com.pacbio.secondary.vis.io.hdf.referenceinfo

Class CMPH5ReferenceInfo

java.lang.Object

com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReferenceInfo

public class CMPH5ReferenceInfo
extends java.lang.Object

Encapsulates concept of cmp.h5's reference metadata storage

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	full_sequence_name
protected int	ref_seq_id
protected java.lang.String	ref_seq_name

Constructor Summary

Constructors

Constructor and Description
CMPH5ReferenceInfo(java.lang.String ref_seq_name, java.lang.String full_sequence_name, int ref_seq_id)

Method Summary

Methods

Modifier and Type	Method and Description
static java.lang.String	getConsensusCallsPath(java.lang.String contig_id)
java.lang.String	getFullSequenceName()
static java.lang.String	getIPDRatioSequencePath(java.lang.String contig_id)
int	getRefSeqID()
java.lang.String	getRefSeqName()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

ref_seq_name

protected java.lang.String ref_seq_name

full_sequence_name

protected java.lang.String full_sequence_name

ref_seq_id

protected int ref_seq_id

Constructor Detail

CMPH5ReferenceInfo

public CMPH5ReferenceInfo(java.lang.String ref_seq_name,
                  java.lang.String full_sequence_name,
                  int ref_seq_id)

Parameters:

ref_seq_name -

full_sequence_name -

ref_seq_id -

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getRefSeqName

public java.lang.String getRefSeqName()

getFullSequenceName

public java.lang.String getFullSequenceName()

getRefSeqID

public int getRefSeqID()

getConsensusCallsPath

public static java.lang.String getConsensusCallsPath(java.lang.String contig_id)

Parameters:

contig_id -

Returns:

getIPDRatioSequencePath

public static java.lang.String getIPDRatioSequencePath(java.lang.String contig_id)

Parameters:

contig_id -

Returns: