Package org.biojava.bio.search

Interface SearchContentHandler

All Known Subinterfaces:
SearchBuilder
All Known Implementing Classes:
BlastLikeHomologyBuilder, BlastLikeSearchBuilder, FastaSearchSAXParser, FilteringContentHandler, SearchContentAdapter, SearchContentFilter, SearchContentHandlerDebugger, SimilarityPairBuilder
public interface SearchContentHandler
SearchContentHandler is a notification interface for objects which listen to search stream parsers. This is applicable to all types of search results which are represented by flat files created by external programs e.g. Fasta, (T)BlastN/PX, EMBOSS programs. This is not limited to sequence similarity searches, but includes any format consisting of a header followed by hits, each of which may, or may not, have subhits.
Since:
1.1
Author:
Keith James

  • Method Summary

    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.
    boolean
    getMoreSearches()
    getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source.
    void
    setDatabaseID(String databaseID)
    setDatabaseID identifies the database searched by a name, ID or URN.
    void
    setMoreSearches(boolean value)
    setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results.
    void
    setQueryID(String queryID)
    setQueryID identifies the query sequence by a name, ID or URN.
    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.

  • Method Details

    • getMoreSearches

      boolean getMoreSearches()
      getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source. Used for handling streams of search results.
      Returns:
      a boolean value.

    • setMoreSearches

      void setMoreSearches(boolean value)
      setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results. Used for handling streams of search results.
      Parameters:
      value - a boolean value.

    • startSearch

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

    • endSearch

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

    • startHeader

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

    • endHeader

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

    • startHit

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

    • endHit

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

    • startSubHit

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

    • endSubHit

      void endSubHit()
      The endSubHit method indicates the end of a formatted subhit.

    • addSearchProperty

      void addSearchProperty(Object key, Object value)
      The addSearchProperty method adds a key/value pair containing some property of the overall search result.
      Parameters:
      key - an Object.
      value - an Object.

    • addHitProperty

      void addHitProperty(Object key, Object value)
      The addHitProperty method adds a key/value pair containing some property of a particular hit.
      Parameters:
      key - an Object.
      value - an Object.

    • addSubHitProperty

      void addSubHitProperty(Object key, Object value)
      The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
      Parameters:
      key - an Object.
      value - an Object.

    • setQueryID

      void setQueryID(String queryID)
      setQueryID identifies the query sequence by a name, ID or URN.
      Parameters:
      queryID - a String which should be an unique identifer for the sequence.

    • setDatabaseID

      void setDatabaseID(String databaseID)
      setDatabaseID identifies the database searched by a name, ID or URN.
      Parameters:
      databaseID - a String which should be an unique identifier for the database searched.