org.biolegato.gdesupport.data
Class Seq

java.lang.Object
  org.biolegato.gdesupport.data.Seq

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public final class Seq
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable

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

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
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 test the sequence is

Author:

Graham Alvare, Brian Fristensky

See Also:

Serialized Form

Nested Class Summary

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

Field Summary

static ColourMask

DEFAULT_MASK The default colour mask for BioLegato

Constructor Summary

Seq()
Constructs new instances of Cell objects.

Seq(Seq.Type type, java.lang.String name, java.lang.StringBuffer sequence)
Constructs new instances of sequence.

Seq(Seq.Type type, java.lang.String name, java.lang.StringBuffer sequence, Seq.Direction direction, Seq.Topology topology, Seq.Strandedness strandedness)
Constructs new instances of sequence.

Seq(Seq.Type type, java.lang.String name, java.lang.StringBuffer sequence, Seq.Direction direction, Seq.Topology topology, Seq.Strandedness strandedness, int groupID, java.lang.String description)
Constructs new instances of sequence.

Seq(Seq.Type type, java.lang.String name, java.lang.StringBuffer sequence, Seq.Direction direction, Seq.Topology topology, Seq.Strandedness strandedness, java.lang.StringBuilder original)
Constructs new instances of sequence.

Seq(Seq data)
Constructs new instances of sequence.

Method Summary

java.lang.Object	clone() Clones the current sequence object.
static Seq.Type	detectType(java.lang.StringBuffer data) This function detects the type of a sequence
static ColourMask	getDefaultMask() Load the default colour masks (this was the only way I was able to get this code to work properly).
java.lang.String	getDescription()
Seq.Direction	getDirection()
int	getGroupID()
ColourMask	getMask()
java.lang.String	getName()
java.lang.StringBuilder	getOriginal()
boolean	getProtectAlignment()
boolean	getProtectAmbiguous()
boolean	getProtectUnambiguous()
java.lang.StringBuffer	getSequence()
Seq.Strandedness	getStrandedness()
Seq.Topology	getTopology()
Seq.Type	getType()
void	modified()
java.lang.String	toString() Creates a string representation of the Cell and its fields

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MASK

public static final ColourMask DEFAULT_MASK

The default colour mask for BioLegato

Constructor Detail

Seq

public Seq()

Constructs new instances of Cell objects.

Seq

public Seq(Seq.Type type,
           java.lang.String name,
           java.lang.StringBuffer sequence)

Constructs new instances of sequence.

Parameters:

type - the type of data to store

name - the name of the data sequence

sequence - the text of the sequence

Seq

public Seq(Seq.Type type,
           java.lang.String name,
           java.lang.StringBuffer sequence,
           Seq.Direction direction,
           Seq.Topology topology,
           Seq.Strandedness strandedness)

Constructs new instances of sequence.

Parameters:

type - the type of data to store

name - the name of the data sequence

sequence - the text of the sequence

direction - the direction of the sequence

topology - the topology of the sequence

strandedness - the strandedness of the sequence

Seq

public Seq(Seq.Type type,
           java.lang.String name,
           java.lang.StringBuffer sequence,
           Seq.Direction direction,
           Seq.Topology topology,
           Seq.Strandedness strandedness,
           java.lang.StringBuilder original)

Constructs new instances of sequence.

Parameters:

type - the type of data to store

name - the name of the data sequence

sequence - the text of the sequence

direction - the direction of the sequence

topology - the topology of the sequence

strandedness - the strandedness of the sequence

original - the original genbank file entry of the sequence

Seq

public Seq(Seq.Type type,
           java.lang.String name,
           java.lang.StringBuffer sequence,
           Seq.Direction direction,
           Seq.Topology topology,
           Seq.Strandedness strandedness,
           int groupID,
           java.lang.String description)

Constructs new instances of sequence.

Parameters:

type - the type of data to store

name - the name of the data sequence

sequence - the text of the sequence

direction - the direction of the sequence

topology - the topology of the sequence

strandedness - the strandedness of the sequence

groupID - the group ID for the sequence

description - the description of the sequence

Seq

public Seq(Seq data)

Constructs new instances of sequence.

Parameters:

data - the sequence to copy

Method Detail

modified

public final void modified()

getType

public final Seq.Type getType()

getName

public final java.lang.String getName()

getSequence

public final java.lang.StringBuffer getSequence()

getDirection

public final Seq.Direction getDirection()

getTopology

public final Seq.Topology getTopology()

getStrandedness

public final Seq.Strandedness getStrandedness()

getProtectAlignment

public final boolean getProtectAlignment()

getProtectAmbiguous

public final boolean getProtectAmbiguous()

getProtectUnambiguous

public final boolean getProtectUnambiguous()

getMask

public final ColourMask getMask()

getGroupID

public final int getGroupID()

getOriginal

public final java.lang.StringBuilder getOriginal()

getDescription

public final java.lang.String getDescription()

toString

public java.lang.String toString()

Creates a string representation of the Cell and its fields

Overrides:

toString in class java.lang.Object

Returns:

the corresponding sequence

clone

public java.lang.Object clone()

Clones the current sequence object.

Overrides:

clone in class java.lang.Object

Returns:

a cloned copy of the sequence.

detectType

public static Seq.Type detectType(java.lang.StringBuffer data)

This function detects the type of a sequence

Parameters:

data - the sequence to detect the type for.

Returns:

the sequence type

getDefaultMask

public static ColourMask getDefaultMask()

Load the default colour masks (this was the only way I was able to get this code to work properly).