de.charite.compbio.jannovar.reference

Class TranscriptProjectionDecorator

java.lang.Object

de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator

public final class TranscriptProjectionDecorator
extends Object

Wraps a TranscriptModel object and allow the coordinate conversion.

Author:

Manuel Holtgrewe

Field Summary

Fields

Modifier and Type	Field and Description
static int	INVALID_EXON_ID constant for invalid exon index
static int	INVALID_INTRON_ID constant for invalid intron index

Constructor Summary

Constructors

Constructor and Description
TranscriptProjectionDecorator(TranscriptModel transcript) Initialize the object with the given TranscriptModel

Method Summary

Modifier and Type	Method and Description
GenomePosition	cdsToGenomePos(CDSPosition pos) Coordinate conversion from CDS to genome position.
TranscriptPosition	cdsToTranscriptPos(CDSPosition pos) Coordinate conversion from CDS to transcript position.
int	exonIDInReferenceOrder(int exonID) Returns the index of the (0-based) exon in the reference (forward) order.
CDSPosition	genomeToCDSPos(GenomePosition pos) Coordinate conversion from genome position to CDS position.
TranscriptPosition	genomeToTranscriptPos(GenomePosition pos) Coordinate conversion from genome position to transcript position.
String	getCDSTranscript()
TranscriptModel	getTranscript()
String	getTranscriptStartingAtCDS()
int	locateExon(GenomePosition pos) Returns (0-based) index of the exon (in the order determined by the transcript's strand).
int	locateExon(TranscriptPosition pos) Returns (0-based) index of the exon (in the order determined by the transcript's strand).
int	locateIntron(GenomePosition pos) Returns (0-based) index of the intron (in the order determined by the transcript's strand).
CDSInterval	projectGenomeToCDSInterval(GenomeInterval interval) Translate GenomeInterval to CDSInterval for transcript.
CDSPosition	projectGenomeToCDSPosition(GenomePosition pos) Translate GenomePosition to CDSPosition for transcript.
TranscriptInterval	projectGenomeToTXInterval(GenomeInterval interval) Translate GenomeInterval to TranscriptInterval for transcript.
TranscriptPosition	projectGenomeToTXPosition(GenomePosition pos) Translate GenomePosition to TranscriptPosition for transcript.
GenomePosition	transcriptToGenomePos(TranscriptPosition pos) Coordinate conversion from transcript to genome position.

Methods inherited from class java.lang.Object

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

Field Detail

INVALID_EXON_ID

public static final int INVALID_EXON_ID

constant for invalid exon index

See Also:

Constant Field Values

INVALID_INTRON_ID

public static final int INVALID_INTRON_ID

constant for invalid intron index

See Also:

Constant Field Values

Constructor Detail

TranscriptProjectionDecorator

public TranscriptProjectionDecorator(TranscriptModel transcript)

Initialize the object with the given TranscriptModel

Parameters:

transcript - the TranscriptModel to decorate

Method Detail

getTranscript

public TranscriptModel getTranscript()

Returns:

the transcript

getCDSTranscript

public String getCDSTranscript()

Returns:

the CDS transcript string

getTranscriptStartingAtCDS

public String getTranscriptStartingAtCDS()

Returns:

the CDS transcript string extended to the right for the full transcript

genomeToTranscriptPos

public TranscriptPosition genomeToTranscriptPos(GenomePosition pos)
                                         throws ProjectionException

Coordinate conversion from genome position to transcript position.

Parameters:

pos - genome position to convert

Returns:

position on transcript corresponding to pos

Throws:

ProjectionException - if the genome position was not valid

genomeToCDSPos

public CDSPosition genomeToCDSPos(GenomePosition pos)
                           throws ProjectionException

Coordinate conversion from genome position to CDS position. This is computed from the transcript position and the offset of the CDS start position.

Parameters:

pos - genome position to convert

Returns:

position on transcript corresponding to pos

Throws:

ProjectionException - if the genome position was not valid

cdsToTranscriptPos

public TranscriptPosition cdsToTranscriptPos(CDSPosition pos)

Coordinate conversion from CDS to transcript position.

Parameters:

pos - the position in the CDS transcript

Returns:

the corresponding genome position for pos, will be on the same strand as the transcript

cdsToGenomePos

public GenomePosition cdsToGenomePos(CDSPosition pos)
                              throws ProjectionException

Coordinate conversion from CDS to genome position.

Parameters:

pos - the position in the CDS transcript

Returns:

the corresponding genome position for pos, will be on the same strand as the transcript

Throws:

ProjectionException - on problems with the coordinate transformation (outside of the transcript)

transcriptToGenomePos

public GenomePosition transcriptToGenomePos(TranscriptPosition pos)
                                     throws ProjectionException

Coordinate conversion from transcript to genome position.

Parameters:

pos - the position on the transcript

Returns:

the corresponding genome position for pos, will be on the same strand as the transcript

Throws:

ProjectionException - on problems with the coordinate transformation (outside of the transcript)

exonIDInReferenceOrder

public int exonIDInReferenceOrder(int exonID)

Returns the index of the (0-based) exon in the reference (forward) order.

Parameters:

exonID - the 0-based exonID in transcript order (reverse order in the case of transcripts on the reverse strand)

Returns:

the exon ID in reference (forward order)

locateIntron

public int locateIntron(GenomePosition pos)

Returns (0-based) index of the intron (in the order determined by the transcript's strand).

Parameters:

pos - the GenomePosition to use for querying

Returns:

(0-based) index of the selected intron, or INVALID_INTRON_ID if pos is not in exonic region but in transcript interval

locateExon

public int locateExon(GenomePosition pos)

Returns (0-based) index of the exon (in the order determined by the transcript's strand).

Parameters:

pos - the GenomePosition to use for querying

Returns:

(0-based) index of the selected exon, or INVALID_EXON_ID if pos is not in exonic region but in transcript interval

locateExon

public int locateExon(TranscriptPosition pos)
               throws ProjectionException

Returns (0-based) index of the exon (in the order determined by the transcript's strand).

Parameters:

pos - the TranscriptPosition to use for querying

Returns:

(0-based) index of the selected exon

Throws:

ProjectionException - if there was a problem with pos (somehow falls out of transcript region, can only happen if negative or right of transcript end)

projectGenomeToCDSPosition

public CDSPosition projectGenomeToCDSPosition(GenomePosition pos)

Translate GenomePosition to CDSPosition for transcript. Positions upstream of CDS region are projected to the CDS begin position, downstream of CDS are projected to the CDS end, positions in CDS introns are projected to first position of the next CDS exon.

Parameters:

pos - the position to translate

Returns:

the corresponding position in the transcript sequence

projectGenomeToCDSInterval

public CDSInterval projectGenomeToCDSInterval(GenomeInterval interval)

Translate GenomeInterval to CDSInterval for transcript. Positions upstream of CDS region are projected to the CDS begin position, downstream of CDS are projected to the CDS end.

Parameters:

interval - the GenomeInterval to project

Returns:

the corresponding position in the transcript sequence

projectGenomeToTXPosition

public TranscriptPosition projectGenomeToTXPosition(GenomePosition pos)

Translate GenomePosition to TranscriptPosition for transcript. Positions upstream of TX region are projected to the TX begin position, downstream of TX are projected to the TX end, positions in introns are projected to first position of the next CDS exon.

Parameters:

pos - the position to translate

Returns:

the corresponding position in the transcript sequence

projectGenomeToTXInterval

public TranscriptInterval projectGenomeToTXInterval(GenomeInterval interval)

Translate GenomeInterval to TranscriptInterval for transcript. Positions upstream of TX region are projected to the TX begin position, downstream of TX are projected to the TX end.

Parameters:

interval - the GenomeInterval to project

Returns:

the corresponding position in the transcript sequence