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FilteringContentHandler (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.bio.search.SearchContentAdapter
      • org.biojava.bio.search.FilteringContentHandler
  • All Implemented Interfaces:
    BlastLikeSearchFilter.Node, SearchContentHandler
    public class FilteringContentHandler
extends SearchContentAdapter
implements BlastLikeSearchFilter.Node

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      class  FilteringContentHandler.FilterVisitor

      Visitor class that parses the filter tree

    • Constructor Summary

      Constructors 
      Constructor Description
      FilteringContentHandler​(BlastLikeSearchFilter filter)  
      FilteringContentHandler​(BlastLikeSearchFilter filter, SearchContentHandler delegate)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addHitProperty​(Object key, Object value)

      The addHitProperty method adds a key/value pair containing some property of a particular hit.
      void addSearchProperty​(Object key, Object value)

      The addSearchProperty method adds a key/value pair containing some property of the overall search result.
      void addSubHitProperty​(Object key, Object value)

      The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
      void endHeader()

      The endHeader method indicates the end of a formatted header.
      void endHit()

      The endHit method indicates the end of a formatted hit.
      void endSearch()

      The endSearch method indicates the end of useful search information.
      void endSubHit()

      The endSubHit method indicates the end of a formatted subhit.
      Object getHitProperty​(Object key)  
      Object getSearchProperty​(Object key)  
      Object getSubHitProperty​(Object key)  
      void setDatabaseID​(String id)

      setDatabaseID identifies the database searched by a name, ID or URN.
      void setQueryID​(String queryID)

      setQueryID identifies the query sequence by a name, ID or URN.
      void setSearchContentHandler​(SearchContentHandler delegate)  
      void startHeader()

      The startHeader method indicates the start of a formatted header.
      void startHit()

      The startHit method indicates the start of a formatted hit.
      void startSearch()

      The startSearch method indicates the start of useful search information.
      void startSubHit()

      The startSubHit method indicates the start of a formatted subhit.

      • Methods inherited from class org.biojava.bio.search.SearchContentAdapter

        getMoreSearches, setMoreSearches

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • FilteringContentHandler

        public FilteringContentHandler​(BlastLikeSearchFilter filter,
                               SearchContentHandler delegate)
                        throws BioException
        Throws:
        BioException

      • FilteringContentHandler

        public FilteringContentHandler​(BlastLikeSearchFilter filter)
                        throws BioException
        Throws:
        BioException

    • Method Detail

      • getSearchProperty

        public Object getSearchProperty​(Object key)
        Specified by:
        getSearchProperty in interface BlastLikeSearchFilter.Node

      • getHitProperty

        public Object getHitProperty​(Object key)
        Specified by:
        getHitProperty in interface BlastLikeSearchFilter.Node

      • getSubHitProperty

        public Object getSubHitProperty​(Object key)
        Specified by:
        getSubHitProperty in interface BlastLikeSearchFilter.Node

      • setSearchContentHandler

        public void setSearchContentHandler​(SearchContentHandler delegate)

      • startHeader

        public void startHeader()

        The startHeader method indicates the start of a formatted header. This usually contains information relevant to the search as a whole.

        Specified by:
        startHeader in interface SearchContentHandler
        Overrides:
        startHeader in class SearchContentAdapter

      • setDatabaseID

        public void setDatabaseID​(String id)

        setDatabaseID identifies the database searched by a name, ID or URN.

        Specified by:
        setDatabaseID in interface SearchContentHandler
        Overrides:
        setDatabaseID in class SearchContentAdapter
        Parameters:
        id - a String which should be an unique identifier for the database searched.

      • endHeader

        public void endHeader()

        The endHeader method indicates the end of a formatted header.

        Specified by:
        endHeader in interface SearchContentHandler
        Overrides:
        endHeader in class SearchContentAdapter

      • startSearch

        public void startSearch()

        The startSearch method indicates the start of useful search information.

        Specified by:
        startSearch in interface SearchContentHandler
        Overrides:
        startSearch in class SearchContentAdapter

      • setQueryID

        public void setQueryID​(String queryID)

        setQueryID identifies the query sequence by a name, ID or URN.

        Specified by:
        setQueryID in interface SearchContentHandler
        Overrides:
        setQueryID in class SearchContentAdapter
        Parameters:
        queryID - a String which should be an unique identifer for the sequence.

      • addSearchProperty

        public void addSearchProperty​(Object key,
                              Object value)

        The addSearchProperty method adds a key/value pair containing some property of the overall search result.

        Specified by:
        addSearchProperty in interface SearchContentHandler
        Overrides:
        addSearchProperty in class SearchContentAdapter
        Parameters:
        key - an Object.
        value - an Object.

      • startHit

        public void startHit()

        The startHit method indicates the start of a formatted hit. This could be a single line, or a block of lines.

        Specified by:
        startHit in interface SearchContentHandler
        Overrides:
        startHit in class SearchContentAdapter

      • addHitProperty

        public void addHitProperty​(Object key,
                           Object value)

        The addHitProperty method adds a key/value pair containing some property of a particular hit.

        Specified by:
        addHitProperty in interface SearchContentHandler
        Overrides:
        addHitProperty in class SearchContentAdapter
        Parameters:
        key - an Object.
        value - an Object.

      • startSubHit

        public void startSubHit()

        The startSubHit method indicates the start of a formatted subhit. There may be zero or more of these per hit.

        Specified by:
        startSubHit in interface SearchContentHandler
        Overrides:
        startSubHit in class SearchContentAdapter

      • addSubHitProperty

        public void addSubHitProperty​(Object key,
                              Object value)

        The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.

        Specified by:
        addSubHitProperty in interface SearchContentHandler
        Overrides:
        addSubHitProperty in class SearchContentAdapter
        Parameters:
        key - an Object.
        value - an Object.

      • endSubHit

        public void endSubHit()

        The endSubHit method indicates the end of a formatted subhit.

        Specified by:
        endSubHit in interface SearchContentHandler
        Overrides:
        endSubHit in class SearchContentAdapter

      • endHit

        public void endHit()

        The endHit method indicates the end of a formatted hit.

        Specified by:
        endHit in interface SearchContentHandler
        Overrides:
        endHit in class SearchContentAdapter

      • endSearch

        public void endSearch()

        The endSearch method indicates the end of useful search information.

        Specified by:
        endSearch in interface SearchContentHandler
        Overrides:
        endSearch in class SearchContentAdapter