Package org.biojava.nbio.core.search.io

Class Result

java.lang.Object

org.biojava.nbio.core.search.io.Result

All Implemented Interfaces:

Iterable<Hit>

Direct Known Subclasses:

BlastResult

public abstract class Result
extends Object
implements Iterable<Hit>

This class models a search result. You will find one of this for every query sequence specified in the run. Designed by Paolo Pavan. You may want to find my contacts on Github and LinkedIn for code info or discuss major changes. https://github.com/paolopavan

Author:

Paolo Pavan

Constructor Summary

Constructors

Constructor	Description
Result(String program, String version, String reference, String dbFile, HashMap<String,String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object obj)	Experimental.
String	getDbFile()
int	getHitCounter()
int	getIterationNumber()
String	getProgram()
String	getProgramSpecificParameter(String key)
Set<String>	getProgramSpecificParametersList()
String	getQueryDef()
String	getQueryID()
int	getQueryLength()
Sequence	getQuerySequence()	returns the reference to the original and whole sequence used to query the database.
String	getReference()
String	getVersion()
int	hashCode()
Iterator<Hit>	iterator()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

Result

public Result(String program,
              String version,
              String reference,
              String dbFile,
              HashMap<String,String> programSpecificParameters,
              int iterationNumber,
              String queryID,
              String queryDef,
              int queryLength,
              List<Hit> hits,
              Sequence querySequence)

Method Detail

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Experimental. Wants to return an hashcode designed to allow conceptual comparisons of search results. Wants to implement conceptual comparisons of search results. Fields unrelated to search are deliberately not considered.

Overrides:

equals in class Object

Returns:

getIterationNumber

public int getIterationNumber()

getQueryID

public String getQueryID()

getQueryDef

public String getQueryDef()

getQueryLength

public int getQueryLength()

getHitCounter

public int getHitCounter()

getProgram

public String getProgram()

getVersion

public String getVersion()

getReference

public String getReference()

getDbFile

public String getDbFile()

getProgramSpecificParametersList

public Set<String> getProgramSpecificParametersList()

getProgramSpecificParameter

public String getProgramSpecificParameter(String key)

getQuerySequence

public Sequence getQuerySequence()

returns the reference to the original and whole sequence used to query the database. Available only if the ResultFactory implements setQueryReferences and it was used before the parsing with SearchIO

Returns:

Sequence object

iterator

public Iterator<Hit> iterator()

Specified by:

iterator in interface Iterable<Hit>