net.sf.jannot
Class Entry

java.lang.Object
  net.sf.jannot.Entry

All Implemented Interfaces:

java.lang.Comparable<Entry>, java.lang.Iterable<DataKey>

public class Entry
extends java.lang.Object
implements java.lang.Comparable<Entry>, java.lang.Iterable<DataKey>

Each Entry contains information about a specific genome/chromossomes or any chunck of DNA. With the chunk we associate a sequence, feature annotation, a description, graph annotation and alignment annotation. In order to load data to an Entry set, you should use the class Filesource. e.g.: EntrySet set = new FileSource(new File("sequence.fasta")).read(); will read a sequence from a fasta to Entryset set. new FileSource(new File("sequence.gff")).read(set); will read notations from the .gff file to Entryset set.

Author:

Thomas Abeel

Field Summary

Description

description

Constructor Summary

Entry(java.lang.String id)

Method Summary

void	add(DataKey key, Data<?> newData)
int	compareTo(Entry o)
boolean	contains(DataKey dataKey)
Data<?>	get(DataKey dataKey)
java.lang.String	getID() Shortcut to access the id
int	getMaximumLength() Returns the highest position for which there is data
MemoryFeatureAnnotation	getMemoryAnnotation(DataKey type)
java.util.Iterator<DataKey>	iterator()
void	remove(DataKey dataKey)
Sequence	sequence()
void	setSequence(Sequence seq)
java.lang.Iterable<ReadGroup>	shortReads()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

description

public final Description description

Constructor Detail

Entry

public Entry(java.lang.String id)

Method Detail

getMaximumLength

public int getMaximumLength()

Returns the highest position for which there is data

Returns:

add

public void add(DataKey key,
                Data<?> newData)

get

public Data<?> get(DataKey dataKey)

Parameters:

dataKey -

Returns:

iterator

public java.util.Iterator<DataKey> iterator()

Specified by:

iterator in interface java.lang.Iterable<DataKey>

shortReads

public java.lang.Iterable<ReadGroup> shortReads()

Returns:

getMemoryAnnotation

public MemoryFeatureAnnotation getMemoryAnnotation(DataKey type)

Parameters:

type -

Returns:

sequence

public Sequence sequence()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getID

public java.lang.String getID()

Shortcut to access the id

Returns:

compareTo

public int compareTo(Entry o)

Specified by:

compareTo in interface java.lang.Comparable<Entry>

contains

public boolean contains(DataKey dataKey)

Parameters:

dataKey -

Returns:

setSequence

public void setSequence(Sequence seq)

remove

public void remove(DataKey dataKey)

Parameters:

dataKey -