BlastXMLParser

java.lang.Object
- org.biojava.nbio.core.search.io.blast.BlastXMLParser

All Implemented Interfaces:

ResultFactory
```
public class BlastXMLParser
extends java.lang.Object
implements ResultFactory
```
Re-designed by Paolo Pavan on the footprint of: org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis 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 and Description

BlastXMLParser()

Constructors
Constructor and Description
`BlastXMLParser()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.util.List<Result>`	`createObjects(double maxEScore)` Launch the parsing and get back a list of Result objects representing the search result in the specified file.
`java.util.List<java.lang.String>`	`getFileExtensions()` returns a list of file extensions associated to this ResultFactory
`void`	`setDatabaseReferences(java.util.List<Sequence> sequences)` Specify the collection of sequences objects used as database in the Search run.
`void`	`setFile(java.io.File f)`
`void`	`setQueryReferences(java.util.List<Sequence> sequences)` Specify the collection of sequences objects used as queries in the Search run.
`void`	`storeObjects(java.util.List<Result> results)` The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - BlastXMLParser
```
public BlastXMLParser()
```
- Method Detail
  - setFile
```
public void setFile(java.io.File f)
```
    Specified by:
    
    setFile in interface ResultFactory
  - createObjects
```
public java.util.List<Result> createObjects(double maxEScore)
                                     throws java.io.IOException,
                                            java.text.ParseException
```
    Description copied from interface: ResultFactory
    
    Launch the parsing and get back a list of Result objects representing the search result in the specified file.
    
    Specified by:
    
    createObjects in interface ResultFactory
    
    Returns:
    
    Throws:
    
    java.io.IOException
    
    java.text.ParseException
  - getFileExtensions
```
public java.util.List<java.lang.String> getFileExtensions()
```
    Description copied from interface: ResultFactory
    
    returns a list of file extensions associated to this ResultFactory
    
    Specified by:
    
    getFileExtensions in interface ResultFactory
    
    Returns:
  - setQueryReferences
```
public void setQueryReferences(java.util.List<Sequence> sequences)
```
    Description copied from interface: ResultFactory
    
    Specify the collection of sequences objects used as queries in the Search run. They will be associated back to the query during the construction of the Result object.
    
    Specified by:
    
    setQueryReferences in interface ResultFactory
  - setDatabaseReferences
```
public void setDatabaseReferences(java.util.List<Sequence> sequences)
```
    Description copied from interface: ResultFactory
    
    Specify the collection of sequences objects used as database in the Search run. They will be associated back to the Hit during the construction of the Hit object.
    
    Specified by:
    
    setDatabaseReferences in interface ResultFactory
  - storeObjects
```
public void storeObjects(java.util.List<Result> results)
                  throws java.io.IOException,
                         java.text.ParseException
```
    Description copied from interface: ResultFactory
    
    The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.
    
    Specified by:
    
    storeObjects in interface ResultFactory
    
    Throws:
    
    java.io.IOException
    
    java.text.ParseException

Class BlastXMLParser

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BlastXMLParser

Method Detail

setFile

createObjects

getFileExtensions

setQueryReferences

setDatabaseReferences

storeObjects