#include <stdio.h>#include <stdlib.h>#include <time.h>#include <math.h>#include <string.h>#include <inttypes.h>#include <errno.h>#include <ctype.h>#include "global.h"#include "constants.h"#include "vbyte.h"#include "memSingleBlock.h"#include "memBlocks.h"#include "readFile.h"#include "encoding.h"#include "writedb.h"#include "readNcbidb.h"#include "readdb.h"#include "parameters.h"#include "scoreMatrix.h"#include "PSSMatrix.h"#include "karlin.h"#include "statistics.h"#include "qPosList.h"#include "wordLookupDFA.h"#include "nucleotideLookup.h"#include "readFasta.h"#include "hitMatrix.h"#include "ungappedExtension.h"#include "gappedExtension.h"#include "fasterGappedExtension.h"#include "descriptions.h"#include "bytepackGappedScoring.h"#include "fasterBytepackGappedScoring.h"#include "tableGappedScoring.h"#include "oldSemiGappedScoring.h"#include "oldGappedScoring.h"#include "semiGappedScoring.h"#include "gappedScoring.h"#include "nuGappedScoring.h"#include "smithWatermanScoring.h"#include "smithWatermanTraceback.h"#include "alignments.h"#include "unpack.h"#include "print.h"#include "index.h"#include "postings.h"#include "hashcounter.h"#include "search.h"#include "wildcards.h"#include "dust.h"#include "seg.h"Include dependency graph for blast.h:
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Defines | |
| #define | int4 int32_t |
| #define | uint4 uint32_t |
| #define | int8 int64_t |
| #define | uint8 uint64_t |
| #define | int2 int16_t |
| #define | uint2 uint16_t |
| #define int2 int16_t |
Definition at line 17 of file blast.h.
Referenced by fasterGappedExtension_dpAfterSeed(), fasterGappedExtension_dpBeforeSeed(), gappedExtension_dpAfterSeed(), gappedExtension_dpBeforeSeed(), gappedScoring_dpAfterSeed(), gappedScoring_dpBeforeSeed(), nucleotideLookup_build(), nuGappedScoring_dpAfterSeed(), nuGappedScoring_dpBeforeSeed(), nuGappedScoring_printAfterRow(), nuGappedScoring_printBeforeRow(), oldGappedScoring_dpAfterSeed(), oldGappedScoring_dpBeforeSeed(), oldSemiGappedScoring_dpAfterSeed(), oldSemiGappedScoring_dpBeforeSeed(), parameters_processArguments(), PSSMatrix_create(), PSSMatrix_reverse(), qPosList_processLists(), scoreMatrix_create(), scoreMatrix_load(), search_nucleotide(), search_nucleotide_longWord(), semiGappedScoring_dpAfterSeed(), semiGappedScoring_dpBeforeSeed(), smithWatermanScoring_dynamicProgramming(), smithWatermanTraceback_dynamicProgramming(), tableGappedScoring_buildTable(), ungappedExtension_extend(), ungappedExtension_findProteinSeed(), ungappedExtension_oneHitExtend(), wildcards_scoreCandidates(), and wordLookupDFA_build().
| #define int4 int32_t |
Definition at line 13 of file blast.h.
Referenced by alignments_checkForJoin(), alignments_expandCluster(), alignments_findFinalAlignments(), alignments_findGoodAlignments(), alignments_findTopFinalAlignments(), alignments_getTracebacks(), alignments_loadSubjectsIntoMemory(), alignments_printFinalAlignments(), alignments_printGoodAlignments(), alignments_regularGappedAlignment(), blast_search(), BlastComputeLengthAdjustment(), BlastKarlinLambdaBis(), BlastKarlinLambdaNR(), BlastKarlinLHtoK(), BlastKarlinLtoH(), bytepackGappedScoring_dpAfterSeed(), bytepackGappedScoring_dpBeforeSeed(), bytepackGappedScoring_score(), cluster_addChild(), cluster_averageWildcodeScore(), cluster_buildCluster(), cluster_buildPSSM(), cluster_calculateSavings(), cluster_clusterSequences(), cluster_freePSSM(), cluster_mergeParents(), cluster_printCluster(), cluster_processList(), cluster_processSequenceMatches(), cluster_score(), cluster_spexClusterSequences(), determineDbAlphabetType(), encoding_bytePackSequence(), encoding_byteUnpackRegion(), encoding_determineAlphabetType(), encoding_encodeSequence(), encoding_initialize(), encoding_replaceWildcards(), fasterBytepackGappedScoring_dpAfterSeed(), fasterBytepackGappedScoring_dpBeforeSeed(), fasterGappedExtension_build(), fasterGappedExtension_dpAfterSeed(), fasterGappedExtension_dpBeforeSeed(), fasterGappedExtension_joinTraces(), fasterGappedExtension_printAfterRow(), fasterGappedExtension_printBeforeRow(), fasterGappedExtension_prune(), fasterGappedExtension_traceAfterSeed(), fasterGappedExtension_traceBeforeSeed(), gappedExtension_build(), gappedExtension_dpAfterSeed(), gappedExtension_dpBeforeSeed(), gappedExtension_joinTraces(), gappedExtension_printAfterRow(), gappedExtension_printBeforeRow(), gappedExtension_prune(), gappedExtension_traceAfterSeed(), gappedExtension_traceBeforeSeed(), gappedScoring_dpAfterSeed(), gappedScoring_dpBeforeSeed(), gappedScoring_score(), global_int4toString(), global_int8toString(), hitMatrix_initialize(), hitMatrix_reinitialize(), identityAlign_print(), identityAlign_score(), main(), memBlocks_initialize(), memBlocks_newEntries(), memBlocks_newEntry(), nucleotideLookup_build(), nucleotideLookup_print(), nuGappedScoring_dpAfterSeed(), nuGappedScoring_dpBeforeSeed(), nuGappedScoring_printAfterRow(), nuGappedScoring_printBeforeRow(), nuGappedScoring_score(), oldGappedScoring_dpAfterSeed(), oldGappedScoring_dpBeforeSeed(), oldGappedScoring_score(), oldSemiGappedScoring_dpAfterSeed(), oldSemiGappedScoring_dpBeforeSeed(), oldSemiGappedScoring_score(), parameters_getDefaultPenalties(), parameters_printArguments(), parameters_processArguments(), print_constructAlignment(), print_formatDescription(), print_gappedAlignmentsBrief(), print_gappedAlignmentsFull(), print_gappedExtension(), print_singleSequence(), print_tabularGappedExtension(), print_XMLgappedExtension(), PSSMatrix_create(), PSSMatrix_print(), qPosList_print(), qPosList_processList(), qPosList_processLists(), rsdb_calculateSavings(), rsdb_printCluster(), rsdb_score(), rsdb_spexClusterSequences(), rsdb_updateDiagonalMatches(), scoreMatrix_create(), scoreMatrix_load(), scoreMatrix_print(), search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), search_nucleotideSsearch(), search_protein1hit(), search_protein2hit(), search_proteinSsearch(), semiGappedScoring_dpAfterSeed(), semiGappedScoring_dpBeforeSeed(), semiGappedScoring_score(), smithWatermanScoring_dynamicProgramming(), smithWatermanTraceback_dynamicProgramming(), smithWatermanTraceback_print(), smithWatermanTraceback_trace(), statistics_calcLengthAdjust(), statistics_calcLengthAdjustNew(), statistics_calculateUngappedKarlinParameters(), statistics_lookupPrecomputedParams(), statistics_ungappedNucleotideTrigger(), tableGappedScoring_buildTable(), tableGappedScoring_compareBlocks(), tableGappedScoring_dpAfterSeed(), tableGappedScoring_dpBeforeSeed(), tableGappedScoring_printCarry(), tableGappedScoring_score(), ungappedExtension_extend(), ungappedExtension_findNucleotideSeed(), ungappedExtension_findProteinSeed(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), ungappedExtension_simpleScoring(), unpack_extendRegionEnd(), unpack_extendRegionStart(), unpack_getRegions(), unpack_loadSubject(), unpack_unpackSubject(), wildcards_scoreResidueWildMatch(), wordLookupDFA_build(), wordLookupDFA_calcFrequencyGroups(), wordLookupDFA_findNeighbours(), wordLookupDFA_getCodes(), wordLookupDFA_getCodeword(), wordLookupDFA_getNeighbours(), wordLookupDFA_print(), and wordLookupDFA_printCodes().
| #define uint2 uint16_t |
Definition at line 18 of file blast.h.
Referenced by nucleotideLookup_build(), search_protein1hit(), search_protein2hit(), tableGappedScoring_buildTable(), tableGappedScoring_dpAfterSeed(), tableGappedScoring_dpBeforeSeed(), wordLookupDFA_build(), and wordLookupDFA_print().
| #define uint4 uint32_t |
Definition at line 14 of file blast.h.
Referenced by alignments_free(), chooseWilds_printOccurenceMatrix(), cluster_buildCluster(), cluster_buildPSSM(), cluster_clusterSequences(), cluster_getEdits(), cluster_getWildcode(), cluster_mergeParents(), cluster_overlap(), cluster_printList(), cluster_processList(), cluster_removeChildren(), cluster_score(), cluster_simpleClusterSequences(), cluster_spexClusterSequences(), cluster_updateWildcode(), cluster_updateWildcodes(), cluster_writeClusters(), determineDbAlphabetType(), encoding_insertWilds(), fasterGappedExtension_traceAfterSeed(), fasterGappedExtension_traceBeforeSeed(), gappedExtension_traceAfterSeed(), gappedExtension_traceBeforeSeed(), index_addSubject(), index_addWord(), index_finishBuild(), index_generateCodeword(), index_initializeBuild(), index_print(), index_processQuery(), main(), nucleotideLookup_build(), postings_addEntry(), postings_addPosting(), postings_decodeList(), postings_getSortedLists(), postings_initialize(), print_encodeGreaterLessThan(), print_gappedAlignmentsFull(), print_untilWhitespace(), PSSMatrix_reverse(), readdb_getChildren(), readdb_nextVolume(), readdb_open(), readFasta_readSequence(), readNcbidb_getDescription(), readNcbidb_getSequence(), readNcbidb_open(), readNcbidb_readInt(), rsdb_printList(), rsdb_processList(), rsdb_score(), rsdb_slottedSpex(), rsdb_spexClusterSequences(), rsdb_winnowingSpex(), rsdb_writeClusters(), search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), search_nucleotideSsearch(), search_protein1hit(), search_protein2hit(), search_proteinSsearch(), smithWatermanScoring_scoreReverse(), smithWatermanTraceback_trace(), ungappedExtension_checkHit(), unpack_getRegions(), unpack_loadSubject(), unpack_unpackSubject(), wildcards_compareWilds(), wildcards_countBits(), wildcards_countOccurences(), wildcards_getOccurences(), wildcards_getSubset(), wildcards_initialize(), wildcards_initializeCountOccurences(), wildcards_outputWildcards(), wildcards_printWildcard(), wildcards_readWildcards(), wildcards_removeSubset(), wildcards_scoreCandidates(), wordLookupDFA_calcFrequencyGroups(), wordLookupDFA_getCodeword(), wordLookupDFA_print(), writedb_addSequence(), and writedb_close().
| #define uint8 uint64_t |
Definition at line 16 of file blast.h.
Referenced by alignments_getTracebacks(), main(), postings_addEntry(), postings_hash64bit(), readNcbidb_read64Int(), and vbyte_get64vbyte().
1.5.2