com.pacbio.secondary.vis.io.indexer.gff.metadata

Class GFFMetadataInfo

java.lang.Object

com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo

All Implemented Interfaces:

java.io.Serializable

public class GFFMetadataInfo
extends java.lang.Object
implements java.io.Serializable

Author:

Marco Milletti supports private serialization

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
int	avg_row_lenght
java.lang.String	file_path
long	gff_slice_size
java.util.ArrayList<GFFIndexInfo>	indexes
int	max_read_length

Constructor Summary

Constructors

Constructor and Description
GFFMetadataInfo() default constructor required for de-serialization
GFFMetadataInfo(long gff_slice_size)

Method Summary

Methods

Modifier and Type	Method and Description
long	avg_reads_per_slice()
java.util.TreeMap<java.lang.Integer,Locus>	getContigsMap() Get map containing list of all contigs in file and start/end for each contig
int	getTotalSlicesInContig(int contig) Get number of slices for specific contig
java.lang.String	printIndexes()
java.lang.String	printStatistics()

Methods inherited from class java.lang.Object

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

Field Detail

file_path

public java.lang.String file_path

indexes

public java.util.ArrayList<GFFIndexInfo> indexes

avg_row_lenght

public int avg_row_lenght

max_read_length

public int max_read_length

gff_slice_size

public long gff_slice_size

Constructor Detail

GFFMetadataInfo

public GFFMetadataInfo()

default constructor required for de-serialization

GFFMetadataInfo

public GFFMetadataInfo(long gff_slice_size)

Method Detail

avg_reads_per_slice

public long avg_reads_per_slice()

getContigsMap

public java.util.TreeMap<java.lang.Integer,Locus> getContigsMap()

Get map containing list of all contigs in file and start/end for each contig

Returns:

map of contigs

getTotalSlicesInContig

public int getTotalSlicesInContig(int contig)

Get number of slices for specific contig

Returns:

number of datapoints per contig

printIndexes

public java.lang.String printIndexes()

printStatistics

public java.lang.String printStatistics()