#include <global.h>
Data Fields | |
| int4 | length |
| int4 | strandLength |
| int4 | highestValue |
| int4 | lowestValue |
| int2 ** | matrix |
| unsigned char * | queryCodes |
| unsigned char * | bestMatchCodes |
| unsigned char * | bytePackedCodes |
| unsigned char * | xorCodes |
Definition at line 21 of file global.h.
| int4 PSSMatrix::length |
Definition at line 23 of file global.h.
Referenced by alignments_expandCluster(), alignments_getTracebacks(), blast_search(), bytepackGappedScoring_dpAfterSeed(), bytepackGappedScoring_score(), fasterBytepackGappedScoring_dpAfterSeed(), fasterGappedExtension_build(), fasterGappedExtension_dpAfterSeed(), gappedExtension_build(), gappedScoring_dpAfterSeed(), gappedScoring_score(), index_processQuery(), nucleotideLookup_build(), nuGappedScoring_dpAfterSeed(), nuGappedScoring_score(), oldGappedScoring_dpAfterSeed(), oldGappedScoring_score(), oldSemiGappedScoring_dpAfterSeed(), oldSemiGappedScoring_score(), print_gappedExtension(), print_tabularGappedExtension(), print_XMLgappedExtension(), print_XMLheader(), PSSMatrix_chop(), PSSMatrix_print(), PSSMatrix_reverse(), PSSMatrix_strandEnd(), semiGappedScoring_dpAfterSeed(), semiGappedScoring_score(), smithWatermanScoring_dynamicProgramming(), smithWatermanScoring_score(), smithWatermanTraceback_dynamicProgramming(), statistics_initialize(), statistics_ungappedNucleotideTrigger(), tableGappedScoring_dpAfterSeed(), ungappedExtension_checkHit(), ungappedExtension_nucleotideExtend(), wordLookupDFA_build(), and wordLookupDFA_calcFrequencyGroups().
Definition at line 24 of file global.h.
Referenced by bytepackGappedScoring_score(), fasterGappedExtension_build(), gappedExtension_build(), gappedScoring_score(), index_processQuery(), nucleotideLookup_build(), nuGappedScoring_score(), oldGappedScoring_score(), oldSemiGappedScoring_score(), print_gappedExtension(), print_tabularGappedExtension(), print_XMLgappedExtension(), PSSMatrix_chop(), PSSMatrix_reverse(), PSSMatrix_strandEnd(), PSSMatrix_strandStart(), semiGappedScoring_score(), statistics_initialize(), ungappedExtension_checkHit(), and ungappedExtension_nucleotideExtend().
Definition at line 25 of file global.h.
Referenced by PSSMatrix_chop(), PSSMatrix_create(), PSSMatrix_reverse(), statistics_calculateUngappedKarlinParameters(), and unpack_getRegions().
Definition at line 26 of file global.h.
Referenced by PSSMatrix_chop(), PSSMatrix_create(), PSSMatrix_reverse(), and statistics_calculateUngappedKarlinParameters().
| int2** PSSMatrix::matrix |
Definition at line 27 of file global.h.
Referenced by fasterGappedExtension_build(), fasterGappedExtension_dpAfterSeed(), fasterGappedExtension_dpBeforeSeed(), gappedExtension_build(), gappedScoring_dpAfterSeed(), gappedScoring_dpBeforeSeed(), gappedScoring_score(), nuGappedScoring_dpAfterSeed(), nuGappedScoring_dpBeforeSeed(), nuGappedScoring_score(), oldGappedScoring_dpAfterSeed(), oldGappedScoring_dpBeforeSeed(), oldGappedScoring_score(), oldSemiGappedScoring_dpAfterSeed(), oldSemiGappedScoring_dpBeforeSeed(), oldSemiGappedScoring_score(), print_constructAlignment(), PSSMatrix_chop(), PSSMatrix_create(), PSSMatrix_free(), PSSMatrix_freeCopy(), PSSMatrix_print(), PSSMatrix_reverse(), search_protein1hit(), search_protein2hit(), semiGappedScoring_dpAfterSeed(), semiGappedScoring_dpBeforeSeed(), semiGappedScoring_score(), smithWatermanScoring_dynamicProgramming(), smithWatermanTraceback_dynamicProgramming(), statistics_calculateUngappedKarlinParameters(), ungappedExtension_extend(), ungappedExtension_findProteinSeed(), ungappedExtension_oneHitExtend(), wordLookupDFA_findNeighbours(), and wordLookupDFA_getNeighbours().
| unsigned char* PSSMatrix::queryCodes |
Definition at line 28 of file global.h.
Referenced by index_processQuery(), nucleotideLookup_build(), PSSMatrix_chop(), PSSMatrix_free(), PSSMatrix_freeCopy(), PSSMatrix_reverse(), statistics_calculateUngappedKarlinParameters(), and wordLookupDFA_getNeighbours().
| unsigned char* PSSMatrix::bestMatchCodes |
Definition at line 29 of file global.h.
Referenced by index_processQuery(), PSSMatrix_free(), PSSMatrix_reverse(), and wordLookupDFA_getNeighbours().
| unsigned char* PSSMatrix::bytePackedCodes |
Definition at line 30 of file global.h.
Referenced by bytepackGappedScoring_dpAfterSeed(), bytepackGappedScoring_dpBeforeSeed(), bytepackGappedScoring_score(), fasterBytepackGappedScoring_dpAfterSeed(), fasterBytepackGappedScoring_dpBeforeSeed(), PSSMatrix_chop(), PSSMatrix_free(), PSSMatrix_reverse(), search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), ungappedExtension_checkHit(), ungappedExtension_findNucleotideSeed(), and ungappedExtension_nucleotideExtend().
| unsigned char* PSSMatrix::xorCodes |
Definition at line 31 of file global.h.
Referenced by PSSMatrix_chop(), PSSMatrix_free(), PSSMatrix_reverse(), tableGappedScoring_dpAfterSeed(), and tableGappedScoring_dpBeforeSeed().
1.5.2