Search Toolkit Book for IBlastXMLReportData
Interface for filling the top layer of the XML report. More...
#include <algo/blast/format/blastxml_format.hpp>
Inheritance diagram for IBlastXMLReportData:
Public Member Functions | |
| virtual | ~IBlastXMLReportData () |
| Our virtual destructor. More... | |
| virtual string | GetBlastProgramName (void) const =0 |
| Returns BLAST program name as string. More... | |
| virtual blast::EProgram | GetBlastTask (void) const =0 |
| Returns BLAST task as an enumerated value. More... | |
| virtual string | GetDatabaseName (void) const =0 |
| Returns database name. More... | |
| virtual double | GetEvalueThreshold (void) const =0 |
| Returns e-value theshold used in search. More... | |
| virtual int | GetGapOpeningCost (void) const =0 |
| Returns gap opening cost used in search. More... | |
| virtual int | GetGapExtensionCost (void) const =0 |
| Returns gap extension cost used in search. More... | |
| virtual int | GetMatchReward (void) const =0 |
| Returns match reward, for blastn search only. More... | |
| virtual int | GetMismatchPenalty (void) const =0 |
| Returns mismatch penalty, for blastn search only. More... | |
| virtual string | GetPHIPattern (void) const =0 |
| Returns pattern string, for PHI BLAST search only. More... | |
| virtual string | GetFilterString (void) const =0 |
| Returns filtering option string. More... | |
| virtual string | GetMatrixName (void) const =0 |
| Returns matrix name. More... | |
| virtual CBlastFormattingMatrix * | GetMatrix (void) const =0 |
| Returns a 256x256 ASCII-alphabet matrix, needed for formatting. More... | |
| virtual unsigned int | GetNumQueries (void) const =0 |
| Returns number of query sequences. More... | |
| virtual const TMaskedQueryRegions * | GetMaskLocations (int query_index) const =0 |
| Returns list of mask locations for a given query. More... | |
| virtual int | GetDbNumSeqs (void) const =0 |
| Returns number of database sequences. More... | |
| virtual Int8 | GetDbLength (void) const =0 |
| Returns database length. More... | |
| virtual int | GetLengthAdjustment (int query_index) const =0 |
| Returns length adjustment for a given query. More... | |
| virtual Int8 | GetEffectiveSearchSpace (int query_index) const =0 |
| Returns effective search space for a given query. More... | |
| virtual double | GetLambda (int query_index) const =0 |
| Returns Karlin-Altschul Lambda parameter for a given query. More... | |
| virtual double | GetKappa (int query_index) const =0 |
| Returns Karlin-Altschul K parameter for a given query. More... | |
| virtual double | GetEntropy (int query_index) const =0 |
| Returns Karlin-Altschul H parameter for a given query. More... | |
| virtual const objects::CSeq_loc * | GetQuery (int query_index) const =0 |
| Returns a query Seq-loc for a given query index. More... | |
| virtual objects::CScope * | GetScope (int query_index) const =0 |
| Returns scope for a given query. More... | |
| virtual const objects::CSeq_align_set * | GetAlignment (int query_index) const =0 |
| Returns set of alignments found for a given query. More... | |
| virtual bool | GetGappedMode (void) const =0 |
| Returns true if search was gapped, false otherwise. More... | |
| virtual int | GetMasterGeneticCode () const =0 |
| master genetic code More... | |
| virtual int | GetSlaveGeneticCode () const =0 |
| slave genetic code More... | |
| virtual vector< string > | GetMessages () const =0 |
| Get error messages, one element per query (e.g. More... | |
Detailed Description
Interface for filling the top layer of the XML report.
Definition at line 55 of file blastxml_format.hpp.
The documentation for this class was generated from the following file:
- include/algo/blast/format/blastxml_format.hpp
