FastaGeneWriter

java.lang.Object
- org.biojava.nbio.core.sequence.io.FastaGeneWriter

```
public class FastaGeneWriter
extends java.lang.Object
```
A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version. It is also an option to write out the gene sequence where the exon regions are upper case 6/22/2010 FastaWriter needs to be sequence aware to handle writing out a GeneSequence which is negative Strand with the proper sequence

Author:

Scooter Willis

Constructor Summary

Constructors
Constructor and Description
`FastaGeneWriter(java.io.OutputStream os, java.util.Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase)`
`FastaGeneWriter(java.io.OutputStream os, java.util.Collection<GeneSequence> sequences, FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat, boolean showExonUppercase, int 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)`

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

Constructor Detail

FastaGeneWriter

public FastaGeneWriter(java.io.OutputStream os,
                       java.util.Collection<GeneSequence> sequences,
                       FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat,
                       boolean showExonUppercase)

Parameters:: os -; sequences -; headerFormat -; showExonUppercase -

FastaGeneWriter

public FastaGeneWriter(java.io.OutputStream os,
                       java.util.Collection<GeneSequence> sequences,
                       FastaHeaderFormatInterface<GeneSequence,NucleotideCompound> headerFormat,
                       boolean showExonUppercase,
                       int lineLength)

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

Method Detail

process

public void process()
             throws java.lang.Exception

Throws:: java.lang.Exception

getLineLength
```
public int getLineLength()
```
Returns:

the lineLength

setLineLength
```
public void setLineLength(int lineLength)
```
Parameters:

lineLength - the lineLength to set

main

public static void main(java.lang.String[] args)

Class FastaGeneWriter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FastaGeneWriter

FastaGeneWriter

Method Detail

process

getLineLength

setLineLength

main