com.pacbio.secondary.vis.data.db

Class IdeogramDB

java.lang.Object

com.pacbio.secondary.vis.data.db.IdeogramDB

All Implemented Interfaces:

java.io.Serializable

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

Database class for the NCBI ideogram database.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	isAutoGenerated
protected IntervalTree[]	tree

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	IdeogramDB()
	IdeogramDB(int num_contigs)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addDefaultBand(java.lang.String name, int contig, int start, int extent, int band_idx)
protected void	clear(boolean isAutoGenerated) Creates a new set of empty IntervalTrees.
void	generateDefault(ReferenceInfo ref_info)
int	getAutoIdeogramBandSize()
int	getAutoIdeogramNumBands()
IntervalTree[]	getIdeogramDBTree()
boolean	isAutoGenerated()
boolean	isAutoIdeogramUsesFixedNumBands()
static void	main(java.lang.String[] args)
boolean	readIdeogramData(java.io.Reader reader, IProgressNotifier notifier)
void	setAutoIdeogramBandSize(int n)
void	setAutoIdeogramNumBands(int n)
void	setAutoIdeogramUsesFixedNumBands(boolean useFixedNumBands)

Methods inherited from class java.lang.Object

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

Field Detail

tree

protected IntervalTree[] tree

isAutoGenerated

protected boolean isAutoGenerated

Constructor Detail

IdeogramDB

public IdeogramDB(int num_contigs)

IdeogramDB

protected IdeogramDB()

Method Detail

isAutoIdeogramUsesFixedNumBands

public boolean isAutoIdeogramUsesFixedNumBands()

setAutoIdeogramUsesFixedNumBands

public void setAutoIdeogramUsesFixedNumBands(boolean useFixedNumBands)

getAutoIdeogramNumBands

public int getAutoIdeogramNumBands()

setAutoIdeogramNumBands

public void setAutoIdeogramNumBands(int n)

getAutoIdeogramBandSize

public int getAutoIdeogramBandSize()

setAutoIdeogramBandSize

public void setAutoIdeogramBandSize(int n)

clear

protected void clear(boolean isAutoGenerated)

Creates a new set of empty IntervalTrees.

getIdeogramDBTree

public IntervalTree[] getIdeogramDBTree()

isAutoGenerated

public boolean isAutoGenerated()

generateDefault

public void generateDefault(ReferenceInfo ref_info)

addDefaultBand

protected void addDefaultBand(java.lang.String name,
                  int contig,
                  int start,
                  int extent,
                  int band_idx)

readIdeogramData

public boolean readIdeogramData(java.io.Reader reader,
                       IProgressNotifier notifier)
                         throws java.io.IOException,
                                FileFormatException

Parameters:

reader -

notifier -

Returns:

Throws:

java.io.IOException

FileFormatException

main

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

Parameters:

args -