com.biomatters.geneious.publicapi.documents.sequence

Class CompactQualityOnlyGraph

java.lang.Object

com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph

All Implemented Interfaces:

ExtendedNucleotideGraph, NucleotideGraph

public class CompactQualityOnlyGraph
extends Object
implements ExtendedNucleotideGraph

A memory efficient nucleotide graph that only supports quality values in the range 0->256 and does not support traces. Useful for 454 sequences where we want to minimize the memory overhead of each sequence.

Nested Class Summary

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph

NucleotideGraph.ImmutableGraphProvider

Constructor Summary

Constructors

Constructor and Description
CompactQualityOnlyGraph(byte[] qualities) Constructs a new graph.

Method Summary

Methods

Modifier and Type	Method and Description
int	getChromatogramLength() The number of points for which this graph has values, which is typically larger than the length of the nucleotide sequence because a base isn't called at every position in the graph.
int	getChromatogramPositionForResidue(int residueIndex) The graph position (can be used as an argument to NucleotideGraph.getChromatogramValue(int, int)) where the nucleotide at the specified residue index has been called.
int	getChromatogramValue(int nucleotideStateNumber, int graphPosition) Returns the graph value for the specified nucleotide and at the specified position.
int	getLeadingGapsLength() Get the number of leading residues in the sequence this graph corresponds to that are all gaps.
int	getSequenceLength() The length of the nucleotide sequence that can be annotated with this graph.
int	getSequenceQuality(int residueIndex) Returns a measurement of confidence in the residue reported at the specified residueIndex in the sequence.
int	getTrailingGapsLength() Get the number of trailing residues in the sequence this graph corresponds to that are all gaps.
boolean	hasChromatogramPositionsForResidues() Tests whether this NucleotideGraph contains information about the position of the base calls, i.e.
boolean	hasChromatogramValues(int nucleotideStateNumber) Specifies whether it is legal to call NucleotideGraph.getChromatogramValue(int, int) for the specified nucleotide.
boolean	hasSequenceQualities() Tests whether this graph contains information about the confidence in the associated sequence's residues, i.e.

Methods inherited from class java.lang.Object

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

Constructor Detail

CompactQualityOnlyGraph

public CompactQualityOnlyGraph(byte[] qualities)

Constructs a new graph.

Parameters:

qualities - the qualities of the graph. The contents of this array must not change after calling this method. The quality values may be negative values (because Java bytes range in value from -128 to +127). Negative byte values are interpreted as postive integers (by adding 256) when returned from getSequenceQuality(int).

Method Detail

hasSequenceQualities

public boolean hasSequenceQualities()

Description copied from interface: NucleotideGraph

Tests whether this graph contains information about the confidence in the associated sequence's residues, i.e. whether it is legal to call NucleotideGraph.getSequenceQuality(int).

Specified by:

hasSequenceQualities in interface NucleotideGraph

Returns:

true if it is legal to call NucleotideGraph.getSequenceQuality(int) on this graph.

getSequenceQuality

public int getSequenceQuality(int residueIndex)
                       throws IndexOutOfBoundsException,
                              UnsupportedOperationException

Description copied from interface: NucleotideGraph

Returns a measurement of confidence in the residue reported at the specified residueIndex in the sequence. The measure is on a logaritmic scale: P(call correct) = 1 - 10^(-v/10) where v is the quality returned from this method.

If the sequence contains a gap at the specified position, this method should return Integer.MIN_VALUE if it is an end gap. If it is an internal gap, it should return the average quality of the non-gap positions on either side of the gap.

This method may only be called if NucleotideGraph.hasSequenceQualities() returns true.

Specified by:

getSequenceQuality in interface NucleotideGraph

Parameters:

residueIndex - A value 0 <= residueIndex < NucleotideGraph.getSequenceLength() specifying the index in the nucleotide sequence for which to calculate the quality of the graph.

Returns:

The quality score v for the residue at the specified index in the nucleotide sequence, which indicates the reliability of the nucleotide on a logarithmic scale as described above.

Throws:

IndexOutOfBoundsException - if residueIndex < 0 or residueIndex > NucleotideGraph.getSequenceLength().

UnsupportedOperationException - if !hasSequenceQualities().

getSequenceLength

public int getSequenceLength()

Description copied from interface: NucleotideGraph

The length of the nucleotide sequence that can be annotated with this graph. If a class implements both this interface and SequenceDocument, then the return value of this method must be equal to getCharSequence().length() Also if NucleotideGraph.hasChromatogramPositionsForResidues() or NucleotideGraph.hasSequenceQualities() is true, the return value indicates the range of legal values to pass to NucleotideGraph.getChromatogramPositionForResidue(int) and NucleotideGraph.getSequenceQuality(int).

Specified by:

getSequenceLength in interface NucleotideGraph

Returns:

length of the nucleotide sequence belonging to this graph.

getChromatogramLength

public int getChromatogramLength()

Description copied from interface: NucleotideGraph

The number of points for which this graph has values, which is typically larger than the length of the nucleotide sequence because a base isn't called at every position in the graph.

Specified by:

getChromatogramLength in interface NucleotideGraph

Returns:

the length of this graph, or 0 if this graph has no graph values for any nucleotide.

getChromatogramValue

public int getChromatogramValue(int nucleotideStateNumber,
                       int graphPosition)
                         throws IndexOutOfBoundsException

Description copied from interface: NucleotideGraph

Returns the graph value for the specified nucleotide and at the specified position. If the graph is a chromatogram, this is a measure of the support for the specified nucleotide at this position. May only be called if NucleotideGraph.hasChromatogramValues(int) returns true for the specified nucleotide.

Specified by:

getChromatogramValue in interface NucleotideGraph

Parameters:

nucleotideStateNumber - The nucleotide for which to retrieve the graph value, encoded as 0 = A, 1 = C, 2 = G, 3 = T (alphabetic order, same as in Nucleotides)

graphPosition - The position in the sequence for which to query the graph value, with 0 <= graphPosition < graph length

Returns:

the graph value for the specified nucleotide and at the specified position.

Throws:

IndexOutOfBoundsException - if graphPosition < 0 or graphPosition >= NucleotideGraph.getChromatogramLength()

hasChromatogramValues

public boolean hasChromatogramValues(int nucleotideStateNumber)

Description copied from interface: NucleotideGraph

Specifies whether it is legal to call NucleotideGraph.getChromatogramValue(int, int) for the specified nucleotide.

Specified by:

hasChromatogramValues in interface NucleotideGraph

Parameters:

nucleotideStateNumber - A nucleotide state number encoded in the same way as for NucleotideGraph.getChromatogramValue(int, int), i.e. 0 = A, 1 = C, 2 = G, 3 = T

Returns:

true if is legal to call NucleotideGraph.getChromatogramValue(int, int) for the specified nucleotide

getChromatogramPositionForResidue

public int getChromatogramPositionForResidue(int residueIndex)
                                      throws IndexOutOfBoundsException,
                                             UnsupportedOperationException

Description copied from interface: NucleotideGraph

The graph position (can be used as an argument to NucleotideGraph.getChromatogramValue(int, int)) where the nucleotide at the specified residue index has been called. This method may only be called if NucleotideGraph.hasChromatogramPositionsForResidues() returns true. The graph sites are guaranteed to have the same order as the sequence nucleotides. Therefore, any implementation must ensure that if i < j, then getChromatogramPositionForResidue(i) <= getChromatogramPositionForResidue(j).

Specified by:

getChromatogramPositionForResidue in interface NucleotideGraph

Parameters:

residueIndex - A value 0 <= residueIndex < NucleotideGraph.getSequenceLength() specifying the index in the nucleotide sequence for which to calculate the corresponding position in the graph.

Returns:

A value in the range 0 <= value < NucleotideGraph.getChromatogramLength(), specifiying the graph position where the nucleotide that is at position residueIndex has been called. For positions residueIndex where the sequence length consisting of values between 0 and getChromatogramLength()-1 inclusive. For a residueIndex where the sequence holds a '-', the returned site position must always be Integer.MIN_VALUE.

Throws:

IndexOutOfBoundsException - if residueIndex < 0 or residueIndex > NucleotideGraph.getSequenceLength().

UnsupportedOperationException - if !hasChromatogramPositionsForResidues().

hasChromatogramPositionsForResidues

public boolean hasChromatogramPositionsForResidues()

Description copied from interface: NucleotideGraph

Tests whether this NucleotideGraph contains information about the position of the base calls, i.e. whether it is legal to call NucleotideGraph.getChromatogramPositionForResidue(int).

Specified by:

hasChromatogramPositionsForResidues in interface NucleotideGraph

Returns:

true if this NucleotideGraph contains information about the position of the base calls.

getLeadingGapsLength

public int getLeadingGapsLength()

Description copied from interface: ExtendedNucleotideGraph

Get the number of leading residues in the sequence this graph corresponds to that are all gaps. NucleotideGraph.getSequenceQuality(int) and NucleotideGraph.getChromatogramPositionForResidue(int) will both return Integer.MIN_VALUE for residueIndices less than the number of leading gaps.

Note, an implementation may choose to return 0 from this method even if it has leading end gaps or any value less than or equal to the number of leading gaps it has.

Specified by:

getLeadingGapsLength in interface ExtendedNucleotideGraph

Returns:

the number of leading residues in the sequence this graph corresponds to that are all gaps.

getTrailingGapsLength

public int getTrailingGapsLength()

Description copied from interface: ExtendedNucleotideGraph

Get the number of trailing residues in the sequence this graph corresponds to that are all gaps. NucleotideGraph.getSequenceQuality(int) and NucleotideGraph.getChromatogramPositionForResidue(int) will both return Integer.MIN_VALUE for residueIndices within this much of NucleotideGraph.getSequenceLength().

Note, an implementation may choose to return 0 from this method even if it has trailing end gaps or any value less than or equal to the number of trailing gaps it has.

Specified by:

getTrailingGapsLength in interface ExtendedNucleotideGraph

Returns:

the number of trailing residues in the sequence this graph corresponds to that are all gaps.