com.pacbio.secondary.vis.data.db

Class MotifsDB

java.lang.Object

com.pacbio.secondary.vis.data.db.MotifsDB

public class MotifsDB
extends java.lang.Object

stores motif summary data

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.ArrayList<MotifData>	motifs_db

Constructor Summary

Constructors

Constructor and Description
MotifsDB()

Method Summary

Methods

Modifier and Type	Method and Description
int[]	getCenterPositions(java.lang.String motif) returns array of center positions for 1 or 2 motifs passed in, eventually separated by '/'
protected int	getMotifCenterPosition(java.lang.String motif) returns center position for one given motif string
java.lang.String	getMotifsReport() creates html motif report
boolean	readMotifsFile(VioletApp app, java.lang.String filename)
int	size()

Methods inherited from class java.lang.Object

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

Field Detail

motifs_db

protected java.util.ArrayList<MotifData> motifs_db

Constructor Detail

MotifsDB

public MotifsDB()

Method Detail

size

public int size()

readMotifsFile

public boolean readMotifsFile(VioletApp app,
                     java.lang.String filename)

Parameters:

app -

filename -

Returns:

getMotifsReport

public java.lang.String getMotifsReport()

creates html motif report

Returns:

getCenterPositions

public int[] getCenterPositions(java.lang.String motif)

returns array of center positions for 1 or 2 motifs passed in, eventually separated by '/'

Parameters:

motif -

Returns:

getMotifCenterPosition

protected int getMotifCenterPosition(java.lang.String motif)

returns center position for one given motif string

Parameters:

motif -

Returns:

0-based center position