Add parameter --alignment-output-mode, remove alignment mode 5

Author: martin-steinegger

src/alignment/Alignment.cpp

@@ -23,7 +23,8 @@ Alignment::Alignment(const std::string &querySeqDB, const std::string &targetSeq
         covThr(par.covThr), canCovThr(par.covThr), covMode(par.covMode), seqIdMode(par.seqIdMode), evalThr(par.evalThr), seqIdThr(par.seqIdThr),
         alnLenThr(par.alnLenThr), includeIdentity(par.includeIdentity), addBacktrace(par.addBacktrace), realign(par.realign), scoreBias(par.scoreBias), realignScoreBias(par.realignScoreBias), realignMaxSeqs(par.realignMaxSeqs),
         threads(static_cast<unsigned int>(par.threads)), compressed(par.compressed), outDB(outDB), outDBIndex(outDBIndex),
-        maxSeqLen(par.maxSeqLen), compBiasCorrection(par.compBiasCorrection), altAlignment(par.altAlignment), maxAccept(static_cast<unsigned int>(par.maxAccept)), maxReject(static_cast<unsigned int>(par.maxRejected)), wrappedScoring(par.wrappedScoring),
+        maxSeqLen(par.maxSeqLen), compBiasCorrection(par.compBiasCorrection), altAlignment(par.altAlignment), alignmentOutputMode(par.alignmentOutputMode),
+        maxAccept(static_cast<unsigned int>(par.maxAccept)), maxReject(static_cast<unsigned int>(par.maxRejected)), wrappedScoring(par.wrappedScoring),
         lcaAlign(lcaAlign), qdbr(NULL), qDbrIdx(NULL), tdbr(NULL), tDbrIdx(NULL) {
     unsigned int alignmentMode = par.alignmentMode;
     if (alignmentMode == Parameters::ALIGNMENT_MODE_UNGAPPED) {
@@ -34,11 +35,7 @@ Alignment::Alignment(const std::string &querySeqDB, const std::string &targetSeq
     if (addBacktrace == true) {
         alignmentMode = Parameters::ALIGNMENT_MODE_SCORE_COV_SEQID;
     }
-    outputClusterFormat = false;
-    if (par.alignmentMode == Parameters::ALIGNMENT_MODE_CLUSTER) {
-        alignmentMode = Parameters::ALIGNMENT_MODE_SCORE_ONLY;
-        outputClusterFormat = true;
-    }
+
 
     if (lcaAlign == true) {
         lcaSwMode = initSWMode(std::max(alignmentMode, (unsigned int)Parameters::ALIGNMENT_MODE_SCORE_ONLY), 0.0f, 0.0f);
@@ -257,7 +254,7 @@ void Alignment::run() {
 
 void Alignment::run(const std::string &outDB, const std::string &outDBIndex, const size_t dbFrom, const size_t dbSize, bool merge) {
     int dbtype = Parameters::DBTYPE_ALIGNMENT_RES;
-    if(outputClusterFormat){
+    if(alignmentOutputMode == Parameters::ALIGNMENT_OUTPUT_CLUSTER){
         dbtype =  Parameters::DBTYPE_CLUSTER_RES;
     }
     DBWriter dbw(outDB.c_str(), outDBIndex.c_str(), threads, compressed, dbtype);
@@ -506,7 +503,7 @@ void Alignment::run(const std::string &outDB, const std::string &outDBIndex, con
 
                     returnRes = &swRealignResults;
                 }
-                if(outputClusterFormat) {
+                if(alignmentOutputMode == Parameters::ALIGNMENT_OUTPUT_CLUSTER) {
                     for (size_t result = 0; result < returnRes->size(); result++) {
                         alnResultsOutString.append(SSTR((*returnRes)[result].dbKey));
                         alnResultsOutString.push_back('\n');

src/alignment/Alignment.h

@@ -85,9 +85,8 @@ class Alignment {
     int targetSeqType;
     bool compBiasCorrection;
 
-    bool outputClusterFormat;
-
     int altAlignment;
+    int alignmentOutputMode;
 
     const unsigned int maxAccept;
     const unsigned int maxReject;

src/commons/Parameters.cpp

@@ -63,7 +63,8 @@ Parameters::Parameters():
         PARAM_SPACED_KMER_PATTERN(PARAM_SPACED_KMER_PATTERN_ID, "--spaced-kmer-pattern", "Spaced k-mer pattern", "User-specified spaced k-mer pattern", typeid(std::string), (void *) &spacedKmerPattern, "^1[01]*1$", MMseqsParameter::COMMAND_PREFILTER | MMseqsParameter::COMMAND_EXPERT),
         PARAM_LOCAL_TMP(PARAM_LOCAL_TMP_ID, "--local-tmp", "Local temporary path", "Path where some of the temporary files will be created", typeid(std::string), (void *) &localTmp, "", MMseqsParameter::COMMAND_PREFILTER | MMseqsParameter::COMMAND_EXPERT),
         // alignment
-        PARAM_ALIGNMENT_MODE(PARAM_ALIGNMENT_MODE_ID, "--alignment-mode", "Alignment mode", "How to compute the alignment:\n0: automatic\n1: only score and end_pos\n2: also start_pos and cov\n3: also seq.id\n4: only ungapped alignment\n5: score only (output) cluster format", typeid(int), (void *) &alignmentMode, "^[0-5]{1}$", MMseqsParameter::COMMAND_ALIGN),
+        PARAM_ALIGNMENT_MODE(PARAM_ALIGNMENT_MODE_ID, "--alignment-mode", "Alignment mode", "How to compute the alignment:\n0: automatic\n1: only score and end_pos\n2: also start_pos and cov\n3: also seq.id\n4: only ungapped alignment", typeid(int), (void *) &alignmentMode, "^[0-5]{1}$", MMseqsParameter::COMMAND_ALIGN),
+        PARAM_ALIGNMENT_OUTPUT_MODE(PARAM_ALIGNMENT_OUTPUT_MODE_ID, "--alignment-output-mode", "Alignment mode", "How to compute the alignment:\n0: automatic\n1: only score and end_pos\n2: also start_pos and cov\n3: also seq.id\n4: only ungapped alignment\n5: score only (output) cluster format", typeid(int), (void *) &alignmentOutputMode, "^[0-1]{1}$", MMseqsParameter::COMMAND_ALIGN),
         PARAM_E(PARAM_E_ID, "-e", "E-value threshold", "List matches below this E-value (range 0.0-inf)", typeid(double), (void *) &evalThr, "^([-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)|[0-9]*(\\.[0-9]+)?$", MMseqsParameter::COMMAND_ALIGN),
         PARAM_C(PARAM_C_ID, "-c", "Coverage threshold", "List matches above this fraction of aligned (covered) residues (see --cov-mode)", typeid(float), (void *) &covThr, "^0(\\.[0-9]+)?|^1(\\.0+)?$", MMseqsParameter::COMMAND_ALIGN | MMseqsParameter::COMMAND_CLUSTLINEAR),
         PARAM_COV_MODE(PARAM_COV_MODE_ID, "--cov-mode", "Coverage mode", "0: coverage of query and target\n1: coverage of target\n2: coverage of query\n3: target seq. length has to be at least x% of query length\n4: query seq. length has to be at least x% of target length\n5: short seq. needs to be at least x% of the other seq. length", typeid(int), (void *) &covMode, "^[0-5]{1}$", MMseqsParameter::COMMAND_ALIGN),
@@ -336,6 +337,7 @@ Parameters::Parameters():
     align.push_back(&PARAM_SUB_MAT);
     align.push_back(&PARAM_ADD_BACKTRACE);
     align.push_back(&PARAM_ALIGNMENT_MODE);
+    align.push_back(&PARAM_ALIGNMENT_OUTPUT_MODE);
     align.push_back(&PARAM_WRAPPED_SCORING);
     align.push_back(&PARAM_E);
     align.push_back(&PARAM_MIN_SEQ_ID);
@@ -2106,6 +2108,7 @@ void Parameters::setDefaults() {
     spacedKmer = true;
     includeIdentity = false;
     alignmentMode = ALIGNMENT_MODE_FAST_AUTO;
+    alignmentOutputMode = ALIGNMENT_OUTPUT_ALIGNMENT;
     evalThr = 0.001;
     covThr = 0.0;
     covMode = COV_MODE_BIDIRECTIONAL;

src/commons/Parameters.h

@@ -106,7 +106,9 @@ class Parameters {
     static const unsigned int ALIGNMENT_MODE_SCORE_COV = 2;
     static const unsigned int ALIGNMENT_MODE_SCORE_COV_SEQID = 3;
     static const unsigned int ALIGNMENT_MODE_UNGAPPED = 4;
-    static const unsigned int ALIGNMENT_MODE_CLUSTER = 5;
+
+    static const unsigned int ALIGNMENT_OUTPUT_ALIGNMENT = 0;
+    static const unsigned int ALIGNMENT_OUTPUT_CLUSTER = 1;
 
     static const unsigned int EXPAND_TRANSFER_EVALUE = 0;
     static const unsigned int EXPAND_RESCORE_BACKTRACE = 1;
@@ -384,6 +386,7 @@ class Parameters {
     // ALIGNMENT
     int alignmentMode;                   // alignment mode 0=fastest on parameters,
                                          // 1=score only, 2=score, cov, start/end pos, 3=score, cov, start/end pos, seq.id,
+    int alignmentOutputMode;             // alignment output mode 0=alignment, 1=cluster
     double evalThr;                      // e-value threshold for acceptance
     float  covThr;                       // coverage query&target threshold for acceptance
     int    covMode;                      // coverage target threshold for acceptance
@@ -702,6 +705,7 @@ class Parameters {
 
     // alignment
     PARAMETER(PARAM_ALIGNMENT_MODE)
+    PARAMETER(PARAM_ALIGNMENT_OUTPUT_MODE)
     PARAMETER(PARAM_E)
     PARAMETER(PARAM_C)
     PARAMETER(PARAM_COV_MODE)

src/workflow/Search.cpp

@@ -343,7 +343,7 @@ int search(int argc, const char **argv, const Command& command) {
             par.rescoreMode = originalRescoreMode;
         } else {
             cmd.addVariable("ALIGNMENT_PAR", par.createParameterString(par.align).c_str());
-            par.alignmentMode = Parameters::ALIGNMENT_MODE_CLUSTER;
+            par.alignmentOutputMode = Parameters::ALIGNMENT_OUTPUT_CLUSTER;
             cmd.addVariable("ALIGNMENT_IT_PAR", par.createParameterString(par.align).c_str());
         }