Class
RnaRecordA container for RNA structure data.
| Defined in | <seqan/rna_io.h> |
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| Signature |
class RnaRecord;
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Member Function Overview
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void RnaRecord::clearID()Clear value of recordID and set to undefined. -
bool RnaRecord::hasUndefinedID()Test for an undefined recordID value.
Member Variable Overview
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Align<Rna5String,ArrayGaps> RnaRecord::alignAlignment of several sequences (including gaps). -
String<RnaStructureGraph> RnaRecord::bppMatrGraphsVector of base pair probability graphs extracted from the input files. -
CharString RnaRecord::commentComment to be stored together with the record. -
String<RnaStructureGraph> RnaRecord::fixedGraphsVector of fixed structure graphs extracted from the input files. -
CharString RnaRecord::nameSequence name. -
unsigned RnaRecord::offsetStart index of the sequence. -
CharString RnaRecord::qualityQuality values for the sequence. -
StringSet<String<float>> RnaRecord::reactErrorError of the reactivity. -
StringSet<String<float>> RnaRecord::reactivityThe area peak/likelihood estimate that represents the reactivity at each position. -
std::uint32_t RnaRecord::recordIDIdentification of the record. -
StringSet<CharString> RnaRecord::seqIDSequence identifier for aligned sequences. -
TSizeRna5String RnaRecord::seqLenLength of the sequence or alignment stored in this record. -
Rna5String RnaRecord::sequenceString of bases in RNA strand. -
String<std::uint32_t> RnaRecord::typeIDIndices of the assigned type (T..) attributes records from EBPSEQ files.
Detailed Description
The container stores all kinds of data that can be obtained by reading RNA structure file records.
Member Functions Detail
void RnaRecord::clearID()
Data Races
bool RnaRecord::hasUndefinedID()
Returns
bool |
True if recordID is not set. |
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Data Races
Member Variables Detail
Align<Rna5String,ArrayGaps> RnaRecord::align
This member variable is only used in alignment-based records (from STH files).
String<RnaStructureGraph> RnaRecord::bppMatrGraphs
CharString RnaRecord::comment
String<RnaStructureGraph> RnaRecord::fixedGraphs
CharString RnaRecord::name
unsigned RnaRecord::offset
CharString RnaRecord::quality
StringSet<String<float>> RnaRecord::reactError
This member variable is used only if biological validated data is found (T.. fields in EBPSEQ are set).
If reactivity was derived as a consensus of different replicates, this indicates the standard error between samples used. If only one experiment was done, this may be some measure of variation between the data in that experiment, e.g. 0.2 of the standard deviation.
StringSet<String<float>> RnaRecord::reactivity
This member variable is used only if biological validated data is found (T.. fields in EBPSEQ are set).
std::uint32_t RnaRecord::recordID
In an RNA structure file the first record gets ID 0, the following ID 1 and so on.
StringSet<CharString> RnaRecord::seqID
This member variable is only used in alignment-based records (from STH files).
TSizeRna5String RnaRecord::seqLen
Rna5String RnaRecord::sequence
This member variable is only used in sequence-based records (from CT, DBN, DBV, BPSEQ, EBPSEQ files).
String<std::uint32_t> RnaRecord::typeID
This member variable is used only if biological validated data is found (T.. fields in EBPSEQ are set).