hasNext Iterator . next Map < String , Set < String > > . get Set . iterator Iterator . next HashSet . remove HashSet . add |
total number of classifications | Annotation . getNames Vector . cast Vector . size |
annotate the specified node | Annotation . getNode Annotation . cast Annotation . setNode Annotation . getNode Annotation . setNode |
visit the specified annotation | Annotation . getNode Annotation . setNode |
copy the specified comment | Annotation . getNode Node . cast ArrayList < String > . <init> Comment . <init> Node . setLocation |
visit the specified comment | Annotation . getNode Printer . p |
delete the annotation action specified as a <unk> | Annotation . getObject Annotation . getAction Action . <unk> Annotation . getEntries HashMap . remove Dictionary . <unk> Dictionary . <unk> Annotation . <unk> |
update the current annotation action with this entry | Annotation . getObject Annotation . getAction Action . <unk> Dictionary . <unk> Dictionary . <unk> Dictionary . <unk> Annotation . getEntries Dictionary . <unk> HashMap . put Dictionary . <unk> |
update the current annotation action with this entry | Annotation . getObject Annotation . getAction Action . <unk> Dictionary . <unk> Dictionary . <unk> Dictionary . <unk> Annotation . getEntries HashMap . put Dictionary . <unk> |
delete the annotation action specified as a <unk> | Annotation . getObject Annotation . getAction Action . <unk> Hashtable < Object , Object > . remove Dictionary . <unk> Dictionary . <unk> |
delete the annotation action specified as a <unk> | Annotation . getObject Annotation . getAction Annotation . getEntries HashMap < Object , Object > . remove Dictionary . <unk> Dictionary . <unk> Annotation . <unk> |
delete the annotation action specified as a <unk> | Annotation . getObject Annotation . getAction HashMap . remove Dictionary . <unk> Dictionary . <unk> Annotation . <unk> |
return the appearance stream as defined by the ap dictionary key n | Annotation . getObject HashMap . cast Annotation . getObject Name . cast HashMap . cast Stream . instance Form . cast |
return the appearance stream as defined by the ap dictionary key n | Annotation . getObject HashMap . cast HashMap . instance Annotation . getObject Name . cast Stream . cast |
return the appearance stream as defined by the ap dictionary key n | Annotation . getObject HashMap . instance HashMap . cast Annotation . getObject Name . cast HashMap . cast Stream . instance Stream . cast |
return the appearance stream as defined by the ap dictionary key n | Annotation . getObject HashMap . instance HashMap . cast HashMap . instance Annotation . getObject Name . instance Name . cast Stream . instance Stream . cast |
check to see if the annotation has defined a drawable border width | Annotation . getObject List . cast List . size Number . cast Number . floatValue Annotation . <unk> <unk> . <unk> |
check to see if the annotation has defined a drawable border width | Annotation . getObject List . cast List . size Number . floatValue List . get Annotation . <unk> <unk> . <unk> |
check to see if the annotation has defined a drawable border width | Annotation . getObject List . cast Number . floatValue List . get Number . floatValue Annotation . <unk> <unk> . <unk> |
check to see if the annotation has defined a drawable border width | Annotation . getObject List . instance List . cast List . get Number . cast Number . floatValue Annotation . <unk> <unk> . <unk> |
check to see if the annotation has defined a drawable border width | Annotation . getObject List . instance List . cast List . size Number . cast Number . floatValue Annotation . <unk> <unk> . <unk> |
check to see if the annotation has defined a drawable border width | Annotation . getObject List . instance List . cast Number . cast Number . floatValue Annotation . <unk> <unk> . <unk> |
get the annotation rectangle , and defines the location of the annotation on the page in default user space units | Annotation . getObject List . instance |
get the annotation rectangle , and defines the location of the annotation on the page in default user space units | Annotation . getObject Name . getName |
check to see if the annotation has defined a drawable border width | Annotation . getObject Vector . instance Vector . cast Vector . size Number . floatValue Vector . get Number . floatValue Annotation . <unk> |
get the <unk> <unk> sequence of an annotation bases are reported in 5 to three direction | Annotation . getOrientation Annotation . <unk> Sequence . <init> Annotation . getEnd Sequence . <unk> Sequence . <unk> Sequence . append Annotation . getOrientation Sequence . reverse |
reverse the strand of the annotation | Annotation . getOrientation Annotation . setOrientation Annotation . getOrientation Annotation . setOrientation |
comparison methods | Annotation . getOrientation String . equalsIgnoreCase Annotation . <unk> Annotation . <unk> |
todo document | Annotation . getPackageName Annotation . <unk> |
remove this element from parent and dispose | Annotation . getParent Annotation . dispose |
set the float value of this property | Annotation . getPool ConstantPool . <unk> |
set the long value of this property | Annotation . getPool ConstantPool . <unk> |
set the string value of this property | Annotation . getPool ConstantPool . <unk> |
extract the java value | Annotation . getPool ConstantPool . getEntry Annotation . getProject String . cast Annotation . getPool ConstantPool . getEntry Class . forName Method . invoke Class . getName Number . cast Number . byteValue Number . cast Byte . <init> Number . intValue Character . <init> Number . cast Character . <init> Annotation . getProject String . cast Number . shortValue Short . <init> Number . cast |
extract the java value | Annotation . getPool ConstantPool . getEntry Annotation . getProject String . cast ConstantPool . getEntry Class . forName Method . invoke Class . getName Number . intValue Number . cast Byte . <init> Number . cast Byte . <init> Character . <init> Number . cast Number . intValue Character . <init> Annotation . getProject String . cast Number . cast Short . <init> |
test if one annotation completely contains the region of another | Annotation . getPosition Annotation . getLength Annotation . getPosition Annotation . getLength |
test if the covered region of the binary overlaps for the two annotations provided | Annotation . getPosition Annotation . getLength Annotation . getPosition Annotation . getLength |
import an annotation from another instance | Annotation . getProperties Annotation . setProperties |
this method registers a send activity against the <unk> representation | Annotation . getProperties Map < String , Object > . containsKey Map < String , Object > . get String . cast Map < String > . put |
return the operation name for the supplied interaction | Annotation . getProperties Map < String , Object > . get String . cast String . endsWith String . length String . substring |
this method registers a receive activity against the <unk> representation | Annotation . getProperties String . cast Annotation . getProperties String . cast Map < String > . put |
support String , arrays of string else toString , else toString , strips quotes | Annotation . getProperty AnnotationValue . <unk> String . instance String . cast StringBuffer . <init> String . instance String . cast StringBuffer . append StringBuffer . length StringBuffer . delete StringBuffer . toString AnnotationValue . toString |
add a taxon along with its parents to the database | Annotation . getProperty List . cast List . get String . cast Integer . parseInt Connection . prepareStatement PreparedStatement . setInt PreparedStatement . executeQuery ResultSet . getInt Connection . prepareStatement PreparedStatement . setInt String . equals PreparedStatement . setNull PreparedStatement . setString String . equals PreparedStatement . setNull PreparedStatement . setInt Integer . <init> PreparedStatement . setInt PreparedStatement . setNull PreparedStatement . setInt Integer . <init> PreparedStatement . setInt String . equals PreparedStatement . setNull Integer . <init> Integer . intValue PreparedStatement . setInt PreparedStatement . setNull Integer . intValue PreparedStatement . setInt Connection . prepareStatement PreparedStatement . setInt PreparedStatement . setNull PreparedStatement . setString String . equals PreparedStatement . setNull PreparedStatement . setInt Integer . <init> PreparedStatement . setNull Integer . <init> PreparedStatement . setInt PreparedStatement . setNull PreparedStatement . setInt Integer . <init> PreparedStatement . setNull Integer . <init> Integer . intValue PreparedStatement . setInt PreparedStatement . executeUpdate PreparedStatement . close ResultSet . close PreparedStatement . close |
add a taxon along with its parents to the database | Annotation . getProperty List . instance String . cast List . cast String . cast Integer . parseInt Connection . prepareStatement PreparedStatement . setInt PreparedStatement . executeQuery ResultSet . getInt Connection . prepareStatement PreparedStatement . setInt PreparedStatement . setNull PreparedStatement . setString String . equals PreparedStatement . setNull PreparedStatement . setInt Integer . <init> PreparedStatement . setNull Integer . <init> PreparedStatement . setInt PreparedStatement . setNull Integer . <init> PreparedStatement . setInt String . equals PreparedStatement . setNull Integer . intValue PreparedStatement . setInt Connection . prepareStatement PreparedStatement . setInt String . equals PreparedStatement . setNull PreparedStatement . setString String . equals PreparedStatement . setNull Integer . <init> PreparedStatement . setInt PreparedStatement . setNull PreparedStatement . setInt Integer . <init> PreparedStatement . setInt String . equals PreparedStatement . setNull PreparedStatement . setInt Integer . <init> PreparedStatement . setInt String . equals PreparedStatement . setNull Integer . intValue PreparedStatement . setInt PreparedStatement . executeUpdate PreparedStatement . close ResultSet . close PreparedStatement . close |
convert the matrix annotation to a matrix | Annotation . getProperty String . cast Double . parseDouble |
expand all annotations that cover point , and shift the ones that start after | Annotation . getRange Range . getStart Range . setStart Range . getEnd Annotation . getRange Range . setEnd |
trim the peak to max contiguous subsequence of counts above a certain quantile | Annotation . getStart Annotation . getEnd Annotation . setName Annotation . setOrientation |
check if the oriented end of the read falls in the window | Annotation . getStart Annotation . getEnd |
remove annotation from sentence | Annotation . getStartIndex Annotation . getEndIndex ArrayList < Token > . get ArrayList < Annotation > . remove |
compare two annotations , considering one bigger than the other or equal | Annotation . getStartIndex Annotation . getEndIndex |
keep the current token pointer at the right point in the token list | Annotation . getStartNode Annotation . cast Annotation . getStartNode Annotation . cast Annotation . getStartNode Annotation . cast Annotation . getStartNode |
keep the current token pointer at the right point in the token list | Annotation . getStartNode Annotation . cast Annotation . getStartNode |
get the next token after an annotation | Annotation . getStartNode Annotation . cast |
return the number of tokens between the end of annotation one and the beginning of annotation 2 | Annotation . getStartNode Annotation . cast |
get all the annotations of type target type from the source annotation set that lie within the range of the containing annotation | Annotation . getStartNode Annotation . getEndNode Annotation . getStartNode Annotation . getEndNode |
this method verifies if a source annotation can <unk> inserted safety into the a target <unk> set | Annotation . getStartNode Annotation . getEndNode Annotation . getStartNode Long . longValue Iterator < Annotation > . next |
this method verifies if a source annotation can <unk> inserted safety into the a target <unk> set | Annotation . getStartNode Annotation . getEndNode Long . longValue Iterator < Annotation > . hasNext Iterator < Annotation > . next Annotation . getEndNode |
add an annotation to the start offset index | Annotation . getStartNode Annotation . getEndNode Node . getOffset Map < Integer , Object > . get Map < Integer , Object > . put Annotation . instance HashSet < Annotation > . <init> Set < Annotation > . add Node . getId Map < Integer , Object > . put Set < Annotation > . cast Set < Annotation > . add |
add an annotation to the start offset index | Annotation . getStartNode Annotation . getEndNode Node . getOffset Node . getId Map < Integer , Object > . get Node . getId Map < Integer , Object > . put Annotation . instance HashSet < Annotation > . <init> Annotation . cast Set < Annotation > . add Node . getId Map < Integer , Object > . put Set < Annotation > . cast Set < Annotation > . add |
get all the annotations of type target type from the source annotation set that cover the range of the specified annotation | Annotation . getStartNode Annotation . getEndNode |
give an annotation , this method returns the string of that annotation | Annotation . getStartNode Annotation . getEndNode |
return the underlying string for the annotation | Annotation . getStartNode Annotation . getEndNode |
<unk> of mentions : for <unk> phrases , take the number of the last noun before the first <unk> e | Annotation . getStartNode Annotation . getFeatures ArrayList < Annotation > . <init> Collections . sort List < Annotation > . size List < Annotation > . get String . cast Annotation . getFeatures String . cast String . matches List < Annotation > . get String . cast String . matches |
<unk> a <unk> , <unk> reduced and proper sequence features to noun phrase | Annotation . getStartNode ArrayList < String > . <init> String . cast List < String > . add String . split String . startsWith String . length List < String > . add String . trim Annotation . getFeatures |
get the underlying text of the annotation | Annotation . getStartNode Document . getContent |
find position of a token in the input annotations list | Annotation . getStartNode List < Annotation > . get |
remove from the offset indices | Annotation . getStartNode Map < Integer , Object > . get Annotation . instance Map < Integer , Object > . remove Collection < Annotation > . cast Collection < Annotation > . remove Map < Integer , Object > . put |
two annotation are <unk> if their offsets are the same | Annotation . getStartNode Node . getOffset Annotation . getStartNode Node . getOffset Annotation . getEndNode Node . getOffset |
determine if this annotation covers completely in span annotation a | Annotation . getStartOffset Annotation . <unk> |
this method tells if this and annotation a overlap | Annotation . getStartOffset Annotation . <unk> |
update values in the text fields in the edit panel : start , end , id , ref | Annotation . getStartOffset Annotation . getEndOffset Annotation . getStartOffset JTextField . setText Annotation . getEndOffset String . valueOf JTextField . setText Annotation . getAttribute JTextField . setText Annotation . getAttribute JTextField . setText |
add highlighting for words covered by the specified annotation | Annotation . getStartPosition Annotation . getLength |
remove css highlighting for words covered by the specified annotation | Annotation . getStartPosition Annotation . getLength |
this method initializes annotation id dependent on provider | Annotation . getStatus System . currentTimeMillis Annotation . <unk> |
call the annotation edition frame and set the element content | Annotation . getText Annotation . setText |
check if the token could be an initial like a | Annotation . getText Character . isUpperCase String . length |
delete the annotation similarity line that contains an id | Annotation . getText String . indexOf String . substring String . indexOf String . length Annotation . setText |
delete the annotation note line that contains an id | Annotation . getText String . indexOf String . substring String . indexOf String . length String . substring Annotation . setText |
delete the annotation note line that contains an id | Annotation . getText String . indexOf String . substring String . length Annotation . setText |
do the actual tokenization | Annotation . getText String . length String . charAt Character . getType HashMap . <init> String . substring Map < String , Object > . put String . length Map < String , Object > . put Document . <unk> String . substring Map < String , Object > . put Integer . toString Map < String , Object > . put Document . <unk> String . substring HashMap . <init> Map < String , Object > . put String . length Map < String , Object > . put Document . <unk> |
get substring from the char range [ start , end | Annotation . getText String . substring |
explicitly including genes in custom annotation in all <unk> categories of custom ontology | Annotation . getType Annotation . <init> Annotation . getType Annotation . <unk> Annotation . getMap HashMap . keySet HashSet < String > . <init> Map . get HashSet < String > . addAll Map . get HashSet < String > . addAll HashSet . <init> Iterator . next Annotation . <unk> Annotation . add |
explicitly including genes in custom annotation in all <unk> categories of custom ontology | Annotation . getType Annotation . <init> Annotation . getType Annotation . <unk> Annotation . getMap HashMap . keySet HashSet < String > . <init> Map . get HashSet < String > . cast HashSet < String > . addAll Iterator . hasNext HashSet . <init> Iterator . next HashSet < String > . contains Annotation . <unk> Annotation . add |
take in an annotation and if the annotation type is one of the entities that is needed , it process and store it in the entity list | Annotation . getType Annotation . getFeatures Entity . <init> List < Entity > . add Annotation . getFeatures Annotation . getType Annotation . getEndNode String . substring Entity . <init> List < Entity > . add Annotation . getType String . substring List < Entity > . add Annotation . getStartNode String . substring Entity . <init> List < Entity > . add String . substring List < Entity > . add |
add the type of the annotation to the list of annotation types | Annotation . getType HashMap < String , Integer > . containsKey HashMap < String , Integer > . put HashMap < String , Integer > . get HashMap < String , Integer > . put |
remove from the type index | Annotation . getType Map < String > . get Annotation . getType Map < String > . remove |
check if the given annotation is a <unk> annotation and false otherwise | Annotation . getType String . startsWith |
extract feature values | Annotation . getType Type . <unk> Annotation . getStringValue List < String > . add Annotation . <unk> List < String > . add String . valueOf List < String > . add String . valueOf List < String > . add Annotation . <unk> String . valueOf List < String > . add Annotation . <unk> String . valueOf List < String > . add Annotation . <unk> |
extract feature values | Annotation . getType Type . <unk> Annotation . getStringValue List < String > . add String . valueOf List < String > . add Annotation . getFloatValue List < String > . add Annotation . <unk> List < String > . add String . valueOf List < String > . add Annotation . <unk> String . valueOf List < String > . add Annotation . <unk> List < String > . add Annotation . <unk> |
copy the provided annotation into the provided const pool | Annotation . getTypeName Annotation . <init> String . cast Annotation . <unk> Annotation . <unk> |
construct a display location from an annotation of type net | Annotation . getValue HashMap < String , Object > . get String . cast HashMap < String , Object > . get Double . cast HashMap < String , Object > . get Double . cast |
return the byte value of this property , or false if not set | Annotation . getValue Number . byteValue Number . cast |
return the float value of this property , or 0 if not set | Annotation . getValue Number . cast Number . floatValue |
return the int value of this property , or 0 if not set | Annotation . getValue Number . cast Number . intValue |
return the long value of this property , or 0 if not set | Annotation . getValue Number . cast Number . longValue Number . cast |
return the short value of this property , or 0 if not set | Annotation . getValue Number . cast Number . shortValue Number . cast |
return the double value of this property , or 0 if not set | Annotation . getValue Number . doubleValue Number . cast |
return the class value of this property , or null if not set | Annotation . getValue String . cast |
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