BlastLikeSearchBuilder (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojava.bio.program.ssbind.BlastLikeSearchBuilder

All Implemented Interfaces:: SearchBuilder, SearchContentHandler

public class BlastLikeSearchBuilder
extends Object
implements SearchBuilder

BlastLikeSearchBuilder will create SeqSimilaritySearchResults from SAX events via a SeqSimilarityAdapter. The SAX events should describe elements conforming to the BioJava BlastLikeDataSetCollection DTD. Suitable sources are BlastLikeSAXParser or FastaSearchSAXParser. The result objects are placed in the List supplied to the constructor.

The start/end/strand of SeqSimilaritySearchHits are calculated from their constituent SeqSimilaritySearchSubHits as follows:

The query start is the lowest query start coordinate of its sub-hits, regardless of strand
The query end is the highest query end coordinate of its sub-hits, regardless of strand
The hit start is the lowest hit start coordinate of its sub-hits, regardless of strand
The hit end is the highest hit end coordinate of its sub-hits, regardless of strand
The query strand is null for protein sequences. Otherwise it is equal to the query strand of its sub-hits if they are all on the same strand, or StrandedFeature.UNKNOWN if the sub-hits have mixed query strands
The hit strand is null for protein sequences. Otherwise it is equal to the hit strand of its sub-hits if they are all on the same strand, or StrandedFeature.UNKNOWN if the sub-hits have mixed hit strands

This class has special meanings for particular keys: if you want to adapt this class for another parser, you will need to be aware of this. These originate from and are fully described in the BlastLikeDataSetCollection DTD.

Key	Meaning
program	either this value or the subjectSequenceType value must be set. This can take values acceptable to AlphabetResolver. These are BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, DNA and PROTEIN.
databaseId	Identifier of database searched (in SequenceDBInstallation).
subjectSequenceType	type of sequence that hit is. Can be DNA or PROTEIN.
subjectId	id of sequence that is hit
subjectDescription	description of sequence that is hit
queryStrand	Strandedness of query in alignment. Takes values of "plus" and "minus"
subjectStrand	Strandedness of query in alignment. Takes values of "plus" and "minus"
queryFrame	self-evident
subjectFrame	self-evident
querySequenceStart	self-evident
querySequenceEnd	self-evident
subjectSequenceStart	self-evident
subjectSequenceEnd	self-evident
score	self-evident
expectValue	self-evident
pValue	self-evident

Since:: 1.2
Author:: Keith James, Greg Cox

Constructor Summary

Constructors
Constructor and Description
`BlastLikeSearchBuilder(List target)` Creates a new `BlastLikeSearchBuilder` which will instantiate results into the `List` target.
`BlastLikeSearchBuilder(List target, SequenceDB querySeqHolder, SequenceDBInstallation subjectDBs)` Creates a new `BlastLikeSearchBuilder` which will instantiate results into the `List` target.

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.
`SeqSimilaritySearchResult`	`makeSearchResult()` The `makeSearchResult` method returns a `SeqSimilaritySearchResult` instance created from accumulated data.
`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`	`setQuerySeqHolder(SequenceDB querySeqHolder)` `setQuerySeqHolder` sets the query sequence holder to a specific database.
`void`	`setSubjectDBInstallation(SequenceDBInstallation subjectDBs)` `setSubjectDBInstallation` sets the subject database holder to a specific installation.
`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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - BlastLikeSearchBuilder
```
public BlastLikeSearchBuilder(List target)
```
    Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
    
    Parameters:
    target - a List.
  - BlastLikeSearchBuilder
```
public BlastLikeSearchBuilder(List target,
                      SequenceDB querySeqHolder,
                      SequenceDBInstallation subjectDBs)
```
    Creates a new BlastLikeSearchBuilder which will instantiate results into the List target.
    
    Parameters:
    target - a List.
    querySeqHolder - a SequenceDB of query sequences.
    subjectDBs - a SequenceDBInstallation of databases searched.
- Method Detail
  - makeSearchResult
```
public SeqSimilaritySearchResult makeSearchResult()
                                           throws BioException
```
    Description copied from interface: SearchBuilder
    
    The makeSearchResult method returns a SeqSimilaritySearchResult instance created from accumulated data.
    
    Specified by:
    
    makeSearchResult in interface SearchBuilder
    
    Returns:
    a SeqSimilaritySearchResult.
    
    Throws:
    
    BioException - if an error occurs.
  - setQuerySeqHolder
```
public void setQuerySeqHolder(SequenceDB querySeqHolder)
```
    setQuerySeqHolder sets the query sequence holder to a specific database.
    
    Parameters:
    querySeqHolder - a SequenceDB containing the query sequence(s).
  - setSubjectDBInstallation
```
public void setSubjectDBInstallation(SequenceDBInstallation subjectDBs)
```
    setSubjectDBInstallation sets the subject database holder to a specific installation.
    
    Parameters:
    subjectDBs - a SequenceDBInstallation containing the subject database(s)
  - setQueryID
```
public void setQueryID(String queryID)
```
    Description copied from interface: SearchContentHandler
    
    setQueryID identifies the query sequence by a name, ID or URN.
    
    Specified by:
    
    setQueryID in interface SearchContentHandler
    
    Parameters:
    queryID - a String which should be an unique identifer for the sequence.
  - setDatabaseID
```
public void setDatabaseID(String databaseID)
```
    Description copied from interface: SearchContentHandler
    
    setDatabaseID identifies the database searched by a name, ID or URN.
    
    Specified by:
    
    setDatabaseID in interface SearchContentHandler
    
    Parameters:
    databaseID - a String which should be an unique identifier for the database searched.
  - getMoreSearches
```
public boolean getMoreSearches()
```
    Description copied from interface: SearchContentHandler
    
    getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source. Used for handling streams of search results.
    
    Specified by:
    
    getMoreSearches in interface SearchContentHandler
    
    Returns:
    a boolean value.
  - setMoreSearches
```
public void setMoreSearches(boolean value)
```
    Description copied from interface: SearchContentHandler
    
    setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results. Used for handling streams of search results.
    
    Specified by:
    
    setMoreSearches in interface SearchContentHandler
    
    Parameters:
    value - a boolean value.
  - startSearch
```
public void startSearch()
```
    Description copied from interface: SearchContentHandler
    
    The startSearch method indicates the start of useful search information.
    
    Specified by:
    
    startSearch in interface SearchContentHandler
  - endSearch
```
public void endSearch()
```
    Description copied from interface: SearchContentHandler
    
    The endSearch method indicates the end of useful search information.
    
    Specified by:
    
    endSearch in interface SearchContentHandler
  - startHeader
```
public void startHeader()
```
    Description copied from interface: SearchContentHandler
    
    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
  - endHeader
```
public void endHeader()
```
    Description copied from interface: SearchContentHandler
    
    The endHeader method indicates the end of a formatted header.
    
    Specified by:
    
    endHeader in interface SearchContentHandler
  - startHit
```
public void startHit()
```
    Description copied from interface: SearchContentHandler
    
    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
  - endHit
```
public void endHit()
```
    Description copied from interface: SearchContentHandler
    
    The endHit method indicates the end of a formatted hit.
    
    Specified by:
    
    endHit in interface SearchContentHandler
  - startSubHit
```
public void startSubHit()
```
    Description copied from interface: SearchContentHandler
    
    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
  - endSubHit
```
public void endSubHit()
```
    Description copied from interface: SearchContentHandler
    
    The endSubHit method indicates the end of a formatted subhit.
    
    Specified by:
    
    endSubHit in interface SearchContentHandler
  - addSearchProperty
```
public void addSearchProperty(Object key,
                     Object value)
```
    Description copied from interface: SearchContentHandler
    
    The addSearchProperty method adds a key/value pair containing some property of the overall search result.
    
    Specified by:
    
    addSearchProperty in interface SearchContentHandler
    
    Parameters:
    key - an Object.
    value - an Object.
  - addHitProperty
```
public void addHitProperty(Object key,
                  Object value)
```
    Description copied from interface: SearchContentHandler
    
    The addHitProperty method adds a key/value pair containing some property of a particular hit.
    
    Specified by:
    
    addHitProperty in interface SearchContentHandler
    
    Parameters:
    key - an Object.
    value - an Object.
  - addSubHitProperty
```
public void addSubHitProperty(Object key,
                     Object value)
```
    Description copied from interface: SearchContentHandler
    
    The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.
    
    Specified by:
    
    addSubHitProperty in interface SearchContentHandler
    
    Parameters:
    key - an Object.
    value - an Object.

Class BlastLikeSearchBuilder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BlastLikeSearchBuilder

BlastLikeSearchBuilder

Method Detail

makeSearchResult

setQuerySeqHolder

setSubjectDBInstallation

setQueryID

setDatabaseID

getMoreSearches

setMoreSearches

startSearch

endSearch

startHeader

endHeader

startHit

endHit

startSubHit

endSubHit

addSearchProperty

addHitProperty

addSubHitProperty