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| #define minimum | ( | a, | |||
| b | ) | ((a < b) ? a : b) |
| void global_free | ( | ) |
Definition at line 138 of file global.c.
References global_string.
Referenced by main().
00139 { 00140 free(global_string); 00141 }
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| void global_initialize | ( | ) |
Definition at line 39 of file global.c.
References blast_copyTime, blast_dynamicGappedNominalCutoff, blast_dynamicNominalR1cutoff, blast_finalizeTime, blast_gappedExtendTime, blast_gappedNominalCutoff, blast_gappedScoreTime, blast_nominalR1cutoff, blast_nominalR2cutoff, blast_numAttemptedJoin, blast_numExpandedSequences, blast_numExtensionsPruned, blast_numGapped, blast_numGoodAlignments, blast_numGoodExtensions, blast_numHits, blast_numSemiGapped, blast_numSuccessfullyJoined, blast_numTriggerExtensions, blast_numTriggerSequences, blast_numUngappedExtensions, blast_prepTime, blast_searchTime, blast_semiGappedScoreTime, blast_totalCopied, blast_totalUnpacked, and blast_unpackTime.
Referenced by main().
00040 { 00041 blast_prepTime = 0; blast_searchTime = 0; 00042 blast_gappedScoreTime = 0; blast_gappedExtendTime = 0; blast_finalizeTime = 0; 00043 blast_semiGappedScoreTime = 0; blast_copyTime = 0; blast_unpackTime = 0; 00044 00045 // BLAST statistics 00046 blast_numHits = 0; 00047 blast_numUngappedExtensions = 0; blast_numTriggerExtensions = 0; blast_numTriggerSequences = 0; 00048 blast_numGapped = 0; 00049 blast_numSemiGapped = 0; 00050 blast_numExtensionsPruned = 0; 00051 blast_numExtensionsPruned; 00052 blast_numAttemptedJoin = 0; blast_numSuccessfullyJoined = 0; 00053 blast_numGoodAlignments = 0; 00054 blast_numGoodExtensions = 0; 00055 blast_totalUnpacked = 0; 00056 blast_totalCopied = 0; 00057 blast_numExpandedSequences = 0; 00058 00059 // BLAST global variables 00060 blast_gappedNominalCutoff = 0; blast_nominalR1cutoff = 0; blast_nominalR2cutoff = 0; 00061 blast_dynamicGappedNominalCutoff = 0; blast_dynamicNominalR1cutoff = 0; 00062 00063 }
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| char* global_int4toString | ( | uint4 | number | ) |
Definition at line 66 of file global.c.
References global_realloc(), global_string, int4, and Matrix::length.
Referenced by blast_search(), and rsdb_spexClusterSequences().
00067 { 00068 char string1[50]; 00069 int4 length, count1, count2; 00070 00071 // Convert integer to string 00072 sprintf(string1, "%u", number); 00073 length = strlen(string1); 00074 00075 // Declare second string large enough to hold number with commas 00076 global_string = (char*)global_realloc(global_string, sizeof(char) * length * 4 / 3 + 1); 00077 global_string[0] = '\0'; 00078 00079 count1 = count2 = 0; 00080 00081 // Convert number to version with commas 00082 while (count1 < length) 00083 { 00084 global_string[count2] = string1[count1]; 00085 count1++; 00086 count2++; 00087 00088 if (number >= 10000 && ((length - count1) % 3 == 0 && count1 < length)) 00089 { 00090 global_string[count2] = ','; 00091 count2++; 00092 } 00093 } 00094 00095 // Null terminate string2 00096 global_string[count2] = '\0'; 00097 00098 return global_string; 00099 }
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| char* global_int8toString | ( | uint8 | number | ) |
Definition at line 102 of file global.c.
References global_realloc(), global_string, int4, and Matrix::length.
Referenced by blast_search().
00103 { 00104 char string1[50]; 00105 int4 length, count1, count2; 00106 00107 // Convert integer to string 00108 sprintf(string1, "%llu", number); 00109 length = strlen(string1); 00110 00111 // Declare second string large enough to hold number with commas 00112 global_string = (char*)global_realloc(global_string, sizeof(char) * length * 4 / 3 + 1); 00113 global_string[0] = '\0'; 00114 00115 count1 = count2 = 0; 00116 00117 // Convert number to version with commas 00118 while (count1 < length) 00119 { 00120 global_string[count2] = string1[count1]; 00121 count1++; 00122 count2++; 00123 00124 if (number >= 10000 && ((length - count1) % 3 == 0 && count1 < length)) 00125 { 00126 global_string[count2] = ','; 00127 count2++; 00128 } 00129 } 00130 00131 // Null terminate string2 00132 global_string[count2] = '\0'; 00133 00134 return global_string; 00135 }
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| void* global_malloc | ( | size_t | size | ) |
Definition at line 146 of file global.c.
References global_totalMalloc.
Referenced by blast_search(), BlastKarlinLHtoK(), bytepackGappedScoring_dpAfterSeed(), bytepackGappedScoring_dpBeforeSeed(), cluster_addChild(), cluster_averageWildcodeScore(), cluster_buildCluster(), cluster_buildPSSM(), cluster_clusterSequences(), cluster_getEdits(), cluster_newParent(), cluster_removeChildren(), cluster_simpleClusterSequences(), cluster_spexClusterSequences(), cluster_writeClusters(), descriptions_getDescription(), dust_dustSequence(), encoding_byteUnpack(), encoding_initialize(), fasterBytepackGappedScoring_dpAfterSeed(), fasterBytepackGappedScoring_dpBeforeSeed(), fasterGappedExtension_build(), fasterGappedExtension_dpAfterSeed(), fasterGappedExtension_dpBeforeSeed(), fasterGappedExtension_traceAfterSeed(), fasterGappedExtension_traceBeforeSeed(), gappedExtension_build(), gappedExtension_dpAfterSeed(), gappedExtension_dpBeforeSeed(), gappedExtension_traceAfterSeed(), gappedExtension_traceBeforeSeed(), gappedScoring_dpAfterSeed(), gappedScoring_dpBeforeSeed(), hashcounter_new(), hitMatrix_initialize(), identityAlign_score(), index_initializeBuild(), index_processQuery(), main(), memBlocks_initialize(), memBlocks_newEntries(), memBlocks_newEntry(), memSingleBlock_initialize(), memSingleBlock_initializeExisting(), nucleotideLookup_build(), nuGappedScoring_dpAfterSeed(), nuGappedScoring_dpBeforeSeed(), oldGappedScoring_dpAfterSeed(), oldGappedScoring_dpBeforeSeed(), oldSemiGappedScoring_dpAfterSeed(), oldSemiGappedScoring_dpBeforeSeed(), parameters_findScoringMatrix(), parameters_loadDefaults(), postings_addEntry(), postings_addPosting(), postings_getSortedLists(), postings_initialize(), print_encodeGreaterLessThan(), print_formatDescription(), print_gappedAlignmentsBrief(), print_gappedAlignmentsFull(), print_gappedExtension(), print_tabularGappedExtension(), print_untilWhitespace(), print_XMLgappedExtension(), PSSMatrix_create(), PSSMatrix_reverse(), qPosList_initialize(), qPosList_processList(), readdb_getChildren(), readdb_open(), readFasta_open(), readNcbidb_getDescription(), readNcbidb_getSequence(), readNcbidb_open(), rsdb_newParent(), rsdb_spexClusterSequences(), rsdb_writeClusters(), scoreMatrix_create(), scoreMatrix_load(), semiGappedScoring_dpAfterSeed(), semiGappedScoring_dpBeforeSeed(), smithWatermanScoring_dynamicProgramming(), smithWatermanScoring_scoreReverse(), smithWatermanTraceback_build(), smithWatermanTraceback_dynamicProgramming(), smithWatermanTraceback_trace(), statistics_calculateUngappedKarlinParameters(), tableGappedScoring_buildTable(), tableGappedScoring_dpAfterSeed(), tableGappedScoring_dpBeforeSeed(), unpack_extendRegionStart(), unpack_loadSubject(), unpack_unpackSubject(), wildcards_getOccurences(), wildcards_getSubset(), wildcards_initializeCountOccurences(), wildcards_readWildcards(), wildcards_scoreCandidates(), wordLookupDFA_build(), wordLookupDFA_calcFrequencyGroups(), wordLookupDFA_getCodes(), writedb_addSequence(), and writedb_initialize().
00147 { 00148 void* newMemory; 00149 00150 newMemory = malloc(size); 00151 00152 // printf("[%d]\n", size); 00153 00154 /* if (size > 20000000) 00155 { 00156 char* a; 00157 a = NULL; 00158 *a = 0; 00159 }*/ 00160 00161 if (newMemory == NULL && size != 0) 00162 { 00163 // Report error allocating memory 00164 fprintf(stderr, "Error allocating %d bytes: ", size); 00165 fprintf(stderr, strerror(errno)); 00166 fprintf(stderr, "\n"); fflush(stderr); 00167 exit(-1); 00168 } 00169 00170 global_totalMalloc += size; 00171 00172 return newMemory; 00173 }
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| void* global_realloc | ( | void * | ptr, | |
| size_t | size | |||
| ) |
Definition at line 176 of file global.c.
References global_totalMalloc.
Referenced by cluster_addChild(), cluster_mergeParents(), cluster_updateWildcode(), fasterGappedExtension_dpAfterSeed(), fasterGappedExtension_dpBeforeSeed(), fasterGappedExtension_joinTraces(), gappedExtension_dpAfterSeed(), gappedExtension_dpBeforeSeed(), gappedExtension_joinTraces(), global_int4toString(), global_int8toString(), index_addWord(), main(), memBlocks_newEntries(), memBlocks_newEntry(), memSingleBlock_newEntry(), nucleotideLookup_build(), postings_addPosting(), print_gappedAlignmentsBrief(), readdb_getChildren(), readFasta_readSequence(), rsdb_addChild(), unpack_extendRegionEnd(), wildcards_joinSubset(), and wordLookupDFA_build().
00177 { 00178 ptr = realloc(ptr, size); 00179 00180 // printf("[%d*]\n", size); 00181 00182 if (ptr == NULL && size != 0) 00183 { 00184 // Report error allocating memory 00185 fprintf(stderr, "Error allocating %d bytes: ", size); 00186 fprintf(stderr, strerror(errno)); 00187 fprintf(stderr, "\n"); fflush(stderr); 00188 exit(-1); 00189 } 00190 00191 global_totalMalloc += size; 00192 00193 return ptr; 00194 }
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| int4 blast_copyTime |
| int4 blast_dloc |
Definition at line 33 of file global.c.
Referenced by alignments_checkForJoin(), alignments_findGoodAlignments(), alignments_getTracebacks(), alignments_regularGappedAlignment(), bytepackGappedScoring_dpAfterSeed(), bytepackGappedScoring_dpBeforeSeed(), bytepackGappedScoring_score(), fasterBytepackGappedScoring_dpAfterSeed(), fasterBytepackGappedScoring_dpBeforeSeed(), gappedExtension_build(), gappedScoring_dpAfterSeed(), gappedScoring_dpBeforeSeed(), gappedScoring_score(), nuGappedScoring_dpAfterSeed(), nuGappedScoring_dpBeforeSeed(), nuGappedScoring_score(), tableGappedScoring_dpAfterSeed(), tableGappedScoring_dpBeforeSeed(), tableGappedScoring_score(), and ungappedExtension_nucleotideExtend().
Definition at line 32 of file global.c.
Referenced by alignments_findTopFinalAlignments(), blast_search(), and global_initialize().
Definition at line 32 of file global.c.
Referenced by alignments_findTopFinalAlignments(), blast_search(), and global_initialize().
| int4 blast_finalizeTime |
Definition at line 13 of file global.c.
Referenced by alignments_getTracebacks(), blast_search(), and global_initialize().
Definition at line 31 of file global.c.
Referenced by alignments_findFinalAlignments(), alignments_getTracebacks(), alignments_regularGappedAlignment(), blast_search(), global_initialize(), search_nucleotideSsearch(), and search_proteinSsearch().
Definition at line 31 of file global.c.
Referenced by alignments_findFinalAlignments(), alignments_findGoodAlignments(), blast_search(), and global_initialize().
Definition at line 31 of file global.c.
Referenced by alignments_findFinalAlignments(), blast_search(), and global_initialize().
| uint4 blast_numAttemptedJoin |
Definition at line 22 of file global.c.
Referenced by alignments_checkForJoin(), blast_search(), and global_initialize().
Definition at line 27 of file global.c.
Referenced by alignments_expandCluster(), blast_search(), and global_initialize().
Definition at line 21 of file global.c.
Referenced by alignments_pruneRegion(), blast_search(), and global_initialize().
| uint4 blast_numGapped |
Definition at line 19 of file global.c.
Referenced by blast_search(), gappedScoring_score(), and global_initialize().
| uint4 blast_numGoodAlignments |
Definition at line 23 of file global.c.
Referenced by alignments_findGoodAlignments(), blast_search(), and global_initialize().
| uint4 blast_numGoodExtensions |
Definition at line 24 of file global.c.
Referenced by alignments_findGoodAlignments(), alignments_initialize(), and global_initialize().
| uint4 blast_numHits |
Definition at line 17 of file global.c.
Referenced by blast_search(), global_initialize(), index_processQuery(), search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), search_protein1hit(), and search_protein2hit().
| uint4 blast_numSemiGapped |
Definition at line 20 of file global.c.
Referenced by blast_search(), bytepackGappedScoring_score(), global_initialize(), semiGappedScoring_score(), and tableGappedScoring_score().
Definition at line 22 of file global.c.
Referenced by alignments_checkForJoin(), blast_search(), and global_initialize().
Definition at line 18 of file global.c.
Referenced by blast_search(), global_initialize(), search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), search_protein1hit(), and search_protein2hit().
Definition at line 18 of file global.c.
Referenced by alignments_createNew(), blast_search(), and global_initialize().
Definition at line 18 of file global.c.
Referenced by blast_search(), global_initialize(), search_nucleotide(), search_nucleotide_largeTable(), search_nucleotide_longWord(), search_protein1hit(), and search_protein2hit().
| int4 blast_prepTime |
| char* blast_queryDescription |
Definition at line 34 of file global.c.
Referenced by main(), print_gappedAlignmentsFull(), and print_XMLheader().
| int4 blast_searchTime |
| uint4 blast_totalCopied |
Definition at line 26 of file global.c.
Referenced by blast_search(), global_initialize(), and unpack_loadSubject().
| uint4 blast_totalUnpacked |
Definition at line 25 of file global.c.
Referenced by blast_search(), global_initialize(), and unpack_unpackSubject().
Definition at line 30 of file global.c.
Referenced by blast_search(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), and ungappedExtension_oneHitExtend().
| int4 blast_unpackTime |
Definition at line 14 of file global.c.
Referenced by alignments_getTracebacks(), and global_initialize().
| uint4 global_totalMalloc |
Definition at line 143 of file global.c.
Referenced by global_malloc(), global_realloc(), and rsdb_spexClusterSequences().
1.5.2