FastaWriter

java.lang.Object
- org.biojava.nbio.core.sequence.io.FastaWriter<S,C>

```
public class FastaWriter<S extends Sequence<?>,C extends Compound>
extends java.lang.Object
```
The FastaWriter writes a collection of sequences to an outputStream. FastaWriterHelper should be used to write out sequences. Each sequence loaded from a fasta file retains the original Fasta header and that is used when writing to the stream. This behavior can be overwritten by implementing a custom FastaHeaderFormatInterface.

Author:

Scooter Willis

Constructor Summary

Constructors
Constructor and Description
`FastaWriter(java.io.OutputStream os, java.util.Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat)` Use default line length of 60
`FastaWriter(java.io.OutputStream os, java.util.Collection<S> sequences, FastaHeaderFormatInterface<S,C> headerFormat, int lineLength)` Set custom lineLength

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`getLineLength()`
`static void`	`main(java.lang.String[] args)`
`void`	`process()`
`void`	`setLineLength(int lineLength)`
`void`	`setLineSeparator(java.lang.String lineSeparator)` Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option

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

Constructor Detail

FastaWriter

public FastaWriter(java.io.OutputStream os,
                   java.util.Collection<S> sequences,
                   FastaHeaderFormatInterface<S,C> headerFormat)

Use default line length of 60

Parameters:: os -; sequences -; headerFormat -

FastaWriter

public FastaWriter(java.io.OutputStream os,
                   java.util.Collection<S> sequences,
                   FastaHeaderFormatInterface<S,C> headerFormat,
                   int lineLength)

Set custom lineLength

Parameters:: os -; sequences -; headerFormat -; lineLength -

Method Detail
- setLineSeparator
```
public void setLineSeparator(java.lang.String lineSeparator)
```
  Allow an override of operating system line separator for programs that needs a specific CRLF or CR or LF option
  
  Parameters:
  
  lineSeparator -
- process
```
public void process()
             throws java.io.IOException
```
  Throws:
  
  java.io.IOException
- main
```
public static void main(java.lang.String[] args)
```
- getLineLength
```
public int getLineLength()
```
  Returns:
  
  the lineLength
- setLineLength
```
public void setLineLength(int lineLength)
```
  Parameters:
  
  lineLength - the lineLength to set

Class FastaWriter<S extends Sequence<?>,C extends Compound>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FastaWriter

FastaWriter

Method Detail

setLineSeparator

process

main

getLineLength

setLineLength