net.maizegenetics.pangenome.api

Class GraphIO

java.lang.Object

net.maizegenetics.pangenome.api.GraphIO

public class GraphIO
extends Object

Author:

Terry Casstevens Created August 29, 2017

Method Summary

Modifier and Type	Method and Description
static void	writeAnchorsFasta(HaplotypeGraph graph, String filename) Writes only anchor sequences from HaplotypeNodes in given graph to fasta format.
static void	writeFasta(HaplotypeGraph graph, String filename) Writes all sequences from HaplotypeNodes in given graph to fasta format.
static void	writeFasta(HaplotypeGraph graph, String filename, boolean includeAnchors, boolean includeInnerAnchors)
static void	writeInnerAnchorsFasta(HaplotypeGraph graph, String filename) Writes only inner-anchor sequences from HaplotypeNodes in given graph to fasta format.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

writeFasta

public static void writeFasta(HaplotypeGraph graph,
                              String filename)

Writes all sequences from HaplotypeNodes in given graph to fasta format. The information line for each sequence is the haplotypes.haplotypes_id

Parameters:

graph - graph

filename - output filename

writeAnchorsFasta

public static void writeAnchorsFasta(HaplotypeGraph graph,
                                     String filename)

Writes only anchor sequences from HaplotypeNodes in given graph to fasta format. The information line for each sequence is the haplotypes.haplotypes_id

Parameters:

graph - graph

filename - output filename

writeInnerAnchorsFasta

public static void writeInnerAnchorsFasta(HaplotypeGraph graph,
                                          String filename)

Writes only inner-anchor sequences from HaplotypeNodes in given graph to fasta format. The information line for each sequence is the haplotypes.haplotypes_id

Parameters:

graph - graph

filename - output filename

writeFasta

public static void writeFasta(HaplotypeGraph graph,
                              String filename,
                              boolean includeAnchors,
                              boolean includeInnerAnchors)