Cleanup in many different places

.gitignore

@@ -31,3 +31,4 @@ src/workflow/time_test
 
 build/
 .idea/
+cmake-build-*/

src/alignment/BlastScoreUtils.cpp

@@ -555,27 +555,27 @@ BlastScoreUtils::BlastStat BlastScoreUtils::getAltschulStatsForMatrix(std::strin
         double (*mat)[10];
         long val;
 
-        if (matrix.compare("blosum45") == 0) {
+        if (matrix.compare("blosum45.out") == 0) {
                 mat = blosum45_values;
                 val = BLOSUM45_VALUES_MAX;
         }
-        else if (matrix.compare("blosum50") == 0) {
+        else if (matrix.compare("blosum50.out") == 0) {
                 mat = blosum50_values;
                 val = BLOSUM50_VALUES_MAX;
         }
-        else if (matrix.compare("blosum62") == 0) {
+        else if (matrix.compare("blosum62.out") == 0) {
                 mat = blosum62_values;
                 val = BLOSUM62_VALUES_MAX;
         }
-        else if (matrix.compare("blosum62_20") == 0) {
+        else if (matrix.compare("blosum62_20.out") == 0) {
                 mat = blosum62_20_values;
                 val = BLOSUM62_20_VALUES_MAX;
         }
-        else if (matrix.compare("blosum80") == 0) {
+        else if (matrix.compare("blosum80.out") == 0) {
                 mat = blosum80_values;
                 val = BLOSUM80_VALUES_MAX;
         }
-        else if (matrix.compare("blosum90") == 0) {
+        else if (matrix.compare("blosum90.out") == 0) {
                 mat = blosum90_values;
                 val = BLOSUM90_VALUES_MAX;
         }

src/commons/DBReader.h

@@ -17,7 +17,7 @@ class DBReader {
     struct Index {
         T id;
         size_t offset;
-        static bool compareById(Index x, Index y){
+        static bool compareById(const Index& x, const Index& y){
             return (x.id <= y.id);
         }
     };
@@ -158,7 +158,7 @@ class DBReader {
     bool dataMapped;
     int accessType;
 
-    // needed to avoid compiler to optimize away the loop
+    // needed to prevent the compiler from optimizing away the loop
     size_t magicBytes;
 };
 

src/commons/DBWriter.cpp

@@ -101,20 +101,21 @@ void DBWriter::mergeFiles(DBReader<unsigned int> &qdbr,
     }
 
     for (size_t id = 0; id < qdbr.getSize(); id++) {
+        unsigned int key = qdbr.getDbKey(id);
         std::ostringstream ss;
         // get all data for the id from all files
         for (size_t i = 0; i < fileCount; i++) {
-            char *data = filesToMerge[i]->getDataByDBKey(qdbr.getDbKey(id));
+            const char *data = filesToMerge[i]->getDataByDBKey(key);
             if (data != NULL) {
                 if(i < prefixes.size()) {
                     ss << prefixes[i];
                 }
-                ss << filesToMerge[i]->getDataByDBKey(qdbr.getDbKey(id));
+                ss << data;
             }
         }
         // write result
         std::string result = ss.str();
-        writeData(result.c_str(), result.length(), SSTR(qdbr.getDbKey(id)).c_str(), 0);
+        writeData(result.c_str(), result.length(), SSTR(key).c_str(), 0);
     }
 
     // close all reader
@@ -288,20 +289,27 @@ void DBWriter::mergeFilePair(const char *inData1, const char *inIndex1,
                              const char *inData2, const char *inIndex2) {
     FILE *file1 = fopen(inData1, "r");
     FILE *file2 = fopen(inData2, "r");
+
+    if (file1 == NULL || file2 == NULL) {
+        Debug(Debug::ERROR) << "Could not read merge input files!\n";
+        EXIT(EXIT_FAILURE);
+    }
+
 #if HAVE_POSIX_FADVISE
-    if (posix_fadvise (fileno(file1), 0, 0, POSIX_FADV_SEQUENTIAL) != 0){
-       Debug(Debug::ERROR) << "posix_fadvise returned an error\n";
+    if ((int status = posix_fadvise (fileno(file1), 0, 0, POSIX_FADV_SEQUENTIAL)) != 0){
+       Debug(Debug::ERROR) << "posix_fadvise returned an error: " << strerror(status) << "\n";
     }
-    if (posix_fadvise (fileno(file2), 0, 0, POSIX_FADV_SEQUENTIAL) != 0){
-       Debug(Debug::ERROR) << "posix_fadvise returned an error\n";
+    if ((int status = posix_fadvise (fileno(file2), 0, 0, POSIX_FADV_SEQUENTIAL)) != 0){
+       Debug(Debug::ERROR) << "posix_fadvise returned an error: " << strerror(status) << "\n";;
     }
 #endif
+
     int c1, c2;
     char * buffer = dataFilesBuffer[0];
     size_t writePos = 0;
     int dataFilefd =  fileno(dataFiles[0]);
-    while((c1=getc_unlocked(file1)) != EOF) {
-        if(c1 == '\0'){
+    while ((c1=getc_unlocked(file1)) != EOF) {
+        if (c1 == '\0'){
             while((c2=getc_unlocked(file2)) != EOF && c2 != '\0') {
                 buffer[writePos] = (char) c2;
                 writePos++;
@@ -312,11 +320,11 @@ void DBWriter::mergeFilePair(const char *inData1, const char *inIndex1,
             }
             buffer[writePos] = '\0';
             writePos++;
-            if(writePos == bufferSize){
+            if (writePos == bufferSize){
                 write(dataFilefd, buffer, bufferSize);
                 writePos = 0;
             }
-        }else{
+        } else {
             buffer[writePos] = (char) c1;;
             writePos++;
             if(writePos == bufferSize){
@@ -325,12 +333,13 @@ void DBWriter::mergeFilePair(const char *inData1, const char *inIndex1,
             }
         }
     }
-    if(writePos != 0){ // if there are data in the buffer that are not yet written
+
+    if(writePos != 0) { // if there are data in the buffer that are not yet written
         write(dataFilefd, (const void *) dataFilesBuffer[0], writePos);
     }
-
-    fclose(file1);
     fclose(file2);
+    fclose(file1);
+
     Debug(Debug::WARNING) << "Merge file " << inData1 << " and " << inData2 << "\n";
     DBReader<unsigned int> reader1(inIndex1, inIndex1,
                                    DBReader<std::string>::USE_INDEX);
@@ -343,12 +352,13 @@ void DBWriter::mergeFilePair(const char *inData1, const char *inIndex1,
     unsigned int * seqLen1 = reader1.getSeqLens();
     unsigned int * seqLen2 = reader2.getSeqLens();
     for(size_t id = 0; id < reader1.getSize(); id++){
-        // add lenght for file1 and file2 and substrace -1 for one null byte
+        // add length for file1 and file2 and substract -1 for one null byte
         size_t seqLen = seqLen1[id] + seqLen2[id] - 1;
         seqLen1[id] = seqLen;
         index1[id].offset = currOffset;
         currOffset += seqLen;
     }
+
     writeIndex(indexFiles[0], reader1.getSize(), index1, seqLen1);
     reader2.close();
     reader1.close();

src/commons/HeaderSummarizer.cpp

@@ -6,8 +6,6 @@
 #include <set>
 #include <algorithm>
 
-static PatternCompiler uninformative("hypothetical|unknown|putative|predicted|unnamed|probable|partial|possible|uncharacterized|fragment");
-
 struct UniprotHeader {
     std::string dbType;
     std::string identifier;
@@ -29,10 +27,15 @@ struct UniprotHeader {
         updatePriority();
     };
 
+    PatternCompiler& isUninformative() {
+        static PatternCompiler uninformative("hypothetical|unknown|putative|predicted|unnamed|probable|partial|possible|uncharacterized|fragment");
+        return uninformative;
+    }
+
     void updatePriority() {
         priority = 0;
 
-        if(uninformative.isMatch(identifier.c_str()))
+        if(isUninformative().isMatch(identifier.c_str()))
             return;
 
         if(dbType == "sp") {

src/commons/Parameters.cpp

@@ -80,7 +80,7 @@ PARAM_PCA(PARAM_PCA_ID, "--pca", "Pseudo count a", "pseudo count admixture stren
 PARAM_PCB(PARAM_PCB_ID, "--pcb", "Pseudo count b", "pseudo counts: Neff at half of maximum admixture (0.0,infinity)", typeid(float), (void*) &pcb, "^[0-9]*(\\.[0-9]+)?$", MMseqsParameter::COMMAND_PROFILE),
 //PARAM_FIRST_SEQ_REP_SEQ(PARAM_FIRST_SEQ_REP_SEQ_ID, "--first-seq-as-repr", "first sequence as respresentative", "Use the first sequence of the clustering result as representative sequence", typeid(bool), (void*) &firstSeqRepr, "", MMseqsParameter::COMMAND_PROFILE),
 // result2stats
-PARAM_STAT(PARAM_STAT_ID, "--stat", "Statistics to be computed", "can be one of: linecount, mean, doolittle, charges, seqlen.", typeid(std::string), (void*) &stat, ""),
+PARAM_STAT(PARAM_STAT_ID, "--stat", "Statistics to be computed", "can be one of: linecount, mean, doolittle, charges, seqlen, firstline.", typeid(std::string), (void*) &stat, ""),
 // linearcluster
 PARAM_KMER_PER_SEQ(PARAM_KMER_PER_SEQ_ID, "--kmer-per-seq", "Kmer per sequence", "kmer per sequence", typeid(int), (void*) &kmersPerSequence, "^[1-9]{1}[0-9]*$", MMseqsParameter::COMMAND_CLUSTLINEAR),
 // workflow
@@ -134,8 +134,7 @@ PARAM_MSA_TYPE(PARAM_MSA_TYPE_ID,"--msa-type", "MSA type", "MSA Type: cA3M 0 or
 // extractalignedregion
 PARAM_EXTRACT_MODE(PARAM_EXTRACT_MODE_ID,"--extract-mode", "Extract mode", "Query 1, Target 2", typeid(int), (void *) &extractMode, "^[1-2]{1}$"),
 // convertkb
-PARAM_KB_COLUMNS(PARAM_KB_COLUMNS_ID, "--kb-columns", "UniprotKB Columns", "list of indices of UniprotKB columns to be extracted", typeid(std::string), (void *) &kbColumns, ""),
-PARAM_COUNT_CHARACTER(PARAM_COUNT_CHARACTER_ID, "--count-char", "Count Char", "character to count", typeid(std::string), (void *) &countCharacter, "")
+PARAM_KB_COLUMNS(PARAM_KB_COLUMNS_ID, "--kb-columns", "UniprotKB Columns", "list of indices of UniprotKB columns to be extracted", typeid(std::string), (void *) &kbColumns, "")
 {
     
     // alignment
@@ -224,6 +223,8 @@ PARAM_COUNT_CHARACTER(PARAM_COUNT_CHARACTER_ID, "--count-char", "Count Char", "c
     
     //result2stats
     result2stats.push_back(PARAM_STAT);
+    result2stats.push_back(PARAM_THREADS);
+    result2stats.push_back(PARAM_V);
     
     // format alignment
     convertalignments.push_back(PARAM_FORMAT_MODE);
@@ -375,9 +376,6 @@ PARAM_COUNT_CHARACTER(PARAM_COUNT_CHARACTER_ID, "--count-char", "Count Char", "c
     linearfilter.push_back(PARAM_MAX_SEQ_LEN);
     linearfilter.push_back(PARAM_THREADS);
     linearfilter.push_back(PARAM_V);
-    // result2newick
-    result2newick.push_back(PARAM_THREADS);
-    result2newick.push_back(PARAM_V);
     
     // mergedbs
     mergedbs.push_back(PARAM_MERGE_PREFIXES);
@@ -420,11 +418,6 @@ PARAM_COUNT_CHARACTER(PARAM_COUNT_CHARACTER_ID, "--count-char", "Count Char", "c
     extractalignedregion.push_back(PARAM_THREADS);
     extractalignedregion.push_back(PARAM_V);
     
-    // count
-    count.push_back(PARAM_COUNT_CHARACTER);
-    count.push_back(PARAM_THREADS);
-    count.push_back(PARAM_V);
-    
     // convertkb
     convertkb.push_back(PARAM_KB_COLUMNS);
     convertkb.push_back(PARAM_V);
@@ -937,9 +930,9 @@ void Parameters::setDefaults() {
 
     // linearcluster
     kmersPerSequence = 20;
-    
-    // count
-    countCharacter = "\n";
+
+    // result2stats
+    stat = "";
 }
 
 std::vector<MMseqsParameter> Parameters::combineList(std::vector<MMseqsParameter> &par1,

src/commons/Parameters.h

@@ -253,9 +253,6 @@ class Parameters          // Parameters for gap penalties and pseudocounts
 
     // convertkb
     std::string kbColumns;
-
-    //count
-    std::string countCharacter;
 
     // concatdbs
     bool preserveKeysB;
@@ -361,7 +358,7 @@ class Parameters          // Parameters for gap penalties and pseudocounts
     //PARAMETER(PARAM_FIRST_SEQ_REP_SEQ)
 //    PARAMETER(PARAM_NO_PRUNING)
 
-    // result2stat
+    // result2stats
     PARAMETER(PARAM_STAT)
 
     // linearcluster
@@ -439,9 +436,6 @@ class Parameters          // Parameters for gap penalties and pseudocounts
     // convertkb
     PARAMETER(PARAM_KB_COLUMNS)
 
-    // count
-    PARAMETER(PARAM_COUNT_CHARACTER)
-
     std::vector<MMseqsParameter> empty;
     std::vector<MMseqsParameter> rescorediagonal;
     std::vector<MMseqsParameter> onlyverbosity;
@@ -470,7 +464,6 @@ class Parameters          // Parameters for gap penalties and pseudocounts
     std::vector<MMseqsParameter> filterDb;
     std::vector<MMseqsParameter> swapresults;
     std::vector<MMseqsParameter> subtractdbs;
-    std::vector<MMseqsParameter> result2newick;
     std::vector<MMseqsParameter> diff;
     std::vector<MMseqsParameter> dbconcat;
     std::vector<MMseqsParameter> mergedbs;
@@ -480,7 +473,6 @@ class Parameters          // Parameters for gap penalties and pseudocounts
     std::vector<MMseqsParameter> summarizetabs;
     std::vector<MMseqsParameter> extractdomains;
     std::vector<MMseqsParameter> extractalignedregion;
-    std::vector<MMseqsParameter> count;
     std::vector<MMseqsParameter> convertkb;
 
     std::vector<MMseqsParameter> combineList(std::vector<MMseqsParameter> &par1,

src/commons/SubstitutionMatrix.cpp

@@ -17,7 +17,6 @@ SubstitutionMatrix::SubstitutionMatrix(const char *scoringMatrixFileName_,
         // read amino acid substitution matrix from file
         std::string fileName(scoringMatrixFileName);
         matrixName = Util::base_name(fileName, "/\\");
-        matrixName = Util::remove_extension(matrixName);
         if (fileName.substr(fileName.length() - 4, 4).compare(".out") == 0){
             std::ifstream in(fileName);
             if (in.fail()) {
@@ -28,13 +27,12 @@ SubstitutionMatrix::SubstitutionMatrix(const char *scoringMatrixFileName_,
                             std::istreambuf_iterator<char>());
             readProbMatrix(str);
             in.close();
-        }
-        else {
+        } else {
             Debug(Debug::ERROR) << "Invalid format of the substitution matrix input file! Only .out files are accepted.\n";
             EXIT(EXIT_FAILURE);
         }
     }else{
-        matrixName = "blosum62";
+        matrixName = "blosum62.out";
         std::string submat((const char*)blosum62_out,blosum62_out_len);
         readProbMatrix(submat);
     }

src/commons/Util.cpp

@@ -16,6 +16,10 @@
 
 KSEQ_INIT(int, read)
 
+const std::string& tostringidentity::to_string(const std::string& s) {
+    return s;
+}
+
 size_t Util::countLines(const char *data, size_t length) {
     size_t newlines = 0;
     for (size_t i = 0; i < length; i++ ) {

src/commons/Util.h

@@ -16,12 +16,20 @@
 #endif
 
 #define CHECK_BIT(var,pos) ((var) & (1<<(pos)))
+
 #if __cplusplus <= 199711L
 #define SSTR( x ) \
 dynamic_cast< std::ostringstream& >( \
-( std::ostringstream().flush() << std::dec << x ) ).str()
+( std::ostringstream().flush() << std::dec << (x) ).str()
 #else
-#define SSTR( x ) std::to_string(x)
+#ifndef TOSTRINGIDENTITY
+#define TOSTRINGIDENTITY
+namespace tostringidentity {
+    using std::to_string;
+    const std::string& to_string(const std::string& s);
+}
+#endif
+#define SSTR(x) tostringidentity::to_string((x))
 #endif
 
 #define ARRAY_SIZE(a) (sizeof(a) / sizeof(a[0]))

src/prefiltering/IndexTable.h

@@ -140,16 +140,16 @@ class IndexTable {
     }
 
     // init index table with external data (needed for index readin)
-    void initTableByExternalData(size_t sequenzeCount, size_t tableEntriesNum,
+    void initTableByExternalData(size_t sequenceCount, size_t tableEntriesNum,
                                  char * entries, size_t * entriesSize, SequenceLookup * lookup) {
         this->tableEntriesNum = tableEntriesNum;
-        this->size = sequenzeCount;
-        //        initMemory(sequenzeCount, tableEntriesNum, seqDataSize);
+        this->size = sequenceCount;
+        //        initMemory(sequenceCount, tableEntriesNum, seqDataSize);
         if(lookup != NULL){
             sequenceLookup = lookup;
         }
         this->entries = entries;
-        Debug(Debug::WARNING) << "Cache database  \n";
+        Debug(Debug::INFO) << "Cache database  \n";
         char* it = this->entries;
         // set the pointers in the index table to the start of the list for a certain k-mer
         magicByte = 0; // read each entry to keep them in memory
@@ -161,7 +161,7 @@ class IndexTable {
         }
         table[tableSize] = it;
         externalData = true;
-        Debug(Debug::WARNING) << "Read IndexTable ... Done\n";
+        Debug(Debug::INFO) << "Read IndexTable ... Done\n";
     }
 
     void revertPointer(){