Rework parameter output string

steineggerlab · Feb 5, 2022 · 10b23bf · 10b23bf
1 parent 841369d
commit 10b23bf
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Showing 2 changed files with 25 additions and 5 deletions.
diff --git a/src/commons/LocalParameters.cpp b/src/commons/LocalParameters.cpp
@@ -10,11 +10,29 @@ const int LocalParameters::DBTYPE_TMSCORE = 102;
 LocalParameters::LocalParameters() :
         Parameters(),
         PARAM_TMSCORE_THRESHOLD(PARAM_TMSCORE_THRESHOLD_ID,"--tmscore-threshold", "TMscore threshold", "accept alignments with a tmsore > thr [0.0,1.0]",typeid(float), (void *) &tmScoreThr, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
-        PARAM_ALIGNMENT_TYPE(PARAM_ALIGNMENT_TYPE_ID,"--alignment-type", "Alignment type", "How to compute the alignment:\n0: 3di alignment\n1: TM alignment\n2: 3Di+AA\n",typeid(int), (void *) &alignmentType, "^[0-2]{1}$"),
-        PARAM_CHAIN_NAME_MODE(PARAM_CHAIN_NAME_MODE_ID,"--chain-name-mode", "Chain name mode", "Add chain to name:\n0: auto\n1: always add\n",typeid(int), (void *) &chainNameMode, "^[0-1]{1}$"),
+        PARAM_ALIGNMENT_TYPE(PARAM_ALIGNMENT_TYPE_ID,"--alignment-type", "Alignment type", "How to compute the alignment:\n0: 3di alignment\n1: TM alignment\n2: 3Di+AA",typeid(int), (void *) &alignmentType, "^[0-2]{1}$"),
+        PARAM_CHAIN_NAME_MODE(PARAM_CHAIN_NAME_MODE_ID,"--chain-name-mode", "Chain name mode", "Add chain to name:\n0: auto\n1: always add\n",typeid(int), (void *) &chainNameMode, "^[0-1]{1}$", MMseqsParameter::COMMAND_EXPERT),
         PARAM_TMALIGN_FAST(PARAM_TMALIGN_FAST_ID,"--tmalign-fast", "TMalign fast","turn on fast search in TM-align" ,typeid(int), (void *) &tmAlignFast, "^[0-1]{1}$"),
         PARAM_N_SAMPLE(PARAM_N_SAMPLE_ID, "--n-sample", "Sample size","pick N random sample" ,typeid(int), (void *) &nsample, "^[0-9]{1}[0-9]*$")
 {
+    PARAM_ALIGNMENT_MODE.description = "How to compute the alignment:\n0: automatic\n1: only score and end_pos\n2: also start_pos and cov\n3: also seq.id";
+    PARAM_ALIGNMENT_MODE.regex = "^[0-3]{1}$";
+    PARAM_ALIGNMENT_MODE.category = MMseqsParameter::COMMAND_ALIGN | MMseqsParameter::COMMAND_EXPERT;
+    PARAM_SEARCH_TYPE.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_TRANSLATION_TABLE.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_TRANSLATION_TABLE.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_PCA.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_PCB.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_ZDROP.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_CORR_SCORE_WEIGHT.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_REALIGN.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_REALIGN_SCORE_BIAS.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_REALIGN_MAX_SEQS.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_SCORE_BIAS.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_WRAPPED_SCORING.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_ALPH_SIZE.category = MMseqsParameter::COMMAND_HIDDEN;
+    PARAM_INCLUDE_IDENTITY.category = MMseqsParameter::COMMAND_HIDDEN;
+
     scoringMatrixFile = "3di.out";
     seedScoringMatrixFile = "3di.out";
     substitutionMatrices.emplace_back("3di.out", mat3di_out, mat3di_out_len);

diff --git a/src/foldseek.cpp b/src/foldseek.cpp
@@ -36,9 +36,11 @@ std::vector<struct Command> commands = {
         {"easy-search",          easystructuresearch,           &localPar.easystructuresearchworkflow,   COMMAND_EASY,
                 "Sensitive homology search",
                 "# Search a single/multiple PDB file against a set of PDB files\n"
-                "foldseek easy-search examples/d1asha_ examples/ result.m8 tmp\n\n"
-                "# Search a set of PDB files against a set of PDB files\n"
-                "foldseek easy-search examples/d1asha_ examples/ result.m8 tmp\n\n",
+                "foldseek easy-search examples/d1asha_ examples/ result.m8 tmp\n"
+                "# Format output differently\n"
+                "foldseek easy-search examples/d1asha_ examples/ result.m8 tmp --format-output query,target,qStart,tStart,cigar\n"
+                "# Align with TMalign (global)\n"
+                "foldseek easy-search examples/d1asha_ examples/ result.m8 tmp --alignment-type 1\n\n",
                 "Martin Steinegger <[email protected]>",
                 "<i:PDB|mmCIF[.gz]> ... <i:PDB|mmCIF[.gz]>|<i:stdin> <i:targetFastaFile[.gz]>|<i:targetDB> <o:alignmentFile> <tmpDir>",
                 CITATION_SERVER | CITATION_MMSEQS2,{{"fastaFile[.gz|.bz2]", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA|DbType::VARIADIC, &FoldSeekDbValidator::flatfileStdinAndFolder },