org.biolegato.core.data.sequence
Class Sequence

java.lang.Object
  java.util.Dictionary<K,V>
      java.util.Hashtable<java.lang.String,java.lang.Object>
          org.biolegato.core.data.sequence.Sequence

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.util.Map<java.lang.String,java.lang.Object>

public class Sequence
extends java.util.Hashtable<java.lang.String,java.lang.Object>
implements java.lang.Cloneable

This class is used to contain all sequence related functions and data.

This class uses hashtables to pass and store parameters of the sequence. The hashtable has many intrinsic parameters; however accepts any number of additional parameters. The current values used by all known BioLegato plugins and classes are:

Key	Intrinsic	Default setting	Description
accession	No	N/A>	The accession of the sequence
comments	No	N/A>	Comments about the sequence
creation-date	No	N/A>	The date the sequence was first synthesized
creator	No	N/A>	The creator of the sequence
direction	Yes	From 5' to 3'	The direction of the sequence (from 3' to 5' or from 5' to 3')
description	No	N/A>	A description of the sequence
GI	No	N/A>	The GI number of the sequence
modified	Yes	N/A>	Used to indicate the sequence was modified
name	Yes	New sequence	The sequence's name
sequence	Yes	blank	The raw sequence
strandedness	Yes	Single	The strandedness of a sequence
topology	Yes	Linear	The sequence topology
type	Yes	DNA>	The type of data the sequence is

Author:

Graham Alvare, Brian Fristensky

See Also:

Serialized Form

Nested Class Summary

static class	Sequence.CharacterClass Used for typing characters within a sequence.
static class	Sequence.Direction Used for typing/storing sequence direction.
static class	Sequence.Strandedness Used for typing/storing sequence strandedness.
static class	Sequence.Topology Used for typing/storing sequence topology.
static class	Sequence.Type This enum is used for typing/storing sequence types.

Field Summary

static java.awt.datatransfer.DataFlavor

sequenceFlavour A data flavour representing the raw Sequence data type.

Constructor Summary

Sequence()
Constructs new instances of Sequence objects.

Sequence(java.util.Map<java.lang.String,java.lang.Object> data)
Constructs new instances of sequence.

Sequence(java.lang.String string)
Constructs new instances of Sequence objects.

Method Summary

void	addListener(SequenceListener listener) Adds a sequence listener to keep track of sequence modifications.
Sequence.CharacterClass	charType(char test)
java.lang.Object	clone() Clones the current sequence object.
java.lang.Object	get(java.lang.Object key) Obtains a value for a field of the sequence.
static java.lang.Object	getDefault(java.lang.String key) This function obtains the default value of a field for a Sequence.
static java.util.LinkedList<Sequence>	getgroup(java.lang.Integer groupNumber)
static void	group(Sequence[] sequences)
boolean	insertField(java.lang.String field, int column, java.lang.String string) Inserts a string into field within the sequence.
java.lang.Object	put(java.lang.String key, java.lang.Object value) Changes a value of a field in the sequence.
void	removeListener(SequenceListener listener) Removes a sequence listener from keeping track of sequence modifications.
Sequence	subseq(int start) Extracts a portion of the current sequence.
Sequence	subseq(int start, int end) Extracts a portion of the current sequence.
java.lang.String	toString() Creates a string representation of the Sequence and its fields
static void	ungroup(Sequence[] sequences)

Methods inherited from class java.util.Hashtable

clear, contains, containsKey, containsValue, elements, entrySet, equals, hashCode, isEmpty, keys, keySet, putAll, rehash, remove, size, values

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

sequenceFlavour

public static final java.awt.datatransfer.DataFlavor sequenceFlavour

A data flavour representing the raw Sequence data type.

Constructor Detail

Sequence

public Sequence()

Constructs new instances of Sequence objects.

Sequence

public Sequence(java.lang.String string)

Constructs new instances of Sequence objects.

Parameters:

string - the string to use for the "sequence" field in the sequence data.

Sequence

public Sequence(java.util.Map<java.lang.String,java.lang.Object> data)

Constructs new instances of sequence.

Parameters:

data - the map of values to use for the sequence.

Method Detail

addListener

public void addListener(SequenceListener listener)

Adds a sequence listener to keep track of sequence modifications.

Parameters:

listener - the sequence listener to add.

removeListener

public void removeListener(SequenceListener listener)

Removes a sequence listener from keeping track of sequence modifications.

Parameters:

listener - the listener to remove.

get

public java.lang.Object get(java.lang.Object key)

Obtains a value for a field of the sequence. This is the same as calling the get function on the Sequence's superclass (hashtable)

Specified by:

get in interface java.util.Map<java.lang.String,java.lang.Object>

Overrides:

get in class java.util.Hashtable<java.lang.String,java.lang.Object>

Parameters:

key - the field name for the sequence data

Returns:

the value of the field

put

public java.lang.Object put(java.lang.String key,
                            java.lang.Object value)

Changes a value of a field in the sequence. This is the same as calling the "put" function on the Sequence's superclass.

Specified by:

put in interface java.util.Map<java.lang.String,java.lang.Object>

Overrides:

put in class java.util.Hashtable<java.lang.String,java.lang.Object>

Parameters:

key - the name of the field in the sequence.

value - the new value of the field.

insertField

public boolean insertField(java.lang.String field,
                           int column,
                           java.lang.String string)

Inserts a string into field within the sequence.

Parameters:

field - the field to alter.

column - the column number to do the insertion at.

string - the text to insert.

Returns:

true if the operation was successful, otherwise false.

getDefault

public static java.lang.Object getDefault(java.lang.String key)

This function obtains the default value of a field for a Sequence. This is done by accessing the defaults hashtable.

Parameters:

key - the name of the field.

Returns:

the value of the field.

toString

public java.lang.String toString()

Creates a string representation of the Sequence and its fields

Overrides:

toString in class java.util.Hashtable<java.lang.String,java.lang.Object>

Returns:

the corresponding sequence

subseq

public Sequence subseq(int start)

Extracts a portion of the current sequence. This function is similar to java.lang.String.substring except that it deals with sequence objects.

Parameters:

start - the position to start the extraction.

Returns:

the extracted sub-sequence.

See Also:

String.substring(int)

subseq

public Sequence subseq(int start,
                       int end)

Extracts a portion of the current sequence. This function is similar to java.lang.String.substring except that it deals with sequence objects.

Parameters:

start - the position to start the extraction.

end - the position to end the extraction.

Returns:

the extracted sequence.

See Also:

String.substring(int)

clone

public java.lang.Object clone()

Clones the current sequence object.

Overrides:

clone in class java.util.Hashtable<java.lang.String,java.lang.Object>

Returns:

a cloned copy of the sequence.

charType

public Sequence.CharacterClass charType(char test)

group

public static void group(Sequence[] sequences)

ungroup

public static void ungroup(Sequence[] sequences)

getgroup

public static java.util.LinkedList<Sequence> getgroup(java.lang.Integer groupNumber)