org.sdm.spa.actors.piw.viz

Class Sequence

java.lang.Object

org.sdm.spa.actors.piw.viz.Sequence

public class Sequence
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	accessionNumberOriginal
java.lang.String	alignedSequence
TranscriptionFactorBindingSite[]	arrTFBSs
java.lang.String	geneID
int	offset

Constructor Summary

Constructors

Constructor and Description
Sequence(java.lang.String accessionNumberOriginal, java.lang.String geneID, java.lang.String alignedSequence, TranscriptionFactorBindingSite[] arrTFBSs) Construct an instance with offset 0.
Sequence(java.lang.String accessionNumberOriginal, java.lang.String geneID, java.lang.String alignedSequence, TranscriptionFactorBindingSite[] arrTFBSs, int offset) Construct an instance.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object ob)
int	getActualIndex(int index)
int	getTotalNumParticularTFBS(java.lang.String tfbs) Returns the number of times the given tfbs appears in this sequence.
int	lengthNoGaps()
java.lang.String	subsequence(int start, int length) Find the subsequence, filling in hyphens for gaps.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

accessionNumberOriginal

public final java.lang.String accessionNumberOriginal

geneID

public final java.lang.String geneID

alignedSequence

public final java.lang.String alignedSequence

arrTFBSs

public final TranscriptionFactorBindingSite[] arrTFBSs

offset

public final int offset

Constructor Detail

Sequence

public Sequence(java.lang.String accessionNumberOriginal,
                java.lang.String geneID,
                java.lang.String alignedSequence,
                TranscriptionFactorBindingSite[] arrTFBSs)

Construct an instance with offset 0.

See Also:

Sequence(String, String, String, TranscriptionFactorBindingSite[], int)

Sequence

public Sequence(java.lang.String accessionNumberOriginal,
                java.lang.String geneID,
                java.lang.String alignedSequence,
                TranscriptionFactorBindingSite[] arrTFBSs,
                int offset)

Construct an instance.

Parameters:

accessionNumberOriginal - Accession number of the original sequence we submitted to BLAST.

geneID - Gene ID of this sequence.

alignedSequence - Sequence returned by ClustalW with gaps.

arrTFBSs - Transcription factor binding sites relative to this sequence with no gaps.

offset - How much this sequence is shifted.

Method Detail

getActualIndex

public int getActualIndex(int index)

Parameters:

index - Index on a sequence without gaps.

Returns:

Corresponding index on this sequence.

subsequence

public java.lang.String subsequence(int start,
                                    int length)

Find the subsequence, filling in hyphens for gaps.

Parameters:

start - Initial index.

length - Length of sequence to return.

Returns:

subsequence.

getTotalNumParticularTFBS

public int getTotalNumParticularTFBS(java.lang.String tfbs)

Returns the number of times the given tfbs appears in this sequence.

lengthNoGaps

public int lengthNoGaps()

Returns:

Length of sequence with gaps removed.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object ob)

Overrides:

equals in class java.lang.Object