SearchContentHandler (biojava-legacy 1.9.1 API)

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

Methods
Modifier and Type	Method and 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 Detail
  - 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.

Interface SearchContentHandler

Method Summary

Method Detail

getMoreSearches

setMoreSearches

startSearch

endSearch

startHeader

endHeader

startHit

endHit

startSubHit

endSubHit

addSearchProperty

addHitProperty

addSubHitProperty

setQueryID

setDatabaseID