idx int64 0 41.2k | question stringlengths 74 4.21k | target stringlengths 5 888 |
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6,200 | private BioPAXElement getIdentical ( BioPAXElement bpe ) { int key = bpe . hashCode ( ) ; List < BioPAXElement > list = equivalenceMap . get ( key ) ; if ( list != null ) { for ( BioPAXElement other : list ) { if ( other . equals ( bpe ) ) { return other ; } } } return null ; } | Searches the target model for an identical of given BioPAX element and returns this element if it finds it . |
6,201 | private void addIntoEquivalanceMap ( BioPAXElement bpe ) { int key = bpe . hashCode ( ) ; List < BioPAXElement > list = equivalenceMap . get ( key ) ; if ( list == null ) { list = new ArrayList < BioPAXElement > ( ) ; equivalenceMap . put ( key , list ) ; } list . add ( bpe ) ; } | Adds a BioPAX element into the equivalence map . |
6,202 | public static Set < BioPAXElement > runNeighborhood ( Set < BioPAXElement > sourceSet , Model model , int limit , Direction direction , Filter ... filters ) { Graph graph ; if ( model . getLevel ( ) == BioPAXLevel . L3 ) { if ( direction == Direction . UNDIRECTED ) { graph = new GraphL3Undirected ( model , filters ) ; ... | Gets neighborhood of the source set . |
6,203 | public static Set < BioPAXElement > runPathsBetween ( Set < BioPAXElement > sourceSet , Model model , int limit , Filter ... filters ) { Graph graph ; if ( model . getLevel ( ) == BioPAXLevel . L3 ) { graph = new GraphL3 ( model , filters ) ; } else return Collections . emptySet ( ) ; Collection < Set < Node > > source... | Gets the graph constructed by the paths between the given seed nodes . Does not get paths between physical entities that belong the same entity reference . |
6,204 | public static Set < BioPAXElement > runGOI ( Set < BioPAXElement > sourceSet , Model model , int limit , Filter ... filters ) { return runPathsFromTo ( sourceSet , sourceSet , model , LimitType . NORMAL , limit , filters ) ; } | Gets paths between the seed nodes . |
6,205 | public static Set < BioPAXElement > runCommonStream ( Set < BioPAXElement > sourceSet , Model model , Direction direction , int limit , Filter ... filters ) { Graph graph ; if ( model . getLevel ( ) == BioPAXLevel . L3 ) { graph = new GraphL3 ( model , filters ) ; } else return Collections . emptySet ( ) ; Collection <... | Gets the elements in the common upstream or downstream of the seed |
6,206 | private static Set < BioPAXElement > convertQueryResult ( Set < GraphObject > resultWrappers , Graph graph , boolean removeDisconnected ) { Set < Object > result = graph . getWrappedSet ( resultWrappers ) ; Set < BioPAXElement > set = new HashSet < BioPAXElement > ( ) ; for ( Object o : result ) { set . add ( ( BioPAXE... | Converts the query result from wrappers to wrapped BioPAX elements . |
6,207 | public static Set < Node > prepareSingleNodeSet ( Set < BioPAXElement > elements , Graph graph ) { Map < BioPAXElement , Set < PhysicalEntity > > map = getRelatedPhysicalEntityMap ( elements ) ; Set < PhysicalEntity > pes = new HashSet < PhysicalEntity > ( ) ; for ( Set < PhysicalEntity > valueSet : map . values ( ) ) ... | Gets the related wrappers of the given elements in a set . |
6,208 | public static Set < Node > prepareSingleNodeSetFromSets ( Set < Set < BioPAXElement > > sets , Graph graph ) { Set < BioPAXElement > elements = new HashSet < BioPAXElement > ( ) ; for ( Set < BioPAXElement > set : sets ) { elements . addAll ( set ) ; } return prepareSingleNodeSet ( elements , graph ) ; } | Gets the related wrappers of the given elements in the sets . |
6,209 | public static Map < BioPAXElement , Set < PhysicalEntity > > getRelatedPhysicalEntityMap ( Collection < BioPAXElement > elements ) { replaceXrefsWithRelatedER ( elements ) ; Map < BioPAXElement , Set < PhysicalEntity > > map = new HashMap < BioPAXElement , Set < PhysicalEntity > > ( ) ; for ( BioPAXElement ele : elemen... | Maps each BioPAXElement to its related PhysicalEntity objects . |
6,210 | protected static void replaceXrefsWithRelatedER ( Collection < BioPAXElement > elements ) { Set < EntityReference > ers = new HashSet < EntityReference > ( ) ; Set < Xref > xrefs = new HashSet < Xref > ( ) ; for ( BioPAXElement element : elements ) { if ( element instanceof Xref ) { xrefs . add ( ( Xref ) element ) ; f... | Replaces Xref objects with the related EntityReference objects . This is required for the use case when user provides multiple xrefs that point to the same ER . |
6,211 | public static Set < PhysicalEntity > getRelatedPhysicalEntities ( BioPAXElement element , Set < PhysicalEntity > pes ) { if ( pes == null ) pes = new HashSet < PhysicalEntity > ( ) ; if ( element instanceof PhysicalEntity ) { PhysicalEntity pe = ( PhysicalEntity ) element ; if ( ! pes . contains ( pe ) ) { pes . add ( ... | Gets the related PhysicalEntity objects of the given BioPAXElement in level 3 models . |
6,212 | private static void addEquivalentsComplexes ( PhysicalEntity pe , Set < PhysicalEntity > pes ) { addEquivalentsComplexes ( pe , true , pes ) ; } | Adds equivalents and parent complexes of the given PhysicalEntity to the parameter set . |
6,213 | public static Set < Node > getSeedInteractions ( Collection < BioPAXElement > elements , Graph graph ) { Set < Node > nodes = new HashSet < Node > ( ) ; for ( BioPAXElement ele : elements ) { if ( ele instanceof Conversion || ele instanceof TemplateReaction || ele instanceof Control ) { GraphObject go = graph . getGrap... | Extracts the querible interactions from the elements . |
6,214 | public String getColumnValue ( SIFInteraction inter ) { switch ( type ) { case MEDIATOR : return concat ( inter . getMediatorIDs ( ) ) ; case PATHWAY : return concat ( inter . getPathwayNames ( ) ) ; case PATHWAY_URI : return concat ( inter . getPathwayUris ( ) ) ; case PUBMED : return concat ( inter . getPublicationID... | Get the string to write in the output file . |
6,215 | public void writeSBGN ( Model model , String file ) { Sbgn sbgn = createSBGN ( model ) ; try { SbgnUtil . writeToFile ( sbgn , new File ( file ) ) ; } catch ( JAXBException e ) { throw new RuntimeException ( "writeSBGN, SbgnUtil.writeToFile failed" , e ) ; } } | Converts the given model to SBGN and writes in the specified file . |
6,216 | public void writeSBGN ( Model model , OutputStream stream ) { Sbgn sbgn = createSBGN ( model ) ; try { JAXBContext context = JAXBContext . newInstance ( "org.sbgn.bindings" ) ; Marshaller marshaller = context . createMarshaller ( ) ; marshaller . setProperty ( Marshaller . JAXB_FORMATTED_OUTPUT , Boolean . TRUE ) ; mar... | Converts the given model to SBGN and writes in the specified output stream . |
6,217 | private void processControllers ( Set < Control > controls , Glyph process ) { for ( Control ctrl : controls ) { Glyph g = createControlStructure ( ctrl ) ; if ( g != null ) { createArc ( g , process , getControlType ( ctrl ) , null ) ; processControllers ( ctrl . getControlledOf ( ) , g ) ; } } } | Associate all the controllers of this process ; |
6,218 | private String extractGeneSymbol ( Xref xref ) { if ( xref . getDb ( ) != null && ( xref . getDb ( ) . equalsIgnoreCase ( "HGNC Symbol" ) || xref . getDb ( ) . equalsIgnoreCase ( "Gene Symbol" ) || xref . getDb ( ) . equalsIgnoreCase ( "HGNC" ) ) ) { String ref = xref . getId ( ) ; if ( ref != null ) { ref = ref . trim... | Searches for gene symbol in Xref . |
6,219 | public void setRangeRestriction ( Map < Class < ? extends BioPAXElement > , Set < Class < ? extends BioPAXElement > > > restrictedRanges ) { this . restrictedRanges = restrictedRanges ; } | This method sets all range restrictions . |
6,220 | public Collection < BioPAXElement > generate ( Match match , int ... ind ) { Collection < BioPAXElement > gen = new HashSet < BioPAXElement > ( con [ 0 ] . generate ( match , ind ) ) ; Set < BioPAXElement > input = new HashSet < BioPAXElement > ( ) ; Set < BioPAXElement > output = new HashSet < BioPAXElement > ( gen ) ... | Chains the member constraints and returns the output of the last constraint . |
6,221 | public Collection < BioPAXElement > generate ( Match match , int ... ind ) { Control ctrl = ( Control ) match . get ( ind [ 0 ] ) ; return new HashSet < BioPAXElement > ( getRelatedERs ( ctrl ) ) ; } | Navigates to the related ERs of the controllers of the given Control . |
6,222 | public Collection < BioPAXElement > generate ( Match match , int ... ind ) { PhysicalEntity pe = ( PhysicalEntity ) match . get ( ind [ 0 ] ) ; Conversion conv = ( Conversion ) match . get ( ind [ 1 ] ) ; if ( ! ( ( peType == RelType . INPUT && getConvParticipants ( conv , RelType . INPUT ) . contains ( pe ) ) || ( peT... | According to the relation between PhysicalEntity and the Conversion checks of the Control is relevant . If relevant it is retrieved . |
6,223 | public void init ( ) { ControlType type = ctrl . getControlType ( ) ; if ( type != null && type . toString ( ) . startsWith ( "I" ) ) { sign = NEGATIVE ; } else { sign = POSITIVE ; } if ( ctrl instanceof TemplateReactionRegulation ) transcription = true ; } | Extracts the sign and the type of the Control . |
6,224 | private void bindUpstream ( BioPAXElement element ) { AbstractNode node = ( AbstractNode ) graph . getGraphObject ( element ) ; if ( node != null ) { Edge edge = new EdgeL3 ( node , this , graph ) ; node . getDownstreamNoInit ( ) . add ( edge ) ; this . getUpstreamNoInit ( ) . add ( edge ) ; } } | Puts the wrapper of the parameter element to the upstream of this Control . |
6,225 | public Set getValueFromModel ( Model model ) { Set < ? extends BioPAXElement > domains = new HashSet < BioPAXElement > ( model . getObjects ( this . getDomain ( ) ) ) ; return getValueFromBeans ( domains ) ; } | This method runs the path query on all the elements within the model . |
6,226 | private void load ( String filename ) { try { load ( new FileInputStream ( filename ) ) ; } catch ( FileNotFoundException e ) { e . printStackTrace ( ) ; } } | Reads data from the given file . |
6,227 | private void load ( InputStream is ) { try { BufferedReader reader = new BufferedReader ( new InputStreamReader ( is ) ) ; for ( String line = reader . readLine ( ) ; line != null ; line = reader . readLine ( ) ) { String [ ] tok = line . split ( DELIM ) ; if ( tok . length >= 3 ) { addEntry ( tok [ 0 ] , Integer . par... | Reads data from the input stream and loads itself . |
6,228 | public void addEntry ( String id , int score , RelType context ) { this . score . put ( id , score ) ; this . context . put ( id , context ) ; } | Adds a new blacklisted ID . |
6,229 | public void write ( String filename ) { try { write ( new FileOutputStream ( filename ) ) ; } catch ( FileNotFoundException e ) { e . printStackTrace ( ) ; } } | Dumps data to the given file . |
6,230 | public void write ( OutputStream os ) { List < String > ids = new ArrayList < String > ( score . keySet ( ) ) ; final Map < String , Integer > score = this . score ; Collections . sort ( ids , new Comparator < String > ( ) { public int compare ( String o1 , String o2 ) { return score . get ( o2 ) . compareTo ( score . ... | Dumps data to the given output stream . |
6,231 | private RelType convertContext ( String type ) { if ( type . equals ( "I" ) ) return RelType . INPUT ; if ( type . equals ( "O" ) ) return RelType . OUTPUT ; if ( type . equals ( "B" ) ) return null ; throw new IllegalArgumentException ( "Unknown context: " + type ) ; } | Converts text context to enum . |
6,232 | private Set < String > getLeastUbique ( Collection < String > ids ) { Set < String > select = new HashSet < String > ( ) ; int s = getLeastScore ( ids ) ; for ( String id : ids ) { if ( score . get ( id ) == s ) select . add ( id ) ; } return select ; } | Gets the subset with the least score . |
6,233 | private int getLeastScore ( Collection < String > ids ) { int s = Integer . MAX_VALUE ; for ( String id : ids ) { if ( score . get ( id ) < s ) s = score . get ( id ) ; } return s ; } | Gets the least score of the given ids . |
6,234 | private boolean isUbiqueInBothContexts ( String id ) { return context . containsKey ( id ) && context . get ( id ) == null ; } | Checks if the given ID is blacklisted in both contexts together . |
6,235 | private boolean isUbique ( String id , RelType context ) { if ( context == null ) return this . context . containsKey ( id ) ; if ( ! isUbique ( id ) ) return false ; RelType ctx = this . context . get ( id ) ; return ctx == null || ctx . equals ( context ) ; } | Checks if the given ID is blacklisted in the given context . |
6,236 | public boolean isUbique ( PhysicalEntity pe ) { String id = getSMRID ( pe ) ; return id != null && isUbique ( id ) ; } | Checks if the given entity is blacklisted in at least one context . |
6,237 | public boolean isUbiqueInBothContexts ( PhysicalEntity pe ) { String id = getSMRID ( pe ) ; return id != null && isUbiqueInBothContexts ( id ) ; } | Checks if the given entity is blacklisted in both context together . |
6,238 | public boolean isUbique ( PhysicalEntity pe , Conversion conv , ConversionDirectionType dir , RelType context ) { String id = getSMRID ( pe ) ; if ( id == null ) return false ; if ( dir == null ) throw new IllegalArgumentException ( "The conversion direction has to be specified." ) ; if ( context == null ) throw new Il... | Checks if the given entity is blacklisted for the given Conversion assuming the Conversion flows towards the given direction and the entity is in given context . |
6,239 | private String getSMRID ( PhysicalEntity pe ) { if ( pe instanceof SmallMolecule ) { EntityReference er = ( ( SmallMolecule ) pe ) . getEntityReference ( ) ; if ( er != null ) return er . getUri ( ) ; } return null ; } | Gets the ID of the reference of the given entity if it is a small molecule . |
6,240 | protected void addToDownstream ( BioPAXElement pe , Graph graph ) { AbstractNode node = ( AbstractNode ) graph . getGraphObject ( pe ) ; if ( node != null ) { EdgeL3 edge = new EdgeL3 ( this , node , graph ) ; edge . setTranscription ( true ) ; node . getUpstreamNoInit ( ) . add ( edge ) ; this . getDownstreamNoInit ( ... | Binds the given PhysicalEntity to the downstream . |
6,241 | public void initDownstream ( ) { for ( Interaction inter : getDownstreamInteractions ( pe . getParticipantOf ( ) ) ) { AbstractNode node = ( AbstractNode ) graph . getGraphObject ( inter ) ; if ( node == null ) continue ; if ( inter instanceof Conversion ) { Conversion conv = ( Conversion ) inter ; ConversionWrapper co... | Binds to downstream interactions . |
6,242 | protected Set < Interaction > getDownstreamInteractions ( Collection < Interaction > inters ) { Set < Interaction > set = new HashSet < Interaction > ( ) ; for ( Interaction inter : inters ) { if ( inter instanceof Conversion ) { Conversion conv = ( Conversion ) inter ; ConversionDirectionType dir = conv . getConversio... | Gets the downstream interactions among the given set . |
6,243 | private Set < Conversion > getRelatedConversions ( Collection < Interaction > inters ) { Set < Conversion > set = new HashSet < Conversion > ( ) ; for ( Interaction inter : inters ) { if ( inter instanceof Conversion ) { set . add ( ( Conversion ) inter ) ; } else if ( inter instanceof Control ) { getRelatedConversions... | Get all related Conversions of the given Interaction set . |
6,244 | private Set < Conversion > getRelatedConversions ( Control ctrl , Set < Conversion > set ) { for ( Process process : ctrl . getControlled ( ) ) { if ( process instanceof Conversion ) { set . add ( ( Conversion ) process ) ; } else if ( process instanceof Control ) { getRelatedConversions ( ( Control ) process , set ) ;... | Recursively searches the related Conversions of a Control . |
6,245 | public void convert ( InputStream inputStream , OutputStream outputStream , boolean forceInteractionToComplex ) throws IOException , PsimiXmlReaderException { if ( inputStream == null || outputStream == null ) { throw new IllegalArgumentException ( "convert(): " + "one or more null arguments." ) ; } PsimiXmlReader read... | Converts the PSI - MI inputStream into BioPAX outputStream . Streams will be closed by the converter . |
6,246 | public void convertTab ( InputStream inputStream , OutputStream outputStream , boolean forceInteractionToComplex ) throws IOException , PsimiTabException { if ( inputStream == null || outputStream == null ) { throw new IllegalArgumentException ( "convertTab(): " + "one or more null arguments." ) ; } PsimiTabReader read... | Converts the PSI - MITAB inputStream into BioPAX outputStream . Streams will be closed by the converter . |
6,247 | public void convert ( EntrySet entrySet , OutputStream outputStream , boolean forceInteractionToComplex ) { if ( entrySet == null || outputStream == null ) { throw new IllegalArgumentException ( "convert: one or more null arguments." ) ; } if ( entrySet . getLevel ( ) != 2 ) { throw new IllegalArgumentException ( "conv... | Converts the PSI interactions from the EntrySet and places into BioPAX output stream . Stream will be closed by the converter . |
6,248 | public void writeResult ( Map < BioPAXElement , List < Match > > matches , OutputStream out ) throws IOException { OutputStreamWriter writer = new OutputStreamWriter ( out ) ; for ( BioPAXElement ele : matches . keySet ( ) ) { Set < String > syms = new HashSet < String > ( ) ; for ( Match m : matches . get ( ele ) ) { ... | Writes the IDs of interaction then gene symbols of related proteins in a line . |
6,249 | public Collection < BioPAXElement > generate ( Match match , int ... ind ) { Collection < BioPAXElement > gen = con . generate ( match , ind ) ; gen . add ( match . get ( ind [ selfIndex ] ) ) ; return gen ; } | Gets the first mapped element along with the generated elements of wrapped constraint . |
6,250 | public boolean satisfies ( Match match , int ... ind ) { return match . get ( ind [ selfIndex ] ) == match . get ( ind [ ind . length - 1 ] ) || super . satisfies ( match , ind ) ; } | Checks if the last index is either generated or equal to the first element . |
6,251 | public GraphObject getGraphObject ( Object obj ) { String key = getKey ( obj ) ; GraphObject go = objectMap . get ( key ) ; if ( go == null ) { Node node = wrap ( obj ) ; if ( node != null ) { objectMap . put ( key , node ) ; node . init ( ) ; } } return objectMap . get ( key ) ; } | Gets the related wrapper for the given object creates the wrapper if not created before . |
6,252 | public String convert ( SIFInteraction inter ) { String s = inter . toString ( ) ; for ( OutputColumn column : columns ) { s += "\t" + column . getColumnValue ( inter ) ; } return s ; } | Prepares the line in the output file for the given interaction . |
6,253 | private static Map < String , Set < BioPAXElement > > collectEntityRefs ( Collection < SIFInteraction > inters ) { Map < String , Set < BioPAXElement > > map = new HashMap < String , Set < BioPAXElement > > ( ) ; for ( SIFInteraction inter : inters ) { if ( ! map . containsKey ( inter . sourceID ) ) map . put ( inter .... | Collects the sources and targets in given interactions . |
6,254 | private static String concat ( Collection < String > col ) { StringBuilder b = new StringBuilder ( ) ; boolean first = true ; for ( String s : col ) { if ( first ) first = false ; else b . append ( ";" ) ; b . append ( s ) ; } return b . toString ( ) ; } | Concatenates the given collection of strings into a single string where values are separated with a semicolon . |
6,255 | public void initUpstream ( ) { NucleicAcid nuc = tempReac . getTemplate ( ) ; if ( nuc != null ) addToUpstream ( nuc , getGraph ( ) ) ; for ( Control cont : tempReac . getControlledOf ( ) ) { addToUpstream ( cont , graph ) ; } } | Binds to template and controllers . |
6,256 | protected void addToUpstream ( BioPAXElement ele , org . biopax . paxtools . query . model . Graph graph ) { AbstractNode node = ( AbstractNode ) graph . getGraphObject ( ele ) ; if ( node == null ) return ; Edge edge = new EdgeL3 ( node , this , graph ) ; if ( isTranscription ( ) ) { if ( node instanceof ControlWrappe... | Binds the given element to the upstream . |
6,257 | public Set < GraphObject > run ( ) { Map < GraphObject , Integer > candidate = new HashMap < GraphObject , Integer > ( ) ; Set < GraphObject > result = new HashSet < GraphObject > ( ) ; for ( Set < Node > source : sourceSet ) { BFS bfs = new BFS ( source , null , direction , limit ) ; Map < GraphObject , Integer > BFSR... | Method to run the query . |
6,258 | public BioPAXElement get ( String label , Pattern p ) { return variables [ p . indexOf ( label ) ] ; } | Gets element corresponding to the given label in the pattern . |
6,259 | public List < BioPAXElement > get ( String [ ] label , Pattern p ) { if ( label == null ) return Collections . emptyList ( ) ; List < BioPAXElement > list = new ArrayList < BioPAXElement > ( label . length ) ; for ( String lab : label ) { list . add ( variables [ p . indexOf ( lab ) ] ) ; } return list ; } | Gets elements corresponding to the given labels in the pattern . |
6,260 | public String getAName ( BioPAXElement ele ) { String name = null ; if ( ele instanceof Named ) { Named n = ( Named ) ele ; if ( n . getDisplayName ( ) != null && n . getDisplayName ( ) . length ( ) > 0 ) name = n . getDisplayName ( ) ; else if ( n . getStandardName ( ) != null && n . getStandardName ( ) . length ( ) >... | Finds a name for the variable . |
6,261 | public void init ( ) { if ( conv . getConversionDirection ( ) == ConversionDirectionType . REVERSIBLE && this . reverse == null ) { reverse = new ConversionWrapper ( conv , ( GraphL3 ) graph ) ; this . direction = LEFT_TO_RIGHT ; reverse . direction = RIGHT_TO_LEFT ; reverse . reverse = this ; } else if ( conv . getCon... | Extracts the direction creates the reverse if necessary . |
6,262 | public void initUpstream ( ) { if ( direction == LEFT_TO_RIGHT ) { for ( PhysicalEntity pe : conv . getLeft ( ) ) { addToUpstream ( pe , getGraph ( ) ) ; } } else { for ( PhysicalEntity pe : conv . getRight ( ) ) { addToUpstream ( pe , getGraph ( ) ) ; } } for ( Control cont : conv . getControlledOf ( ) ) { if ( cont i... | Binds inputs and controllers . |
6,263 | public void initDownstream ( ) { if ( direction == RIGHT_TO_LEFT ) { for ( PhysicalEntity pe : conv . getLeft ( ) ) { addToDownstream ( pe , getGraph ( ) ) ; } } else { for ( PhysicalEntity pe : conv . getRight ( ) ) { addToDownstream ( pe , getGraph ( ) ) ; } } } | Binds products . |
6,264 | public Pattern getPattern ( ) { if ( pattern == null ) { pattern = constructPattern ( ) ; if ( this instanceof SIFMiner && idFetcher != null && idMap != null ) { pattern . add ( new HasAnID ( idFetcher , idMap ) , ( ( SIFMiner ) this ) . getSourceLabel ( ) ) ; pattern . add ( new HasAnID ( idFetcher , idMap ) , ( ( SIF... | Gets the pattern constructs if null . |
6,265 | public boolean isInhibition ( Control ctrl ) { return ctrl . getControlType ( ) != null && ctrl . getControlType ( ) . toString ( ) . startsWith ( "I" ) ; } | Checks if the type of a Control is inhibition . |
6,266 | public Set < String > toStringSet ( Set < ModificationFeature > set ) { List < ModificationFeature > list = new ArrayList < ModificationFeature > ( set ) ; Collections . sort ( list , new Comparator < ModificationFeature > ( ) { public int compare ( ModificationFeature o1 , ModificationFeature o2 ) { String t1 = getMod... | Sorts the modifications and gets them in a String . |
6,267 | private Set < String > getInString ( List < ModificationFeature > list ) { Set < String > text = new HashSet < String > ( list . size ( ) ) ; for ( ModificationFeature mf : list ) { String term = getModificationTerm ( mf ) ; String loc = getPositionInString ( mf ) ; if ( term != null ) { String s = term + loc ; if ( ! ... | Gets the modifications is a string that is separated with comma . |
6,268 | public String getModificationTerm ( ModificationFeature mf ) { Set vals = TERM_ACC . getValueFromBean ( mf ) ; if ( vals . isEmpty ( ) ) return null ; return vals . iterator ( ) . next ( ) . toString ( ) ; } | Gets the String term of the modification feature . |
6,269 | public int getPositionStart ( ModificationFeature mf ) { Set vals = SITE_ACC . getValueFromBean ( mf ) ; if ( ! vals . isEmpty ( ) ) { return ( ( Integer ) vals . iterator ( ) . next ( ) ) ; } vals = INTERVAL_BEGIN_ACC . getValueFromBean ( mf ) ; if ( ! vals . isEmpty ( ) ) { return ( ( Integer ) vals . iterator ( ) . ... | Gets the first position of the modification feature . |
6,270 | public String getPositionInString ( ModificationFeature mf ) { Set vals = SITE_ACC . getValueFromBean ( mf ) ; if ( ! vals . isEmpty ( ) ) { int x = ( ( Integer ) vals . iterator ( ) . next ( ) ) ; if ( x > 0 ) return "@" + x ; } vals = INTERVAL_BEGIN_ACC . getValueFromBean ( mf ) ; if ( ! vals . isEmpty ( ) ) { int be... | Gets the position of the modification feature as a String . |
6,271 | protected Set < String > getModifications ( Match m , String label ) { PhysicalEntity pe = ( PhysicalEntity ) m . get ( label , getPattern ( ) ) ; return toStringSet ( new HashSet < ModificationFeature > ( FEAT_ACC . getValueFromBean ( pe ) ) ) ; } | Gets modifications of the given element in a string . The element has to be a PhysicalEntity . |
6,272 | protected String concat ( Set < String > set , String sep ) { String s = "" ; int i = set . size ( ) ; for ( String ss : set ) { s += ss ; if ( -- i > 0 ) s += sep ; } return s ; } | Converts the set of string to a single string . |
6,273 | protected int sign ( Control ctrl ) { ControlType type = ctrl . getControlType ( ) ; if ( type != null && type . name ( ) . startsWith ( "I" ) ) return - 1 ; return 1 ; } | Identifies negative and positive controls . Assumes positive by default . |
6,274 | protected int sign ( Match m , String ... ctrlLabel ) { int sign = 1 ; for ( String lab : ctrlLabel ) { Control ctrl = ( Control ) m . get ( lab , getPattern ( ) ) ; sign *= sign ( ctrl ) ; } return sign ; } | Checks the cumulative sign of the chained controls . |
6,275 | protected boolean labeledInactive ( Match m , String simpleLabel , String complexLabel ) { PhysicalEntityChain chain = getChain ( m , simpleLabel , complexLabel ) ; PhysicalEntityChain . Activity activity = chain . checkActivityLabel ( ) ; return activity == PhysicalEntityChain . Activity . INACTIVE ; } | Checks if a PE chain is labeled as inactive . |
6,276 | protected void writeResultDetailed ( Map < BioPAXElement , List < Match > > matches , OutputStream out , int columns ) throws IOException { OutputStreamWriter writer = new OutputStreamWriter ( out ) ; String header = getHeader ( ) ; if ( header != null ) { writer . write ( header ) ; } else { for ( int i = 0 ; i < colu... | Writes the result as a tab delimited format where the column values are customized . |
6,277 | public Set < SIFInteraction > createSIFInteraction ( Match m , IDFetcher fetcher ) { BioPAXElement sourceBpe = m . get ( ( ( SIFMiner ) this ) . getSourceLabel ( ) , getPattern ( ) ) ; BioPAXElement targetBpe = m . get ( ( ( SIFMiner ) this ) . getTargetLabel ( ) , getPattern ( ) ) ; Set < String > sources = fetchIDs (... | Creates a SIF interaction for the given match . |
6,278 | protected Set < String > getIdentifiers ( Match m , String label ) { BioPAXElement el = m . get ( label , getPattern ( ) ) ; if ( idFetcher != null ) return idFetcher . fetchID ( el ) ; Set < String > set = new HashSet < String > ( ) ; if ( el instanceof ProteinReference ) { set . add ( getGeneSymbol ( ( ProteinReferen... | Uses uniprot name or gene symbol as identifier . |
6,279 | public void update ( LGraphObject lGraphObj ) { if ( lGraphObj instanceof CoSEGraph ) { return ; } LNode lNode = ( LNode ) lGraphObj ; this . glyph . getBbox ( ) . setX ( ( float ) lNode . getLeft ( ) ) ; this . glyph . getBbox ( ) . setY ( ( float ) lNode . getTop ( ) ) ; this . placeStateAndInfoGlyphs ( ) ; } | Function that will take place when VNode objects will update in layout process of ChiLay |
6,280 | public void setBounds ( float w , float h ) { this . glyph . getBbox ( ) . setW ( w ) ; this . glyph . getBbox ( ) . setH ( h ) ; } | Sets the bound of this VNode by given width and height |
6,281 | public void setSizeAccordingToClass ( ) { String glyphClass = this . glyph . getClazz ( ) ; if ( glyphClass . equalsIgnoreCase ( NONE ) ) return ; if ( glyphClass . equalsIgnoreCase ( SOURCE_AND_SINK ) ) { setBounds ( SOURCE_AND_SINK_BOUND . getWidth ( ) , SOURCE_AND_SINK_BOUND . getHeight ( ) ) ; } else if ( glyphClas... | Chooses a proper bound for this VNode according to its class . |
6,282 | public int calcReqWidthByStateAndInfos ( List < Glyph > stateORinfoList ) { int wholeSize = 0 ; int count = 0 ; for ( Glyph tmpGlyph : stateORinfoList ) { String text ; if ( tmpGlyph . getState ( ) != null ) { text = tmpGlyph . getState ( ) . getValue ( ) ; if ( tmpGlyph . getState ( ) . getVariable ( ) != null && tmpG... | Calculates required width according to the given list state and info glyphs of this VNode . This method also previously computes the width and height of state and info glyphs according to their label . |
6,283 | public void updateSizeForStateAndInfo ( ) { for ( Glyph glyph : this . glyph . getGlyph ( ) ) { if ( glyph . getClazz ( ) == STATE_VARIABLE ) { stateGlyphs . add ( glyph ) ; } else if ( glyph . getClazz ( ) == UNIT_OF_INFORMATION ) { infoGlyphs . add ( glyph ) ; } } int wholeWidthOfStates = calcReqWidthByStateAndInfos ... | If glyph attribute of this VNode object includes any state of information or unit of information glyphs this method updates the size of VNode accordingly . |
6,284 | public Set < GraphObject > run ( ) { Set < GraphObject > queryResult = new HashSet < GraphObject > ( ) ; if ( direction == Direction . UPSTREAM || direction == Direction . BOTHSTREAM ) { BFS bfsBackward = new BFS ( sourceNodes , null , Direction . UPSTREAM , this . limit ) ; Map < GraphObject , Integer > mapBackward = ... | Executes the query . |
6,285 | private void add ( Constraint constr , int ... ind ) { assert ind . length > 0 ; assert constr . getVariableSize ( ) == ind . length ; for ( int i = 0 ; i < ( constr . canGenerate ( ) ? ind . length - 1 : ind . length ) ; i ++ ) { assert ind [ i ] <= lastIndex ; } constraints . add ( new MappedConst ( constr , ind ) ) ... | Creates a mapped constraint with the given constraint and the indexes it applies . |
6,286 | public void removeLastConstraint ( ) { if ( constraints . isEmpty ( ) ) return ; MappedConst mc = constraints . get ( constraints . size ( ) - 1 ) ; constraints . remove ( mc ) ; if ( mc . canGenerate ( ) && mc . getInds ( ) [ mc . getInds ( ) . length - 1 ] == lastIndex ) { setLastIndexToMaxFound ( ) ; } } | Removes the last constraint added to the pattern . |
6,287 | private void setLastIndexToMaxFound ( ) { int max = - 1 ; for ( MappedConst mc : constraints ) { int [ ] ind = mc . getInds ( ) ; int last = ind [ ind . length - 1 ] ; if ( last > max ) max = last ; } lastIndex = max ; } | This method is used after removal of an generative constraint . Searching the remaining constraints we decide the value of lastIndex . |
6,288 | public void add ( Constraint constr , String ... label ) { checkLabels ( constr . canGenerate ( ) , label ) ; int [ ] ind = convertLabelsToInds ( label ) ; if ( ind . length != constr . getVariableSize ( ) ) { throw new IllegalArgumentException ( "Mapped elements do not match the constraint size." ) ; } add ( constr , ... | Creates a mapped constraint with the given generative constraint and the indexes it applies . Also labels the last given index . |
6,289 | private int [ ] convertLabelsToInds ( String ... label ) { int [ ] ind = new int [ label . length ] ; for ( int i = 0 ; i < label . length ; i ++ ) { if ( hasLabel ( label [ i ] ) ) { ind [ i ] = indexOf ( label [ i ] ) ; } else ind [ i ] = lastIndex + 1 ; } return ind ; } | Converts the labels to the indexes . Assumes the sanity of the labels already checked and if any new label exists it is only one and it is the last one . |
6,290 | private String [ ] convertIndsToLabels ( int ... ind ) { String [ ] label = new String [ ind . length ] ; for ( int i = 0 ; i < ind . length ; i ++ ) { if ( ! hasLabel ( ind [ i ] ) ) throw new IllegalArgumentException ( "The index " + ind [ i ] + " does not have a label." ) ; label [ i ] = getLabel ( ind [ i ] ) ; } r... | Converts the indices to the labels . All indices must have an existing label . |
6,291 | public void add ( Pattern p ) { if ( ! hasLabel ( p . getLabel ( 0 ) ) ) throw new IllegalArgumentException ( "The label of first " + "element of parameter index \"" + p . getLabel ( 0 ) + "\" not found in this pattern." ) ; for ( MappedConst mc : p . getConstraints ( ) ) { add ( mc . getConstr ( ) , p . convertIndsToL... | Appends the constraints in the parameter pattern to the desired location . Indexes in the constraint mappings are translated so that 0 is translated to ind0 and others are translated to orig + indAppend - 1 . All slots of this pattern should already be full before calling this method . This method makes room for the ne... |
6,292 | private String getLabel ( int i ) { for ( String label : labelMap . keySet ( ) ) { if ( labelMap . get ( label ) == i ) return label ; } return null ; } | Gets the label for the element at the specified index . |
6,293 | public void insertPointConstraint ( Constraint con , int ... ind ) { assert con . getVariableSize ( ) == 1 ; for ( int i : ind ) { for ( int j = 0 ; j < constraints . size ( ) ; j ++ ) { int [ ] index = constraints . get ( j ) . getInds ( ) ; if ( index [ index . length - 1 ] == i ) { constraints . add ( j + 1 , new Ma... | A point constraint deals with only one element in a match checks its validity . This method injects the parameter constraint multiple times among the list of mapped constraints to the specified indexes . |
6,294 | public void label ( String labelText , int index ) { if ( labelMap . containsKey ( labelText ) ) throw new IllegalArgumentException ( "Label \"" + labelText + "\" already exists." ) ; if ( labelMap . containsValue ( index ) ) throw new IllegalArgumentException ( "Index \"" + index + "\" already has a label." ) ; labelM... | Puts the given label for the given index . |
6,295 | public int indexOf ( String labelText ) { if ( ! labelMap . containsKey ( labelText ) ) throw new IllegalArgumentException ( "The label \"" + labelText + "\" is absent in pattern." ) ; return labelMap . get ( labelText ) ; } | Gets the index of the given label . The label must exist otherwise a runtime exception is thrown . |
6,296 | public void updateLabel ( String oldLabel , String newLabel ) { if ( hasLabel ( newLabel ) ) throw new IllegalArgumentException ( "The label \"" + newLabel + "\" already exists." ) ; int i = indexOf ( oldLabel ) ; labelMap . remove ( oldLabel ) ; labelMap . put ( newLabel , i ) ; } | Changes a label . The oldLabel has to be an existing label and new label has to be a new label . |
6,297 | public static void main ( String [ ] args ) throws IllegalAccessException , InvocationTargetException { for ( String arg : args ) { log . info ( arg ) ; if ( arg . toLowerCase ( ) . endsWith ( "owl" ) ) { try { processXrefs ( arg ) ; } catch ( FileNotFoundException e ) { e . printStackTrace ( ) ; } } } } | args - a space seperated list of owl files to be processed |
6,298 | private static void processXrefs ( String arg ) throws FileNotFoundException , IllegalAccessException , InvocationTargetException { FileInputStream in = new FileInputStream ( new File ( arg ) ) ; Model level2 = reader . convertFromOWL ( in ) ; Set < unificationXref > unis = level2 . getObjects ( unificationXref . class... | Main conversion method . Demonstrates how to read and write a BioPAX model and accessing its objects . |
6,299 | private static void convert ( unificationXref uni , Model level2 ) { Set < XReferrable > referrables = new HashSet < XReferrable > ( uni . isXREFof ( ) ) ; relationshipXref relationshipXref = level2 . addNew ( relationshipXref . class , uni . getUri ( ) ) ; relationshipXref . setCOMMENT ( uni . getCOMMENT ( ) ) ; relat... | This method converts the given unification xref to a relationship xref |
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