SearchIO

java.lang.Object
- org.biojava.nbio.core.search.io.SearchIO

All Implemented Interfaces:

java.lang.Iterable<Result>
```
public class SearchIO
extends java.lang.Object
implements java.lang.Iterable<Result>
```
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 and Description
`SearchIO(java.io.File f)` Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.
`SearchIO(java.io.File f, ResultFactory factory)` Build a SearchIO reader and specify a ResultFactory object to be used for parsing
`SearchIO(java.io.File f, ResultFactory factory, double maxEvalue)` Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`getEvalueThreshold()`
`java.util.Iterator<Result>`	`iterator()`
`void`	`writeResults()` used to write a search report using the guessed or specified factory

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - SearchIO
```
public SearchIO(java.io.File f)
         throws java.io.IOException,
                java.text.ParseException
```
    Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.
    
    Parameters:
    
    f -
    
    Throws:
    
    java.lang.Exception
    
    java.io.IOException
    
    java.text.ParseException
  - SearchIO
```
public SearchIO(java.io.File f,
                ResultFactory factory)
         throws java.io.IOException,
                java.text.ParseException
```
    Build a SearchIO reader and specify a ResultFactory object to be used for parsing
    
    Parameters:
    
    f -
    
    factory -
    
    Throws:
    
    java.io.IOException - for file access related issues
    
    java.text.ParseException - for file format related issues
  - SearchIO
```
public SearchIO(java.io.File f,
                ResultFactory factory,
                double maxEvalue)
         throws java.io.IOException,
                java.text.ParseException
```
    Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold. This usually increase parsing speed
    
    Parameters:
    
    f -
    
    factory -
    
    maxEvalue -
    
    Throws:
    
    java.io.IOException - for file access related issues
    
    java.text.ParseException - for file format related issues
- Method Detail
  - writeResults
```
public void writeResults()
                  throws java.io.IOException,
                         java.text.ParseException
```
    used to write a search report using the guessed or specified factory
    
    Throws:
    
    java.io.IOException - for file access related issues
    
    java.text.ParseException - for file format related issues
  - getEvalueThreshold
```
public double getEvalueThreshold()
```
  - iterator
```
public java.util.Iterator<Result> iterator()
```
    Specified by:
    
    iterator in interface java.lang.Iterable<Result>

Class SearchIO

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

SearchIO

SearchIO

SearchIO

Method Detail

writeResults

getEvalueThreshold

iterator