public interface PherogramProvider extends DataModel
PherogramArea
.Modifier and Type | Field and Description |
---|---|
static String |
LABEL_OVERCALL_PROBABILITY
Label to be used with
getAnnotation(String, int) to determine the overcall probability |
static String |
LABEL_SUBSTITUTION_PROBABILITY
Label to be used with
getAnnotation(String, int) to determine the substitution probability |
static String |
LABEL_UNDERCALL_PROBABILITY
Label to be used with
getAnnotation(String, int) to determine the undercall probability |
static Set<String> |
PROBABILITY_LABELS
A list that allows to iterate over all probability labels.
|
static Set<Character> |
TRACE_CURVE_NUCLEOTIDES
A list of the nucleotides A, T, C and G to which trace curves exist in a trace file from Sanger sequencing.
|
Modifier and Type | Method and Description |
---|---|
int |
getAnnotation(String label,
int baseIndex)
Returns the specified annotation (e.g.
|
char |
getBaseCall(int baseIndex)
Returns a base from the DNA sequence associated with the stored trace.
|
int |
getBaseCallPosition(int baseIndex)
Returns the position in the trace where the base at the specified index was observed.
|
double |
getMaxTraceValue(char nucleotide)
Returns the maximum trace value the specified curve contains.
|
int |
getQuality(char nucleotide,
int baseIndex)
Returns the quality score associated with the specified nucleotide.
|
int |
getSequenceLength()
Returns the length of the sequence associated with the stored trace.
|
int |
getTraceLength()
Returns the length of the stored trace.
|
double |
getTraceValue(char nucleotide,
int x)
Returns the y value of the specified trace curve at the specified position.
|
PherogramProvider |
reverseComplement()
Returns a reverse complemented view of this model.
|
static final Set<Character> TRACE_CURVE_NUCLEOTIDES
static final String LABEL_SUBSTITUTION_PROBABILITY
getAnnotation(String, int)
to determine the substitution probabilitystatic final String LABEL_OVERCALL_PROBABILITY
getAnnotation(String, int)
to determine the overcall probabilitystatic final String LABEL_UNDERCALL_PROBABILITY
getAnnotation(String, int)
to determine the undercall probabilitystatic final Set<String> PROBABILITY_LABELS
double getTraceValue(char nucleotide, int x)
nucleotide
- the type of trace curve (A, T, C or G)x
- the x position of the curve (The first position is 0 and the last is
getTraceLength()
- 1
.)int getTraceLength()
double getMaxTraceValue(char nucleotide)
#getTraceValue(TraceCurve, int)
.)nucleotide
- the type of trace curve (A, T, C or G)char getBaseCall(int baseIndex)
baseIndex
- the index of the base in the pherogram (base call) sequence (This might differ
from the index of the base in the associated sequence in the alignment. Indices start with 0.)int getBaseCallPosition(int baseIndex)
baseIndex
- the index of the base in the pherogram (base call) sequence (This might differ
from the index of the base in the associated sequence in the alignment. Indices start with 0.)getTraceLength()
- 1
int getQuality(char nucleotide, int baseIndex)
nucleotide
- the nucleotide identifying the trace curve for the quality scorebaseIndex
- the index of the base call position to which the quality score belongs (Indices start with 0.)int getAnnotation(String label, int baseIndex)
label
- the name of the attachment to be returnedbaseIndex
- the index of base call to which the returned attachment score belongs (Indices start with 0.)int getSequenceLength()
PherogramProvider reverseComplement()