fsa-blast

Data Structures

aaFrequencyGroup

alignment

Alphabet

argument

child

chunk

clusterWildcard

codeword

Configuration

coordinate

Database

defaultPenalties

diagonal

dpResults

edit

finalAlignment

finalList

gappedExtension

group

Hashcounter

index_scanner

indexCoordinate

initialQPosList

initialWord

listinfo

lo_info

longList

maskRegion

Matrix

memBlocks

memSingleBlock

neighbour

packedByte

parent

PerScoreVec

postingsList

PSSMatrix

queryPosition

queryWord

readFile

scoreMatrix

ScoreMatrix

ScoreVector

Segment

Sequence

sequence

sequenceData

sequenceLists

sequenceMatch

statisticalParameters

strlist

tableBlock

trace

TransVector

ungappedExtension

unpackRegion

vec

wild

wildcard

wildcardEdit

wildCode

wordList

wordLocation

Data Fields

File List

include/_vec.h

include/alignments.h

include/blast.h

include/bytepackGappedScoring.h

include/constants.h

include/descriptions.h

include/dust.h

include/encoding.h

include/fasterBytepackGappedScoring.h

include/fasterGappedExtension.h

include/gappedExtension.h

include/gappedScoring.h

include/global.h

include/hashcounter.h

include/hitMatrix.h

include/index.h

include/karlin.h

include/memBlocks.h

include/memSingleBlock.h

include/nucleotideLookup.h

include/nuGappedScoring.h

include/oldGappedScoring.h

include/oldSemiGappedScoring.h

include/parameters.h

include/postings.h

include/print.h

include/PSSMatrix.h

include/qPosList.h

include/readdb.h

include/readFasta.h

include/readFile.h

include/readindex.h

include/readNcbidb.h

include/scoreMatrix.h

include/search.h

include/seg.h

include/semiGappedScoring.h

include/smithWatermanScoring.h

include/smithWatermanTraceback.h

include/statistics.h

include/tableGappedScoring.h

include/ungappedExtension.h

include/unpack.h

include/utils.h

include/vbyte.h

include/vbyte2.h

include/vec.h

include/wildcards.h

include/wordLookupDFA.h

include/writedb.h

include/writeFile.h

src/alignments.c

src/blast.c

src/bytepackGappedScoring.c

src/chooseWilds.c

src/cluster.c

src/constants.c

src/createindex.c

src/descriptions.c

src/dust.c

src/dustApp.c

src/encoding.c

src/fasterBytepackGappedScoring.c

src/fasterGappedExtension.c

src/formatdb.c

src/gappedExtension.c

src/gappedScoring.c

src/genwin.c

src/genwin.h

src/global.c

src/hashcounter.c

src/hitMatrix.c

src/identityAlign.c

src/index.c

src/karlin.c

src/lnfac.h

src/memBlocks.c

src/memSingleBlock.c

src/nucleotideLookup.c

src/nuGappedScoring.c

src/oldGappedScoring.c

src/oldSemiGappedScoring.c

src/parameters.c

src/postings.c

src/print.c

src/printDescription.c

src/PSSMatrix.c

src/qPosList.c

src/readdb.c

src/readdbApp.c

src/readFasta.c

src/readFile.c

src/readindex.c

src/readNcbidb.c

src/rsdb.c

src/scoreMatrix.c

src/search.c

src/seg.c

src/semiGappedScoring.c

src/smithWatermanScoring.c

src/smithWatermanTraceback.c

src/statistics.c

src/tableGappedScoring.c

src/ungappedExtension.c

src/unpack.c

src/vbyte.c

src/vbyte2.c

src/vec.c

src/wildcards.c

src/wordLookupDFA.c

src/writedb.c

src/writeFile.c

Globals