From 5d04d3dd619b91e95cac3dfab76e6fa1a3e406a1 Mon Sep 17 00:00:00 2001 From: Segei L Kosakovsky Pond Date: Wed, 18 Mar 2020 23:02:37 -0400 Subject: [PATCH] 2.5.7rc --- CMakeLists.txt | 8 - res/TemplateBatchFiles/GARD.bf | 60 +- .../SelectionAnalyses/MEME.bf | 2 +- res/TemplateBatchFiles/files.lst | 1 + .../libv3/UtilityFunctions.bf | 5 +- res/TemplateBatchFiles/libv3/all-terms.bf | 7 + .../libv3/models/parameters.bf | 29 +- .../libv3/tasks/distances.bf | 2 +- res/TemplateBatchFiles/libv3/tasks/mpi.bf | 23 +- res/TemplateBatchFiles/libv3/tasks/trees.bf | 9 +- src/core/avllistxl_iterator.cpp | 2 - src/core/batchlan.cpp | 246 +- src/core/batchlanhelpers.cpp | 11 +- src/core/batchlanruntime.cpp | 165 + src/core/formula.cpp | 2 +- src/core/fstring.cpp | 5 + src/core/global_things.cpp | 3 +- src/core/include/avllistxl_iterator.h | 6 + src/core/include/batchlan.h | 9 +- src/core/include/defines.h | 4 +- src/core/include/list.h | 6 + src/core/include/matrix.h | 3 +- src/core/include/parser.h | 2 +- src/core/likefunc.cpp | 328 +- src/core/list.cpp | 15 + src/core/matrix.cpp | 22 +- src/core/operation.cpp | 4 +- src/core/parser.cpp | 14 +- src/core/strings.cpp | 6 +- src/core/variable.cpp | 3 + src/utils/hyphyunixutils.cpp | 19 +- tests/hbltests/Results/HIVSweden.out | 578 +- .../Results/HIVSweden.out_MODEL_-1.nex | 54 +- .../Results/HIVSweden.out_MODEL_0.nex | 56 +- .../Results/HIVSweden.out_MODEL_1.nex | 60 +- .../libv3/data/partitioned.nex.slac.json | 9835 ----------------- 36 files changed, 1083 insertions(+), 10521 deletions(-) delete mode 100644 tests/hbltests/libv3/data/partitioned.nex.slac.json diff --git a/CMakeLists.txt b/CMakeLists.txt index 6407236c9..8ceb62a20 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -495,15 +495,7 @@ else(${OPENMP_FOUND}) target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES}) endif(${OPENMP_FOUND}) -if(${MPI_FOUND}) - set_property( - TARGET HYPHYDEBUG - APPEND PROPERTY COMPILE_DEFINITIONS __HYPHYMPI__ - ) - target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES} ${MPI_LIBRARIES} OpenMP::OpenMP_CXX) -else(${MPI_FOUND}) target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES}) -endif(${MPI_FOUND}) add_custom_target(DEBUG DEPENDS HYPHYDEBUG) diff --git a/res/TemplateBatchFiles/GARD.bf b/res/TemplateBatchFiles/GARD.bf index 4e4c14c55..fdc7a2f9c 100644 --- a/res/TemplateBatchFiles/GARD.bf +++ b/res/TemplateBatchFiles/GARD.bf @@ -201,7 +201,10 @@ utility.ForEach (alignments.Extract_site_patterns ("gard.filter"), "_pattern_", gard.variableSiteMap = Transpose (utility.DictToArray (gard.variableSiteMap)) % 0; // sort by 1st column gard.variableSites = Rows (gard.variableSiteMap); -gard.inverseVariableSiteMap = unility.SwapKeysAndValues(gard.variableSiteMap); +gard.inverseVariableSiteMap = {}; +for (index, pattern; in; gard.variableSiteMap) { + gard.inverseVariableSiteMap[pattern] = index; +} gard.numberOfPotentialBreakPoints = gard.variableSites - 1; io.ReportProgressMessage ("", ">Loaded a `gard.dataType` multiple sequence alignment with **`gard.numSeqs`** sequences, **`gard.numSites`** sites (`gard.variableSites` of which are variable) from \`" + @@ -606,21 +609,17 @@ lfunction gard.createLikelihoodFunctionForExport (id, model) { */ lfunction gard.validatePartititon (definition, minSize, totalSites) { lastBP = 0; - //console.log (""); - //console.log (definition); - bpCount = utility.Array1D (definition); - for (i = 0; i < bpCount; i+=1) { - if (definition[i] - lastBP + 1 < minSize) { - //console.log ("FAIL"); + + for (current_bp; in; definition) { + if (current_bp - lastBP + 1 < minSize) { return FALSE; } - lastBP = definition[i]; + lastBP = current_bp; } + if (totalSites - lastBP < minSize) { - //console.log ("FAIL"); return FALSE; } - //console.log ("PASS"); return TRUE; } @@ -631,7 +630,8 @@ lfunction gard.validatePartititon (definition, minSize, totalSites) { */ lfunction gard.modelIsNotInMasterList(masterList, breakPoints) { - return utility.KeyExists(masterList, '' + breakPoints) == FALSE; + return masterList / ('' + breakPoints) == FALSE; + //return utility.KeyExists(masterList, '' + breakPoints) == FALSE; } function gard.concludeAnalysis(bestOverallModel) { @@ -807,7 +807,7 @@ lfunction gard.GA.recombineModels (parentModels, populationSize) { breakPoints = {numberOfBreakPoints, 1}; for (breakPointNumber=0; breakPointNumber < numberOfBreakPoints; breakPointNumber += 1) { - if (random.TRUE_or_FALSE()) { + if (Random(0,1) <= 0.5) { breakPoints[breakPointNumber] = parentModel1[breakPointNumber]; } else { breakPoints[breakPointNumber] = parentModel2[breakPointNumber]; @@ -835,16 +835,10 @@ lfunction gard.GA.recombineModels (parentModels, populationSize) { * @returns nothing... the gard.GA.storeMultiBreakPointModelResults function gets called which updates the intergenerationalModels object */ function gard.GA.evaluateModels (models) { - modelIds = utility.Keys(models); - numberOfModels = Columns(modelIds); - - for(modelIndex=0; modelIndex= 0 && variableSiteMapIndexOfParentBreakPoint < (^"gard.variableSites")) { newBreakPoint = (^"gard.variableSiteMap")[variableSiteMapIndexOfParentBreakPoint]; notValid = FALSE; @@ -1019,14 +1011,4 @@ lfunction gard.Helper.convertMatrixStringToMatrix(matrixString){ //sort numeric Nx1 matrix into assending order. lfunction gard.Helper.sortedMatrix(matrix) { return matrix % 0; - - /*sortedMatrix = {1,Columns(matrix)}; - - for (i=0; i ID + * @returns {Dictionary} a dictionary containing old -> new id map +*/ + +lfunction parameters.ValidateIDs (ids) { + result = {}; + N = utility.Array1D (ids); + for (i = 0; i < N; i+=1) { + try_name = ids [i] && 7; + if (result / try_name ) { + for (k = 2; ; k+=1) { + tagged = try_name + "_" + k; + if (!(result/tagged)) { + try_name = tagged; + break; + } + } + } + result [ids[i]] = try_name; + } + return result; } diff --git a/res/TemplateBatchFiles/libv3/tasks/distances.bf b/res/TemplateBatchFiles/libv3/tasks/distances.bf index b8e2728b5..d215018f1 100644 --- a/res/TemplateBatchFiles/libv3/tasks/distances.bf +++ b/res/TemplateBatchFiles/libv3/tasks/distances.bf @@ -23,7 +23,7 @@ lfunction distances.nucleotide.tn93 (filter, freqs, options) { K2P = TRUE; } else { - K2P = FASLE; + K2P = FALSE; K1 = 2*freqs[0]*freqs[2]/fR; K2 = 2*freqs[1]*freqs[3]/fY; K3 = 2*(fR*fY-freqs[0]*freqs[2]*fY/fR-freqs[1]*freqs[3]*fR/fY); diff --git a/res/TemplateBatchFiles/libv3/tasks/mpi.bf b/res/TemplateBatchFiles/libv3/tasks/mpi.bf index 3e0fa733d..9360f345e 100644 --- a/res/TemplateBatchFiles/libv3/tasks/mpi.bf +++ b/res/TemplateBatchFiles/libv3/tasks/mpi.bf @@ -180,6 +180,8 @@ namespace mpi { send_to_nodes * 0; + queue ["cache"] = {}; + } } @@ -197,6 +199,8 @@ namespace mpi { for (k = 1; k < mpi_node_count; k += 1) { queue [k] = {utility.getGlobalValue("terms.mpi.job_id") : None, utility.getGlobalValue("terms.mpi.callback") : None, utility.getGlobalValue("terms.mpi.arguments"): None}; } + + // this will store jobs that were previously sent to each node; avoiding redefinition if possible } return queue; } @@ -225,8 +229,21 @@ namespace mpi { node = aux._handle_receieve (queue); } - - complete_function_dump = aux.queue_export_function (job); + complete_function_dump = None; + + if (utility.Has (queue, "cache" , "AssociativeList")) { + if ((queue["cache"])[node] == job) { + complete_function_dump = ""; + //console.log ("CACHED MPI preamble"); + } else { + (queue["cache"])[node] = job; + } + } + + if (None == complete_function_dump) { + complete_function_dump = aux.queue_export_function (job); + } + //console.log (complete_function_dump); job_id = get_next_job_id(); //fprintf (stdout, "Sending to node ", node, "\n"); @@ -261,6 +278,8 @@ namespace mpi { } } while (node < mpi_node_count); } + + queue = None } namespace aux { diff --git a/res/TemplateBatchFiles/libv3/tasks/trees.bf b/res/TemplateBatchFiles/libv3/tasks/trees.bf index 409881ca4..e986dba35 100644 --- a/res/TemplateBatchFiles/libv3/tasks/trees.bf +++ b/res/TemplateBatchFiles/libv3/tasks/trees.bf @@ -428,7 +428,10 @@ lfunction trees.ExtractTreeInfo(tree_string) { rooted = utility.Array1D ((flat_tree[(flat_tree[0])["Root"]])["Children"]) == 2; - DeleteObject (flat_tree, branch_lengths, branch_names, branch_count); + flat_tree = None; + branch_lengths = None; + branch_names = None; + branch_count = None; return { ^"terms.trees.newick": Format(T, 1, 0), @@ -1093,12 +1096,12 @@ lfunction tree.infer.NJ (datafilter, distances) { treeNodes[i][2] = njm[i][2]; // branch length } - DeleteObject (njm); + njm = None; } } if (flush_distances) { - DeleteObject (distances); + distances = None; } return tree._matrix2string (treeNodes, N, alignments.GetSequenceNames (datafilter), TRUE); diff --git a/src/core/avllistxl_iterator.cpp b/src/core/avllistxl_iterator.cpp index 9200c83f1..f2fd3c26c 100644 --- a/src/core/avllistxl_iterator.cpp +++ b/src/core/avllistxl_iterator.cpp @@ -39,8 +39,6 @@ #include "avllistxl_iterator.h" -#define AVL_LISTXL_ITERATOR_ENDINDEX (-1L) - AVLListXLIterator::AVLListXLIterator (_AVLListXL const * the_list): current_location (AVL_LISTXL_ITERATOR_ENDINDEX), traversal_lookup (AVL_LISTXL_ITERATOR_ENDINDEX), diff --git a/src/core/batchlan.cpp b/src/core/batchlan.cpp index f6b1e83e6..83940cf71 100644 --- a/src/core/batchlan.cpp +++ b/src/core/batchlan.cpp @@ -140,7 +140,7 @@ globalPolynomialCap ("GLOBAL_POLYNOMIAL_CAP"), //____________________________________________________________________________________ -_String blFor ("for("), // moved +_String blWhile ("while("), // moved blFunction ("function "), // moved blFFunction ("ffunction "), // moved @@ -2127,6 +2127,10 @@ _ElementaryCommand::~_ElementaryCommand (void) { _Formula* f = (_Formula*)simpleParameters(i); delete (f); } + } else if (code == HY_HBL_COMMAND_INIT_ITERATOR) { + if (simpleParameters.get (1) == ASSOCIATIVE_LIST && simpleParameters.countitems() > 2) { + delete (AVLListXLIterator*)simpleParameters.get(2); + } } } @@ -2404,6 +2408,17 @@ BaseRef _ElementaryCommand::toStr (unsigned long) { (*string_form) << "namespace " << parameter_to_string (0) << ";"; break; } + + case HY_HBL_COMMAND_INIT_ITERATOR: { + (*string_form) << "Initialize iterator on " << parameter_to_string (0) << ";"; + break; + } + + case HY_HBL_COMMAND_ADVANCE_ITERATOR: { + (*string_form) << "Advance iterator into "; + (string_form -> AppendNewInstance(parameters.Join(",",0,simpleParameters.get (1)))) << ";"; + break; + } } return string_form; @@ -3658,13 +3673,23 @@ bool _ElementaryCommand::Execute (_ExecutionList& chain) { case HY_HBL_COMMAND_GET_DATA_INFO: HandleGetDataInfo(chain); break; + + case HY_HBL_COMMAND_INIT_ITERATOR: + HandleInitializeIterator(chain); + break; + case HY_HBL_COMMAND_ADVANCE_ITERATOR: + HandleAdvanceIterator(chain); + break; + case HY_HBL_COMMAND_NESTED_LIST: chain.currentCommand++; { ((_ExecutionList*)parameters.GetItem(0))->Execute(&chain); } break; + + default: chain.currentCommand++; @@ -4051,87 +4076,137 @@ long _ElementaryCommand::ExtractConditions (_String const& source, long start_at bool _ElementaryCommand::MakeGeneralizedLoop (_String*p1, _String*p2, _String*p3 , bool for_or_while, _String& source, _ExecutionList&target) { + + const _String kIterator ("in"); + // extract the for enclosure long beginning = target.lLength, - for_return = target.lLength, - index; + for_return = beginning; bool success = true; bool has_increment = false; + bool is_iterator = (p2 && *p2 == kIterator); _SimpleList bc; - - while (success) { - - if (p1 && p1->nonempty()) { // initialization stage + + try { + if (is_iterator) { + if (! (p1 && p3)) { + throw (kEmptyString); + } for_return++; - success = success && target.BuildList (*p1, nil, true); // add init step - } + has_increment = true; + _ElementaryCommand * init = new _ElementaryCommand (HY_HBL_COMMAND_INIT_ITERATOR); + + long refer_to_init = target.countitems(); + + init->parameters << p3; + target < init; + _ElementaryCommand * advance = new _ElementaryCommand (HY_HBL_COMMAND_ADVANCE_ITERATOR); + + ExtractConditions (*p1,0L,advance->parameters,',',false); + if (advance->parameters.countitems() < 1 || advance->parameters.countitems() > 3) { + throw (_String("Must have bewteen 1 and 3 arguments for the 'for' iterator loop")); + } + + advance->simpleParameters <simpleParameters << advance->parameters.countitems(); + init->simpleParameters << target.countitems(); + init->simpleParameters << 0; + target < advance; + + for_return++; + target < new _ElementaryCommand (); - // append condition now + if (source.get_char(0)=='{') { + source.Trim(1,kStringEnd); + } - if (!success) { - break; - } + if (target.BuildList (source, &bc) == false) { // construct the main body + throw (kEmptyString); + } + target << advance; + + _ElementaryCommand * loopback = new _ElementaryCommand; + loopback->MakeJumpCommand (nil,for_return,0,target); + target < loopback; + + // automatically generate + // None != iterator_value, but we don't know + + _StringBuffer iterator_condition; + iterator_condition << "None!=" << (_String*)advance->parameters.GetItem (advance->parameters.countitems() -1); + target.GetIthCommand(for_return)->MakeJumpCommand (&iterator_condition, for_return+1, target.lLength,target); + + } else { + + if (p1 && p1->nonempty()) { // initialization stage + for_return++; + success = success && target.BuildList (*p1, nil, true); // add init step + } + + // append condition now - if (for_or_while) { - if (p2 && p2->nonempty()) { // condition stage - target < new _ElementaryCommand (*p2); + if (!success) { + throw (kEmptyString); } - } - if (source.get_char(0)=='{') { - source.Trim(1,kStringEnd); - } + if (for_or_while) { + if (p2 && p2->nonempty()) { // condition stage + target < new _ElementaryCommand (*p2); + } + } - if ((success = success && target.BuildList (source, &bc)) == false) { // construct the main body - break; - } + if (source.get_char(0)=='{') { + source.Trim(1,kStringEnd); + } - if (p3 && p3->nonempty ()) { // increment stage - success = success && target.BuildList (*p3, nil,true); // add increment step - has_increment = true; - } + if ((success = success && target.BuildList (source, &bc)) == false) { // construct the main body + throw (kEmptyString); + } - if (!success) { - break; - } + if (p3 && p3->nonempty ()) { // increment stage + success = success && target.BuildList (*p3, nil,true); // add increment step + has_increment = true; + } - if (for_or_while) { - _ElementaryCommand * loopback = new _ElementaryCommand; - success = success && loopback->MakeJumpCommand (nil,for_return,0,target); - target < loopback; - if (p2 && p2->nonempty()) { - success = success && (target.GetIthCommand(for_return))->MakeJumpCommand (p2, for_return+1, target.lLength,target); + if (!success) { + throw (kEmptyString); } - } else { - if (p2) { - _ElementaryCommand* loopback = new _ElementaryCommand ; - success = success && loopback->MakeJumpCommand (p2,for_return,target.lLength+1,target); + + if (for_or_while) { + _ElementaryCommand * loopback = new _ElementaryCommand; + loopback->MakeJumpCommand (nil,for_return,0,target); target < loopback; + if (p2 && p2->nonempty()) { + target.GetIthCommand(for_return)->MakeJumpCommand (p2, for_return+1, target.lLength,target); + } + } else { + if (p2) { + _ElementaryCommand* loopback = new _ElementaryCommand ; + success = success && loopback->MakeJumpCommand (p2,for_return,target.lLength+1,target); + target < loopback; + } } } - break; - - } - - if (!success) { // clean up - for (index = beginning; index= beginning; index--) { + target.Delete (index); } - return false; - } else { - // write out the breaks and continues - for (index = 0; index0) { // break - (target.GetIthCommand(loc))->MakeJumpCommand (nil, target.lLength, 0,target); - } else { // continue - (target.GetIthCommand(-loc))->MakeJumpCommand (nil, target.lLength-(has_increment?2:1), 0,target); - } + if (err.nonempty()) { + HandleApplicationError(err); } + return false; } + bc.Each ([&target, has_increment] (long loc, unsigned long) -> void { + if (loc>0) { // break + (target.GetIthCommand(loc))->MakeJumpCommand (nil, target.lLength, 0,target); + } else { // continue + (target.GetIthCommand(-loc))->MakeJumpCommand (nil, target.lLength-(has_increment?2:1), 0,target); + } + }); + return true; } @@ -4605,35 +4680,32 @@ bool _ElementaryCommand::ConstructModel (_String&source, _ExecutionList&targe //____________________________________________________________________________________ -bool _ElementaryCommand::MakeJumpCommand (_String* source, long branch1, long branch2, _ExecutionList& parentList) -{ - long oldFla = 0; - code = 4; +bool _ElementaryCommand::MakeJumpCommand (_String* source, long branch_true, long branch_false, _ExecutionList& parentList) { + long existing_formula_handle = 0L; + code = 4L; if (simpleParameters.lLength==3) { if (source) { - _Formula* f = (_Formula*)simpleParameters(2); - delete (f); - } else { - oldFla = simpleParameters(2); + delete ((_Formula*)simpleParameters.get(2)); + } else { + existing_formula_handle = simpleParameters.get(2); } } - if (branch1==-1) { - if (simpleParameters.lLength == 0) { + if (branch_true==-1) { + if (simpleParameters.empty()) { HandleApplicationError("An if-then-else scoping error. Check opening and closing brackets and double else's."); return false; } - branch1 = simpleParameters[0]; + branch_true = simpleParameters.get (0); } simpleParameters.Clear(); - simpleParameters<= 0L) { - ReportWarning (_String("Overwritten previously defined function:'") & *funcID & '\''); + ReportWarning (_String("Overwritten previously defined function:'") & *funcID & '\''); + if (batchLanguageFunctionClassification.get (mark1) == kBLFunctionLocal) { + // clean up previously used namespaces + _ExecutionList * existing = (_ExecutionList *)batchLanguageFunctions.GetItem(mark1); + _String * nm = existing->GetNameSpace(); + if (nm) { + long best_index; + char match = variableNames.FindBest(nm, best_index); + //printf ("PREVIOUS LOCAL FUNCTION %s\n", nm->get_str()); + if (best_index >= 0) { + _Variable * namespace_start = LocateVar (best_index); + if (namespace_start->GetName()->BeginsWith(*nm)) { + //printf ("Clearing namespace %s starting at %s for function %s \n", nm->get_str(), namespace_start->GetName()->get_str(), funcID->get_str()); + _SimpleList locals; + DeleteTreeVariable (best_index, locals,nm, false); + } + } + if (match == 0) { + DeleteVariable(best_index, true, false); + } + } + } + } _List arguments; @@ -4752,8 +4847,7 @@ bool _ElementaryCommand::ConstructFunction (_String&source, _ExecutionList& c return false; } - _String extraNamespace; - if (isLFunction) + if (isLFunction && extraNamespace.empty()) extraNamespace = _HYGenerateANameSpace(); for (long k = 0UL; k < arguments.lLength; k++) { diff --git a/src/core/batchlanhelpers.cpp b/src/core/batchlanhelpers.cpp index 0db7ce707..d3f3f7726 100644 --- a/src/core/batchlanhelpers.cpp +++ b/src/core/batchlanhelpers.cpp @@ -51,7 +51,8 @@ extern _List batchLanguageFunctionNames; //____________________________________________________________________________________ -_String _HYGenerateANameSpace () { +_String const _HYGenerateANameSpace () { + _String nmsp, capLetters ("ABCDEFGHIJKLMNOPQRSTUVWXYZ_abcdefghijklmnopqrstuvwxyz"); do { @@ -59,10 +60,16 @@ _String _HYGenerateANameSpace () { } while (_HY_HBL_Namespaces.FindKey (nmsp) != kNotFound); - _HY_HBL_Namespaces.Insert (nmsp, 0); + _HY_HBL_Namespaces.Insert (nmsp, 0L); + return nmsp; } +//____________________________________________________________________________________ + +void _HYClearANameSpace (const _String& nm) { + _HY_HBL_Namespaces.Delete(nm); + } //____________________________________________________________________________________ diff --git a/src/core/batchlanruntime.cpp b/src/core/batchlanruntime.cpp index 51910294a..7818d672d 100644 --- a/src/core/batchlanruntime.cpp +++ b/src/core/batchlanruntime.cpp @@ -1740,6 +1740,171 @@ bool _ElementaryCommand::HandleUseModel (_ExecutionList& current_program) { return true; } + +//____________________________________________________________________________________ + +bool _ElementaryCommand::HandleInitializeIterator (_ExecutionList& current_program) { +/* + parameters: + [0] -> the string ID of the object to iterate over + [1] -> the object to iteratre over + + + simpleParameters: + [0] -> command index for the corresponding advance command + [1] -> type of object; 0 - dict, 1 - matrix + [2] -> if dict, then this stores the pointer to AVLListXLIterator +*/ + current_program.advance(); + try { + // clean up previous iterator states + if (parameters.countitems() > 1) { + parameters.Delete (1L); + if (simpleParameters.get (1) == ASSOCIATIVE_LIST) { + delete ((AVLListXLIterator*)simpleParameters.get(2)); + } + } + + if (simpleParameters.countitems() > 2) { + simpleParameters.Delete (2); + } + + + HBLObjectRef iterator_substrate = _ProcessAnArgumentByType (*GetIthParameter(0UL), ASSOCIATIVE_LIST | MATRIX, current_program, ¶meters); + + _ElementaryCommand * advance_command = current_program.GetIthCommand(simpleParameters.get (0)); + + if (!advance_command || advance_command->code != HY_HBL_COMMAND_ADVANCE_ITERATOR) { + throw _String ("Iterator init command is not linked with an advance command"); + } + + advance_command->parameters.DeleteTail(advance_command->simpleParameters.get (1)); + + if (iterator_substrate->ObjectClass() == ASSOCIATIVE_LIST) { + _AssociativeList* source_object = (_AssociativeList*)iterator_substrate; + simpleParameters[1] = ASSOCIATIVE_LIST; // indicate that this is an ASSOCIATIVE_LIST + simpleParameters << (long) new AVLListXLIterator (source_object->ListIterator ()); + } else { // MATRIX + simpleParameters[1] = MATRIX; // indicate that tjis is a MATRIX + } + } catch (const _String& error) { + return _DefaultExceptionHandler (nil, error, current_program); + } + + return true; +} + +//____________________________________________________________________________________ + +bool _ElementaryCommand::HandleAdvanceIterator(_ExecutionList& current_program) { + /* + parameters: + [0-2] -> Id of the variable to store stuff in + [+1] -> the source object + [+2] -> _Variable to store the value in + [+3] -> _Variable to store key/index in (could be nil) + [+4] -> _Variable to store column index in (if the object is _Matrix) + + + + simpleParameters: + [0] -> index of the iterator init command in current_program + [1] -> number of receptable variables + [2] -> for _Matrix iterator, the row index + [3] -> for _Matrix iterator, the column index +*/ + current_program.advance(); + try { + + long reciever_count = simpleParameters.get (1); + + _ElementaryCommand * init_command = current_program.GetIthCommand(simpleParameters.get (0)); + if (!init_command || init_command->code != HY_HBL_COMMAND_INIT_ITERATOR) { + throw (_String ("Iterator advance command is not linked with an iterator initiaizer")); + } + + bool is_matrix = init_command->simpleParameters.get (1) == MATRIX; + bool first_in = false; + if (!is_matrix && reciever_count == 3) { + throw (_String ("Iterators over dictionaries do not support the 3 argument form")); + } + + if (parameters.countitems () == reciever_count || parameters.GetItem(reciever_count) != init_command->parameters.GetItem(1)) { + parameters.DeleteTail (reciever_count, true); + parameters << init_command->parameters.GetItem(1); + first_in = true; + for (long k = 0L; k < reciever_count; k++) { + parameters << _ValidateStorageVariable (current_program, k); + } + if (is_matrix) { + if (simpleParameters.countitems() == 2) { + simpleParameters << 0 << 0; + } else { + simpleParameters[2] = 0; + simpleParameters[3] = 0; + } + } + } + + if (is_matrix) { + _Matrix* source_object = (_Matrix*)parameters.GetItem (reciever_count); + long row = simpleParameters.get (2), + column = simpleParameters.get (3); + + if (!first_in) { + column ++; + if (column >= source_object->GetVDim()) { + column = 0; + row ++; + } + } + + if (row >= source_object->GetHDim()) { + ((_Variable*)parameters.GetItem (reciever_count << 1))->SetValue (new _MathObject, false, false); + } else { + ((_Variable*)parameters.GetItem (reciever_count << 1))->SetValue (source_object->GetMatrixCell(row, column), false, false); + if (reciever_count == 2) { + ((_Variable*)parameters.GetItem (reciever_count+1))->SetValue (new _Constant (row*source_object->GetVDim () + column), false, false); + } else if (reciever_count == 3) { + ((_Variable*)parameters.GetItem (reciever_count+1))->SetValue (new _Constant (row), false, false); + ((_Variable*)parameters.GetItem (reciever_count+2))->SetValue (new _Constant (column ), false, false); + } + } + + simpleParameters[2] = row; + simpleParameters[3] = column; + + + + } else { + AVLListXLIterator * it = (AVLListXLIterator *)init_command->simpleParameters.get (2); + if (first_in) { + it->begin(); + } else { + ++(*it); + } + if (!it->is_done()) { // iterator not finished + AVLListXLIteratorKeyValue state = *(*it); + state.get_object()->AddAReference(); + if (reciever_count > 1) { + ((_Variable*)parameters.GetItem (reciever_count+2))->SetValue ((HBLObjectRef)state.get_object(), false, false); + ((_Variable*)parameters.GetItem (reciever_count+1))->SetValue (new _FString (*state.get_key()), false, false); + } else { + ((_Variable*)parameters.GetItem (reciever_count+1))->SetValue ((HBLObjectRef)state.get_object(), false, false); + } + } else { + ((_Variable*)parameters.GetItem (reciever_count << 1))->SetValue (new _MathObject, false, false); + // iterator done + } + } + } catch (const _String& error) { + return _DefaultExceptionHandler (nil, error, current_program); + } + + return true; +} + + //____________________________________________________________________________________ bool _ElementaryCommand::HandleRequireVersion(_ExecutionList& current_program){ current_program.advance(); diff --git a/src/core/formula.cpp b/src/core/formula.cpp index 88d700935..ffdabafe9 100644 --- a/src/core/formula.cpp +++ b/src/core/formula.cpp @@ -452,7 +452,7 @@ node* _Formula::InternalDifferentiate (node* currentSubExpression, l created_nodes [2] = InternalDifferentiate (currentSubExpression->go_down(2), varID, varRefs, dydx, tgt); if (!created_nodes [2]) { - throw (4); + throw (3); } node* XtimesDY = new node; XtimesDY->add_node (*created_nodes [2],*DuplicateFormula (currentSubExpression->go_down(1),tgt)); diff --git a/src/core/fstring.cpp b/src/core/fstring.cpp index 9828a455f..fb52c03fc 100644 --- a/src/core/fstring.cpp +++ b/src/core/fstring.cpp @@ -684,6 +684,11 @@ HBLObjectRef _FString::ExecuteSingleOp (long opCode, _List* arguments, _hyExecut t = &(new _StringBuffer)->SanitizeForRegExAndAppend(get_str()); break; } + + case 7L: { + t = &(*(new _StringBuffer) << get_str().ConvertToAnIdent(fIDAllowCompound)); + break; + } default: t = new _String( get_str().ChangeCase(kStringLowerCase)); diff --git a/src/core/global_things.cpp b/src/core/global_things.cpp index 6711d763a..41dcafb9b 100644 --- a/src/core/global_things.cpp +++ b/src/core/global_things.cpp @@ -58,6 +58,7 @@ #include #include +//#define __HYPHY_MPI_MESSAGE_LOGGING__ using namespace hy_env; @@ -119,7 +120,7 @@ namespace hy_global { kErrorStringDatasetRefIndexError ("Dataset index reference out of range"), kErrorStringMatrixExportError ("Export matrix called with a non-polynomial matrix argument"), kErrorStringNullOperand ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"), - kHyPhyVersion = _String ("2.5.6"), + kHyPhyVersion = _String ("2.5.7"), kNoneToken = "None", kNullToken = "null", diff --git a/src/core/include/avllistxl_iterator.h b/src/core/include/avllistxl_iterator.h index 96e0e4e76..fa714f763 100644 --- a/src/core/include/avllistxl_iterator.h +++ b/src/core/include/avllistxl_iterator.h @@ -42,6 +42,8 @@ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. #include "avllistxl.h" +#define AVL_LISTXL_ITERATOR_ENDINDEX (-1L) + //_____________________________________________________________________________ class AVLListXLIteratorKeyValue { @@ -135,6 +137,10 @@ class AVLListXLIterator { * Return an object pointed to by the iterator * @return the object pointed to by the iterator */ + + bool is_done (void) const { + return current_location == AVL_LISTXL_ITERATOR_ENDINDEX; + } }; diff --git a/src/core/include/batchlan.h b/src/core/include/batchlan.h index 27859e25e..37df1f34d 100644 --- a/src/core/include/batchlan.h +++ b/src/core/include/batchlan.h @@ -286,7 +286,9 @@ class _ElementaryCommand: public _String // string contains the literal for th bool HandleDoSQL (_ExecutionList&); bool HandleFscanf (_ExecutionList&, bool is_sscanf = false); bool HandleChoiceList (_ExecutionList&); - + bool HandleInitializeIterator (_ExecutionList&); + bool HandleAdvanceIterator (_ExecutionList&); + long get_code (void) const { return code; }; unsigned long parameter_count (void) const { return parameters.countitems();} @@ -691,8 +693,9 @@ void RetrieveModelComponents (long, _Variable*&, _Variable*&, bool &); void ReadModelList (void); _String ProcessStringArgument (_String* data); -const _String _hblCommandAccessor (_ExecutionList*, long); -_String _HYGenerateANameSpace (void); +const _String _hblCommandAccessor (_ExecutionList*, long); +_String const _HYGenerateANameSpace (void); +void _HYClearANameSpace (_String const&); HBLObjectRef ProcessAnArgumentByType (_String const*, _VariableContainer const*, long, _ExecutionList* = nil); diff --git a/src/core/include/defines.h b/src/core/include/defines.h index 83d373fc4..f650d006f 100644 --- a/src/core/include/defines.h +++ b/src/core/include/defines.h @@ -315,8 +315,8 @@ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. #define HY_HBL_COMMAND_REPLICATE_CONSTRAINT 565L #define HY_HBL_COMMAND_NESTED_LIST 566L #define HY_HBL_COMMAND_KEYWORD_ARGUMENT 567L - - +#define HY_HBL_COMMAND_INIT_ITERATOR 568L +#define HY_HBL_COMMAND_ADVANCE_ITERATOR 569L //! HyPhy standard directory locations diff --git a/src/core/include/list.h b/src/core/include/list.h index 7d9dacd49..562ccef8f 100644 --- a/src/core/include/list.h +++ b/src/core/include/list.h @@ -282,6 +282,12 @@ class _List:public _SimpleList { */ void Delete(long, bool = true); + /** + * Delete all items from the starting position to the end of the list + * if the bool flag is false, then only remove the reference to the object + */ + void DeleteTail (long, bool = true); + /** */ virtual void Duplicate(BaseRefConst); diff --git a/src/core/include/matrix.h b/src/core/include/matrix.h index 1f337e5fc..22b5a7a9e 100644 --- a/src/core/include/matrix.h +++ b/src/core/include/matrix.h @@ -437,7 +437,8 @@ class _Matrix: public _MathObject { if the matrix is sparse, only will out the non-void entries */ - _Formula* GetFormula (long, long) const; + _Formula* GetFormula (long, long) const; + HBLObjectRef GetMatrixCell (long, long) const; HBLObjectRef MultByFreqs (long); HBLObjectRef EvaluateSimple (_Matrix* existing_receptacle = nil); HBLObjectRef SortMatrixOnColumn (HBLObjectRef); diff --git a/src/core/include/parser.h b/src/core/include/parser.h index 0ed76c7a9..fd3a85f71 100644 --- a/src/core/include/parser.h +++ b/src/core/include/parser.h @@ -115,7 +115,7 @@ void DeleteVariable (long, bool deleteself, bool do_checks = true); void SetVariablesToOwnValues (_AVLList const & indices); -void DeleteTreeVariable (long, _SimpleList&); +void DeleteTreeVariable (long, _SimpleList&, _String * prefix = nil, bool return_leftovers = true); template void DoForEachVariable(ACTION do_this) { diff --git a/src/core/likefunc.cpp b/src/core/likefunc.cpp index 72792e648..ee0656f8f 100644 --- a/src/core/likefunc.cpp +++ b/src/core/likefunc.cpp @@ -1357,8 +1357,6 @@ long _LikelihoodFunction::SetAllIndependent (_Matrix* v) { for (long k = 0; k < upto; k++) { set_this_many += CheckAndSetIthIndependent (k, v->theData[k]); } - //ObjectToConsole(v); - return set_this_many; } @@ -5039,7 +5037,8 @@ hyFloat _LikelihoodFunction::SetParametersAndCompute (long index, hyFloat value, return -INFINITY; }*/ _Matrix newValue (*baseLine); - newValue.AplusBx (*direction, value); + if (value > 0.) + newValue.AplusBx (*direction, value); SetAllIndependent (&newValue); } @@ -5164,16 +5163,23 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle if (verbosity_level > 100) { char buf [512]; - snprintf (buf, sizeof(buf), "\n\t[_LikelihoodFunction::Bracket (index %ld, eval %ld) INITIAL BRACKET %15.12g <= %15.12g (current %15.12g) <= %15.12g]", index, likeFuncEvalCallCount, middle-leftStep, middle, index>=0?GetIthIndependent (index):0.0, middle+rightStep); + snprintf (buf, sizeof(buf), "\n\t[_LikelihoodFunction::Bracket (index %ld, eval %ld) INITIAL BRACKET %15.12g <= %15.12g (current %15.12g) <= %15.12g]\n", index, likeFuncEvalCallCount, middle-leftStep, middle, index>=0?GetIthIndependent (index):0.0, middle+rightStep); BufferToConsole (buf); + + if (index < 0) { + printf ("[Bracket bounds %g - %g (%g)/%g]\n", lowerBound, upperBound, practicalUB, middle); + for (unsigned long i = 0; i < indexInd.lLength; i++) { + printf ("Gradient for %s is %.16g @ %.16g\n", GetIthIndependentVar(i)->GetName()->get_str(), gradient->get_direct(i), GetIthIndependent(i)); + } + } } while (1) { - while (middle-leftStep < lowerBound) { + while (middle-leftStep <= lowerBound) { if (verbosity_level > 100) { char buf [512]; - snprintf (buf, sizeof(buf), "\n\t[_LikelihoodFunction::Bracket (index %ld) HANDLING LEFT BOUNDARY CASES] : LB = %g, current try = %g, current evaluated midpoint value = %g (%s)", index, lowerBound, middle-leftStep, middleValue, first ? "first" : "NOT first"); + snprintf (buf, sizeof(buf), "\n\t[_LikelihoodFunction::Bracket (index %ld) HANDLING LEFT BOUNDARY CASES] : LB = %g, current try = %.16g, current evaluated midpoint value = %.16g (%s)", index, lowerBound, middle-leftStep, middleValue, first ? "first" : "NOT first"); BufferToConsole (buf); } @@ -5181,14 +5187,18 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle if ( leftStep= 0 || index < 0 && leftStep < STD_GRAD_STEP) { if (!first) { if (go2Bound) { - middle = lowerBound==0.0 ? PERTURBATION_OF_ZERO : lowerBound; + middle = 0.0; + middleValue = stash_middle = SetParametersAndCompute (index, 0.0, ¤tValues, gradient); if (verbosity_level > 100) { char buf [512]; - snprintf (buf, sizeof(buf), "\n\t[_LikelihoodFunction::Bracket LEFT BOUNDARY (index %ld) UPDATED middle from %15.12g to %15.12g, LogL = %15.12g]", index, middle, middleValue); + snprintf (buf, sizeof(buf), "\n\t[_LikelihoodFunction::Bracket LEFT BOUNDARY (index %ld) UPDATED middle to %15.12g, LogL = %15.12g]", index, middle, middleValue); BufferToConsole (buf); } - middleValue = stash_middle = SetParametersAndCompute (index, middle, ¤tValues, gradient); - + /* + if (index < 0) { + _TerminateAndDump(_String ("Failed to improve the log likelihood with gradient descent: ") & _String ((_String*)gradient->toStr())); + } + */ } return -2; } else { @@ -5199,7 +5209,7 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle } - while (rightStep+middle > upperBound) { + while (rightStep+middle >= upperBound) { rightStep*=.125; if (rightStep= 10 || index < 0 && rightStep < STD_GRAD_STEP) { if (!first) { @@ -5467,8 +5477,10 @@ HBLObjectRef _LikelihoodFunction::CovarianceMatrix (_SimpleList* parameterList _Matrix * sigLevels = new _Matrix (parameter_count,7,false,true); // find the appropriate significance level for chi2 + + _String unique_prefix = _HYGenerateANameSpace (); - _String xxc = _HYGenerateANameSpace () & (".x"); + _String xxc = unique_prefix & (".x"); thisVar = CheckReceptacle (&xxc, kEmptyString); thisVar->SetBounds (-1.e30,1.e30); @@ -5598,6 +5610,7 @@ HBLObjectRef _LikelihoodFunction::CovarianceMatrix (_SimpleList* parameterList DoneComputing(); DeleteVariable(thisVar->get_index(), true, false); + _HYClearANameSpace(unique_prefix); return sigLevels; } @@ -5922,6 +5935,7 @@ void _LikelihoodFunction::ComputeGradient (_Matrix& gradient, hyFloat& gradi if (gradientStep==0) return;*/ + if (order==1) { funcValue = Compute(); for (long index=0; index 100) { + printf ("Gradient step for %s is %.16g @%.16g %\n", GetIthIndependentVar(index)->GetName()->get_str(), testStep, currentValue); + }*/ SetIthIndependent(index,currentValue+testStep); gradient[index]=(Compute()-funcValue)/testStep; + if (gradient.theData[index] > 1000.) { + gradient.theData[index] = 1000.; + } else if (gradient.theData[index] < -1000.) { + gradient.theData[index] = -1000.; + } SetIthIndependent(index,currentValue); } else { gradient[index]= 0.; } - - /*if (verbosity_level > 50) - { - printf ("[GRADIENT @ %s, [%g-%g-%g], %g. der = %g]\n", cv->GetName()->sData, lb, currentValue, ub, testStep, gradient[index]); - }*/ } } + /*hyFloat scaler = gradient.AbsValue(); + if (scaler > 1.e2) + gradient *= 10./(scaler);*/ + + /*_Matrix stash; + GetAllIndependent(stash); + _Matrix test (stash); + test.AplusBx(gradient, STD_GRAD_STEP); + SetAllIndependent(&test); + hyFloat testv = Compute(); + if (testv < funcValue) { + _TerminateAndDump("Gradient fubar"); + } else { + printf ("<><><>GRADIENT CHECK %.16g to %.16g<><><>\n", funcValue, testv); + } + SetAllIndependent (&stash);*/ + } else { for (long index=0; index 10.) { + bp = gPrecision / bp; + } else { + bp = gPrecision * 0.1; + } //ObjectToConsole(&bestVal); _Matrix left_vector ; @@ -6546,7 +6585,7 @@ void _LikelihoodFunction::GradientDescent (hyFloat& gPrecision, _Matrix& best } if (maxSoFar < initialValue && !CheckEqual (maxSoFar, initialValue, 100. * kMachineEpsilon)) { - _TerminateAndDump(_String (" _LikelihoodFunction::GradientLocateTheBump: in the Brent loop iteration ") & long(outcome) & ". " & _String (maxSoFar, "%18.16g") & " / " & _String (initialValue,"%18.16g") & ".\n"); + _TerminateAndDump(_String (" _LikelihoodFunction::GradientLocateTheBump: in the Brent loop iteration ") & long(outcome) & ". " & _String (maxSoFar, "%18.16g") & " / " & _String (initialValue,"%18.16g") & ".\n Optimization direction: \n" & _String ((_String*)gradient.toStr()) ); return; } @@ -6605,162 +6644,167 @@ void _LikelihoodFunction::LocateTheBump (long index,hyFloat gPrecision, hyFlo unsigned long bracketCount = likeFuncEvalCallCount - inCount; if (outcome != -1) { // successfull bracket - if (right - left < 4*brentPrec) { - brentPrec = (right-left) * 0.2; - //printf ("\nResetting brentPrec to %g\n", brentPrec, "\n"); - } - - hyFloat U,V,W,X=middle,E=0.,FX,FW,FV,XM,R,Q,P,ETEMP,D=0.,FU; - W = middle; - V = middle; - FX = -middleValue; - FV = FX; - FW = FX; - outcome = 0; + if (outcome == -2) { // boundary case; leave the value where it is + maxSoFar = middleValue; + } else { + if (right - left < 4*brentPrec) { + brentPrec = (right-left) * 0.2; + //printf ("\nResetting brentPrec to %g\n", brentPrec, "\n"); + } + + + hyFloat U,V,W,X=middle,E=0.,FX,FW,FV,XM,R,Q,P,ETEMP,D=0.,FU; + W = middle; + V = middle; + FX = -middleValue; + FV = FX; + FW = FX; + outcome = 0; - while (outcome < 20) { - XM = .5*(left+right); + while (outcome < 20) { + XM = .5*(left+right); - bool parabolic_step = false; + bool parabolic_step = false; - if (verbosity_level > 50) { - char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) (current max = %15.12g) GOLDEN RATIO INTERVAL CHECK: %g <= %g (%g = %g) <= %g, span = %g]", index, -FX, left, XM, X, fabs(X-XM), right, right-left); - BufferToConsole (buf); - } + if (verbosity_level > 50) { + char buf [256]; + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) (current max = %15.12g) GOLDEN RATIO INTERVAL CHECK: %g <= %g (%g = %g) <= %g, span = %g]", index, -FX, left, XM, X, fabs(X-XM), right, right-left); + BufferToConsole (buf); + } - if (fabs(X-XM) <= brentPrec && outcome > 0) { - break; - } + if (fabs(X-XM) <= brentPrec && outcome > 0) { + break; + } - hyFloat tol1 = fabs (X) * Minimum (brentPrec, 1e-7) + kMachineEpsilon, - tol2 = 2.*tol1; + hyFloat tol1 = fabs (X) * Minimum (brentPrec, 1e-7) + kMachineEpsilon, + tol2 = 2.*tol1; - if (fabs(E)>tol1) { - R = (X-W)*(FX-FV); - Q = (X-V)*(FX-FW); - P = (X-V)*Q-(X-W)*R; - Q = 2.0 * (Q-R); - if (Q>0.) { - P = -P; - } - Q = fabs(Q); - ETEMP = E; - E = D; - if (!(fabs (P) > fabs (.5*Q*ETEMP) || P <= Q * (left-X) || P >= Q *( right-X))) { - parabolic_step = true; - D = P/Q; - U = X+D; - if (U - left< tol2 || right - U < tol2) { - D = (XM - X >= 0.) ? tol1 : -tol1; - } + if (fabs(E)>tol1) { + R = (X-W)*(FX-FV); + Q = (X-V)*(FX-FW); + P = (X-V)*Q-(X-W)*R; + Q = 2.0 * (Q-R); + if (Q>0.) { + P = -P; + } + Q = fabs(Q); + ETEMP = E; + E = D; + if (!(fabs (P) > fabs (.5*Q*ETEMP) || P <= Q * (left-X) || P >= Q *( right-X))) { + parabolic_step = true; + D = P/Q; + U = X+D; + if (U - left< tol2 || right - U < tol2) { + D = (XM - X >= 0.) ? tol1 : -tol1; + } + } } - } - - if (!parabolic_step) { - E = (X >= XM ? left : right) - X; - D = GOLDEN_RATIO_C * E; - } - U = fabs (D) >= tol1 ? X + D : X + (D > 0. ? tol1 : -tol1); + if (!parabolic_step) { + E = (X >= XM ? left : right) - X; + D = GOLDEN_RATIO_C * E; + } - //U = X + D; - SetIthIndependent (index,U); - FU = -Compute(); + U = fabs (D) >= tol1 ? X + D : X + (D > 0. ? tol1 : -tol1); - if (verbosity_level > 50) { - char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) GOLDEN RATIO TRY: param %20.16g, log L %20.16g]", index, U, -FU); - BufferToConsole (buf); - } + //U = X + D; + SetIthIndependent (index,U); + FU = -Compute(); - if (FU<=FX) { // value at U is the new minimum if (verbosity_level > 50) { char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (eval %ld) ACCEPT new try, confirm value %20.16g (delta = %20.16g)", likeFuncEvalCallCount, GetIthIndependent(index), FX-FU); + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) GOLDEN RATIO TRY: param %20.16g, log L %20.16g]", index, U, -FU); BufferToConsole (buf); } - if (U>=X) { - left = X; - } else { - right = X; - } - V = W; - FV = FW; - W = X; - FW = FX; - X = U; - FX = FU; - } else { // value at X remains the minimum - if (verbosity_level > 50) { - char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (eval %ld) REJECT new try (%20.16g) (delta = %20.16g)", likeFuncEvalCallCount, U, FX-FU); - BufferToConsole (buf); - } + if (FU<=FX) { // value at U is the new minimum + if (verbosity_level > 50) { + char buf [256]; + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (eval %ld) ACCEPT new try, confirm value %20.16g (delta = %20.16g)", likeFuncEvalCallCount, GetIthIndependent(index), FX-FU); + BufferToConsole (buf); + } - if (U < X) { - left = U; - } else { - right = U; - } - if (FU<=FW || W==X) { + if (U>=X) { + left = X; + } else { + right = X; + } V = W; FV = FW; - W = U; - FW = FU; - } else { - if (FU<=FV || V==X || V==W) { - V = U; - FV = FU; + W = X; + FW = FX; + X = U; + FX = FU; + } else { // value at X remains the minimum + if (verbosity_level > 50) { + char buf [256]; + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (eval %ld) REJECT new try (%20.16g) (delta = %20.16g)", likeFuncEvalCallCount, U, FX-FU); + BufferToConsole (buf); } - } - } - outcome++; - } + if (U < X) { + left = U; + } else { + right = U; + } + if (FU<=FW || W==X) { + V = W; + FV = FW; + W = U; + FW = FU; + } else { + if (FU<=FV || V==X || V==W) { + V = U; + FV = FU; + } + } + } + outcome++; - if (verbosity_level > 50) { - char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) GOLDEN RATIO SEARCH SUCCESSFUL: precision %g, parameter moved from %15.12g to %15.12g, Log L new/old = %15.12g/%15.12g ]\n\n", index, brentPrec, bestVal, X, -FX, maxSoFar); - BufferToConsole (buf); - } - middleValue = -FX; - middle = X; + } - if (middleValue 50) { - char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) RESETTING THE VALUE (worse log likelihood obtained; current value %20.16g, best value %20.16g) ]\n\n", index, GetIthIndependent(index), bestVal); - BufferToConsole (buf); - } - if (CheckEqual(GetIthIndependent(index), bestVal) && fabs (middleValue-maxSoFar) > 1e-9) { - char buf[256]; - snprintf (buf, 256, " \n\tERROR: [_LikelihoodFunction::LocateTheBump (index %ld) current value %20.16g (parameter = %20.16g), best value %20.16g (parameter = %20.16g)); delta = %20.16g ]\n\n", index, middleValue, GetIthIndependent(index), maxSoFar, bestVal, maxSoFar - middleValue); - _TerminateAndDump (_String (buf) & "\n" & "\nParameter name " & *GetIthIndependentName(index)); + char buf [256]; + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) GOLDEN RATIO SEARCH SUCCESSFUL: precision %g, parameter moved from %15.12g to %15.12g, Log L new/old = %15.12g/%15.12g ]\n\n", index, brentPrec, bestVal, X, -FX, maxSoFar); + BufferToConsole (buf); } - SetIthIndependent(index,bestVal); - } else { - if (!CheckEqual(GetIthIndependent(index),middle)) { + middleValue = -FX; + middle = X; + + if (middleValue 50) { - char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) moving parameter value (should trigger LL update) %15.12g to %15.12g ]\n\n", index, GetIthIndependent(index), middle); - BufferToConsole (buf); + char buf [256]; + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) RESETTING THE VALUE (worse log likelihood obtained; current value %20.16g, best value %20.16g) ]\n\n", index, GetIthIndependent(index), bestVal); + BufferToConsole (buf); } - SetIthIndependent (index,middle); + if (CheckEqual(GetIthIndependent(index), bestVal) && fabs (middleValue-maxSoFar) > 1e-9) { + char buf[256]; + snprintf (buf, 256, " \n\tERROR: [_LikelihoodFunction::LocateTheBump (index %ld) current value %20.16g (parameter = %20.16g), best value %20.16g (parameter = %20.16g)); delta = %20.16g ]\n\n", index, middleValue, GetIthIndependent(index), maxSoFar, bestVal, maxSoFar - middleValue); + _TerminateAndDump (_String (buf) & "\n" & "\nParameter name " & *GetIthIndependentName(index)); + } + SetIthIndependent(index,bestVal); } else { - if (verbosity_level > 50) { - char buf [256]; - snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) KEEPS parameter value (no LL update) %15.12g == %15.12g ]\n\n", index, GetIthIndependent(index), middle); - BufferToConsole (buf); + if (!CheckEqual(GetIthIndependent(index),middle)) { + if (verbosity_level > 50) { + char buf [256]; + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) moving parameter value (should trigger LL update) %15.12g to %15.12g ]\n\n", index, GetIthIndependent(index), middle); + BufferToConsole (buf); + } + SetIthIndependent (index,middle); + } else { + if (verbosity_level > 50) { + char buf [256]; + snprintf (buf, 256, "\n\t[_LikelihoodFunction::LocateTheBump (index %ld) KEEPS parameter value (no LL update) %15.12g == %15.12g ]\n\n", index, GetIthIndependent(index), middle); + BufferToConsole (buf); + } } + maxSoFar = middleValue; } - maxSoFar = middleValue; } } diff --git a/src/core/list.cpp b/src/core/list.cpp index 8bb8e6cbd..6b145a7c9 100644 --- a/src/core/list.cpp +++ b/src/core/list.cpp @@ -411,6 +411,21 @@ void _List::Delete (long index, bool delete_object) } +// Delete item at index (>=0) +void _List::DeleteTail (long from, bool delete_object) { + if (from>=0 && from= from; k--) { + DeleteObject (((BaseRef*)list_data)[k]); + } + lLength = from; + //memcpy ((hyPointer)list_data+sizeof(BaseRef)*(index),(hyPointer)list_data+sizeof(BaseRef)*(index+1),sizeof(BaseRef)*(lLength-index)); + } + + _UpdateStorageType(); + +} + // Delete item at index (>=0) void _List::DeleteList (const _SimpleList& toDelete) { diff --git a/src/core/matrix.cpp b/src/core/matrix.cpp index 34b3e0d13..329d1c6a3 100644 --- a/src/core/matrix.cpp +++ b/src/core/matrix.cpp @@ -3308,16 +3308,14 @@ void _Matrix::Multiply (_Matrix& storage, hyFloat c) _Constant * cc = new _Constant (c); if (storageType == 2) { - _String star ('*'); - _Operation * cOp = new _Operation (cc), - * mOp = new _Operation (star,2); + _String const star ('*'); for (long i=0; iGetList().AppendNewInstance (cOp); - f->GetList().AppendNewInstance (mOp); + f->GetList().AppendNewInstance (new _Operation (cc)); + f->GetList().AppendNewInstance (new _Operation (star,2)); } } else { if (storageType != 3) { @@ -5022,7 +5020,15 @@ HBLObjectRef _Matrix::MAccess (HBLObjectRef p, HBLObjectRef p2) { } if (ind2>=0) { // element access - if (storageType == 2) { // formulas + return GetMatrixCell (ind1, ind2); + } + + return new _Constant (0.0); +} + +//_____________________________________________________________________________________________ +HBLObjectRef _Matrix::GetMatrixCell (long ind1, long ind2) const { + if (storageType == _FORMULA_TYPE) { // formulas if (!theIndex) { _Formula * entryFla = (((_Formula**)theData)[ind1*vDim+ind2]); if (entryFla) { @@ -5061,11 +5067,9 @@ HBLObjectRef _Matrix::MAccess (HBLObjectRef p, HBLObjectRef p2) { return cell; } } - } - - return new _Constant (0.0); } + //_____________________________________________________________________________________________ _Formula* _Matrix::GetFormula (long ind1, long ind2) const { diff --git a/src/core/operation.cpp b/src/core/operation.cpp index 1b16f5bb8..4e80deb19 100644 --- a/src/core/operation.cpp +++ b/src/core/operation.cpp @@ -259,9 +259,7 @@ _Operation::_Operation (bool isVar, _String& stuff, bool isG, _VariableContaine //__________________________________________________________________________________ -_Operation::~_Operation (void) -{ - +_Operation::~_Operation (void) { if (theNumber) { DeleteObject (theNumber); } diff --git a/src/core/parser.cpp b/src/core/parser.cpp index 3a6ba7f95..89cdfb6fd 100644 --- a/src/core/parser.cpp +++ b/src/core/parser.cpp @@ -442,7 +442,7 @@ void DeleteVariable (long dv, bool deleteself, bool do_checks) { } //__________________________________________________________________________________ -void DeleteTreeVariable (long tree_variable_index, _SimpleList & parms) { +void DeleteTreeVariable (long tree_variable_index, _SimpleList & parms, _String * prefix, bool leftovers) { if (tree_variable_index>=0) { /* @@ -452,7 +452,7 @@ void DeleteTreeVariable (long tree_variable_index, _SimpleList & parms) { */ - _String const *tree_name = (_String const*)variableNames.Retrieve (tree_variable_index), + _String const *tree_name = prefix ? prefix : (_String const*)variableNames.Retrieve (tree_variable_index), kDot = ".", tree_prefix = *tree_name&kDot; @@ -528,11 +528,19 @@ void DeleteTreeVariable (long tree_variable_index, _SimpleList & parms) { UpdateChangingFlas(all_subdomain_indices); // reset compiled formulas that may contain variable indices being deleted - SetVariablesToOwnValues (will_keep_these); + if (leftovers) { + SetVariablesToOwnValues (will_keep_these); + } else { + indices_to_delete << parms; + } + if (touched_dependent_variables.countitems()) { SetVariablesToOwnValues (touched_dependent_variables); } + /*if (prefix) { + printf ("CLEARING %d variables\n", indices_to_delete.countitems() ); + }*/ indices_to_delete.Each ([] (long var_idx, unsigned long) -> void { _Variable * delvar = LocateVar (var_idx); diff --git a/src/core/strings.cpp b/src/core/strings.cpp index 590bd6704..fc7a30b91 100644 --- a/src/core/strings.cpp +++ b/src/core/strings.cpp @@ -50,14 +50,10 @@ #include "hy_string_buffer.h" -_String compileDate = __DATE__, - __HYPHY__VERSION__ = _String ("2.5.6"); +_String compileDate = __DATE__; using namespace hy_global; - - - struct _hy_Valid_ID_Chars_Type { unsigned char valid_chars[256]; diff --git a/src/core/variable.cpp b/src/core/variable.cpp index dd9e289ce..836c1f325 100644 --- a/src/core/variable.cpp +++ b/src/core/variable.cpp @@ -431,6 +431,9 @@ void _Variable::SetValue (HBLObjectRef theP, bool dup, bool do_checks) { // set } if (theValueupperBound) { + /*if (verbosity_level >= 100) { + printf ("\n<========== OUT OF BOUNDS FOR VARIABLE %s : value %.16g, range [%.16g, %.16g] =========>\n" , theName->get_str(), theValue, lowerBound, upperBound); + }*/ if (theValue <= lowerBound+1e-50) { theValue = lowerBound; } else { diff --git a/src/utils/hyphyunixutils.cpp b/src/utils/hyphyunixutils.cpp index cd4b9fee7..4d83d30ae 100644 --- a/src/utils/hyphyunixutils.cpp +++ b/src/utils/hyphyunixutils.cpp @@ -224,7 +224,7 @@ void ObjectToConsole (BaseRef obj, void * extra) { #ifdef __HYPHYMPI__ //__________________________________________________________________________________ -void mpiNormalLoop (int rank, int size, _String & baseDir) +void mpiNormalLoop (int rank, int size, _String & baseDir) { long senderID = 0; @@ -232,6 +232,8 @@ void mpiNormalLoop (int rank, int size, _String & baseDir) _String* theMessage = MPIRecvString (-1,senderID); // listen for messages from any node _StringBuffer * resStr = nil; + + //int loop_count = 0; while (theMessage->nonempty()) { hy_env :: EnvVariableSet (hy_env ::mpi_node_id, new _Constant (rank), false); @@ -256,6 +258,7 @@ void mpiNormalLoop (int rank, int size, _String & baseDir) } else { if (theMessage->BeginsWith ("#NEXUS")) { _String msgCopy (*theMessage); + //printf ("\n\nMPI Node %d; message \n %s\n", rank, theMessage->get_str()); ReportWarning ("[MPI] Received a likelihood function"); //ReportWarning (msgCopy); ReadDataSetFile (nil,true,theMessage); @@ -286,9 +289,14 @@ void mpiNormalLoop (int rank, int size, _String & baseDir) } } else { //ReportWarning(_String ("[MPI] Received commands\n") & *theMessage & "\n"); + //printf ("\n\nMPI Node %d; message \n %s\n", rank, theMessage->get_str()); + //printf ("\n\nMPI Node %d; likefuncs \n %s\n", rank, ((_String*)likeFuncNamesList.toStr())->get_str()); _ExecutionList exL (*theMessage); + + //ReportWarning (_String ((_String*)batchLanguageFunctionNames.toStr())); HBLObjectRef res = exL.Execute(); + //printf ("\n==>%d\n", hy_env::EnvVariableTrue (preserveSlaveNodeState)); if (res) { resStr = new _StringBuffer ((_String*)res->toStr()); } else { @@ -298,7 +306,16 @@ void mpiNormalLoop (int rank, int size, _String & baseDir) MPISendString(*resStr,senderID); + /*loop_count++; + printf ("\n\nMPI Node %d; variable array length %d\n", rank, variableNames.countitems()); + if (loop_count == 20) { + printf ("%s\n", ((_String*)variableNames.toStr())->get_str()); + abort(); + }*/ + + if (hy_env::EnvVariableTrue (preserveSlaveNodeState) == false) { + printf ("\n\nMPI Node %d; PURGING\n", rank); PurgeAll (true); InitializeGlobals (); PushFilePath(baseDir, false, false); diff --git a/tests/hbltests/Results/HIVSweden.out b/tests/hbltests/Results/HIVSweden.out index aa5076ebb..c61b27d9e 100644 --- a/tests/hbltests/Results/HIVSweden.out +++ b/tests/hbltests/Results/HIVSweden.out @@ -2,28 +2,28 @@ *** RUNNING SINGLE RATE MODEL *** ################################# ->Done in 2 seconds +>Done in 4 seconds --1137.68956410902 +-1137.68853135406 ----------------------------------- -dN/dS = 0.911942160103597 +dN/dS = 0.9061405978972703 *** RUNNING MODEL 1 (Neutral) *** ###################################### ->Done in 1 seconds +>Done in 3 seconds --1114.64193743151 +-1114.64193265268 ------------------------------------------------ -dN/dS = 0.5547174896006717 (sample variance = 0.2119990101724308) +dN/dS = 0.5548980976980185 (sample variance = 0.2120545595471635) -Rate[1]= 0.07861747 (weight=0.4832765) -Rate[2]= 1.00000000 (weight=0.5167235) +Rate[1]= 0.07848009 (weight=0.4830085) +Rate[2]= 1.00000000 (weight=0.5169915) ------------------------------------------------ @@ -37,215 +37,215 @@ Import the following part into a data processing program for further analysis -Rate/Site Rate=0.07861747394474425 Rate=1 -1 0.0004171756387820546 0.9995828243612179 -2 0.949611180423643 0.05038881957635705 -3 0.8529582665262366 0.1470417334737633 -4 0.9773633760259754 0.02263662397402449 -5 0.7092394317199029 0.2907605682800972 -6 0.9706897558751614 0.02931024412483861 -7 0.8414164703263 0.1585835296737001 -8 0.6451559578781774 0.3548440421218226 -9 0.009053093997565813 0.9909469060024342 -10 0.2520815880881419 0.747918411911858 -11 0.9364333332734404 0.06356666672655968 -12 0.8042918335986166 0.1957081664013834 -13 0.95939640123464 0.04060359876536005 -14 0.6834467195021842 0.3165532804978159 -15 0.9687681772026803 0.0312318227973196 -16 0.9687681772026803 0.0312318227973196 -17 0.949611180423643 0.05038881957635705 -18 0.09646765254675914 0.9035323474532408 -19 0.8049164583959884 0.1950835416040116 -20 0.4262277110914361 0.573772288908564 -21 0.00117010716164424 0.9988298928383559 -22 0.001185885671369777 0.9988141143286303 -23 0.949611180423643 0.05038881957635705 -24 7.114291691814195e-05 0.9999288570830819 -25 0.8602756841775846 0.1397243158224154 -26 2.254023116609902e-05 0.999977459768834 -27 0.7161023719541011 0.283897628045899 -28 1.841502917909819e-08 0.9999999815849708 -29 0.9786485364590117 0.02135146354098819 -30 0.582686436699258 0.417313563300742 -31 0.002390526277210891 0.9976094737227892 -32 0.8414164703263 0.1585835296737001 -33 0.9364333332734404 0.06356666672655968 -34 0.6987750467418727 0.3012249532581273 -35 0.7790944916468581 0.2209055083531419 -36 0.01429371172876378 0.9857062882712362 -37 0.06361880439585066 0.9363811956041493 -38 0.6920562631865748 0.3079437368134252 -39 0.001928852282323563 0.9980711477176765 -40 0.003983409392734671 0.9960165906072653 -41 0.5303647162053932 0.4696352837946067 -42 0.8386350866813885 0.1613649133186115 -43 0.5925778177481617 0.4074221822518382 -44 0.2090344698105323 0.7909655301894677 -45 0.4821621443281067 0.5178378556718933 -46 0.0186132834313224 0.9813867165686775 -47 0.7641182996309834 0.2358817003690167 -48 0.1408545442834629 0.8591454557165371 -49 0.07692057903640417 0.9230794209635959 -50 0.5574343005631943 0.4425656994368057 -51 4.43894305142888e-06 0.9999955610569485 -52 0.9687681772026803 0.0312318227973196 -53 0.9339651771078613 0.06603482289213859 -54 0.05736048090793156 0.9426395190920684 -55 0.6742031250765356 0.3257968749234645 -56 0.9786485364590117 0.02135146354098819 -57 0.03651732125304075 0.9634826787469593 -58 0.9367559323807118 0.06324406761928837 -59 0.02371625697620915 0.9762837430237908 -60 0.7161023719541011 0.283897628045899 -61 0.2746100472926215 0.7253899527073786 -62 0.1724226760582058 0.8275773239417942 -63 0.06723211289807503 0.932767887101925 -64 0.1596925722997463 0.8403074277002537 -65 0.137719193721605 0.862280806278395 -66 2.859979909597426e-08 0.9999999714002009 -67 0.5393261114055373 0.4606738885944627 -68 0.0006659882940167302 0.9993340117059832 -69 2.893625055714912e-05 0.9999710637494429 -70 0.3241355652436183 0.6758644347563817 -71 0.2253810959593394 0.7746189040406605 -72 0.1625994437141345 0.8374005562858655 -73 0.1397520405558187 0.8602479594441813 -74 0.949611180423643 0.05038881957635705 -75 0.02467516020300521 0.9753248397969949 -76 6.461014423877886e-05 0.9999353898557611 -77 0.9716211799621152 0.02837882003788475 -78 0.7865525944924113 0.2134474055075888 -79 0.7335964702945454 0.2664035297054545 -80 0.9706897558751614 0.02931024412483861 -81 0.8613830849212658 0.1386169150787341 -82 0.7671107376950946 0.2328892623049054 -83 5.70998409009067e-05 0.9999429001590991 -84 0.006758971772704963 0.993241028227295 -85 0.9684512653381456 0.03154873466185435 -86 0.9687681772026803 0.0312318227973196 -87 1.538636892488436e-05 0.999984613631075 -88 0.7671107376950946 0.2328892623049054 -89 0.9317446770502245 0.06825532294977553 -90 0.03875792645356601 0.961242073546434 -91 0.5875108306075472 0.4124891693924528 +Rate/Site Rate=0.07848009442627751 Rate=1 +1 0.0004141627737393899 0.9995858372262606 +2 0.9495507761166344 0.05044922388336558 +3 0.8528260981220774 0.1471739018779226 +4 0.977336809418012 0.02266319058198787 +5 0.7090142858255384 0.2909857141744615 +6 0.9706531409883263 0.02934685901167367 +7 0.8412766164479658 0.1587233835520342 +8 0.6449123361581577 0.3550876638418423 +9 0.009012961357288882 0.9909870386427112 +10 0.2515729424244136 0.7484270575755865 +11 0.9363702099327275 0.06362979006727264 +12 0.8041053903906372 0.1958946096093627 +13 0.9593526850851177 0.04064731491488227 +14 0.6832046611929595 0.3167953388070405 +15 0.9687339067482328 0.03126609325176713 +16 0.9687339067482328 0.03126609325176713 +17 0.9495507761166344 0.05044922388336558 +18 0.09621979767807776 0.9037802023219222 +19 0.8047551995260132 0.1952448004739868 +20 0.4255908932311135 0.5744091067688865 +21 0.001160534715700721 0.9988394652842993 +22 0.001178358441974197 0.9988216415580258 +23 0.9495507761166344 0.05044922388336558 +24 7.044308679104039e-05 0.999929556913209 +25 0.8601400514212729 0.1398599485787271 +26 2.233330534975041e-05 0.9999776666946502 +27 0.7158774071585552 0.2841225928414448 +28 1.814572561314607e-08 0.9999999818542744 +29 0.978622387807438 0.021377612192562 +30 0.5824231418891556 0.4175768581108444 +31 0.00237558476150917 0.9976244152384909 +32 0.8412766164479658 0.1587233835520342 +33 0.9363702099327275 0.06362979006727264 +34 0.6981521129230133 0.3018478870769867 +35 0.7785774055196519 0.221422594480348 +36 0.0141997693474109 0.985800230652589 +37 0.06335483930146486 0.9366451606985351 +38 0.6914590641265288 0.3085409358734711 +39 0.001916542089042451 0.9980834579109574 +40 0.003957232945689599 0.9960427670543104 +41 0.5295988458779451 0.4704011541220548 +42 0.8384853845147031 0.161514615485297 +43 0.5922512023061266 0.4077487976938734 +44 0.2082494606050932 0.7917505393949068 +45 0.4813091605864432 0.5186908394135568 +46 0.01853010394262396 0.981469896057376 +47 0.7639285300172881 0.236071469982712 +48 0.1402915130084854 0.8597084869915146 +49 0.07646879613615927 0.9235312038638407 +50 0.5567010416920375 0.4432989583079625 +51 4.38781266231358e-06 0.9999956121873377 +52 0.9687339067482328 0.03126609325176713 +53 0.9338845331540193 0.06611546684598059 +54 0.0571100401353745 0.9428899598646255 +55 0.6735510244959739 0.3264489755040261 +56 0.978622387807438 0.021377612192562 +57 0.03636120456731126 0.9636387954326887 +58 0.9366812121781629 0.063318787821837 +59 0.02361036641878327 0.9763896335812168 +60 0.7158774071585552 0.2841225928414448 +61 0.2740565218601556 0.7259434781398444 +62 0.1720174591372408 0.8279825408627591 +63 0.06693903026898131 0.9330609697310187 +64 0.1590378602552624 0.8409621397447377 +65 0.1371440849894134 0.8628559150105867 +66 2.819790040501375e-08 0.9999999718020995 +67 0.539061732923397 0.460938267076603 +68 0.0006617027640124549 0.9993382972359874 +69 2.861976646572587e-05 0.9999713802335343 +70 0.3234993872541173 0.6765006127458828 +71 0.2248936280082245 0.7751063719917756 +72 0.1618837241544665 0.8381162758455335 +73 0.1393947929351173 0.8606052070648827 +74 0.9495507761166344 0.05044922388336558 +75 0.02456263811730525 0.9754373618826948 +76 6.397125781098976e-05 0.999936028742189 +77 0.9715858306482195 0.02841416935178053 +78 0.7863765522620176 0.2136234477379824 +79 0.73305042949157 0.2669495705084301 +80 0.9706531409883263 0.02934685901167367 +81 0.8612649202389893 0.1387350797610108 +82 0.766920094547312 0.233079905452688 +83 5.660497622357921e-05 0.9999433950237764 +84 0.006733024659336842 0.9932669753406631 +85 0.9684153079123856 0.03158469208761443 +86 0.9687339067482328 0.03126609325176713 +87 1.524578544240529e-05 0.9999847542145577 +88 0.766920094547312 0.233079905452688 +89 0.9316847221090162 0.06831527789098374 +90 0.03858887239454834 0.9614111276054517 +91 0.5872485448869876 0.4127514551130124 *** RUNNING MODEL 2 (Selection) *** ###################################### ->Done in 6 seconds +>Done in 8 seconds --1106.44530886821 +-1106.44559840278 ------------------------------------------------ -dN/dS = 1.12766514584006 (sample variance = 1.581198405980767) +dN/dS = 1.130650219340381 (sample variance = 1.591003529725344) -Rate[1]= 0.05908674 (weight=0.3752705) -Rate[2]= 1.00000000 (weight=0.4420542) -Rate[3]= 3.63178596 (weight=0.1826753) +Rate[1]= 0.05827256 (weight=0.3740950) +Rate[2]= 1.00000000 (weight=0.4431616) +Rate[3]= 3.64275352 (weight=0.1827434) ------------------------------------------------ Sites with dN/dS>1 (Posterior cutoff = 0.9) -26 (0.9068529264412361) -28 (0.999194331685321) -66 (0.9984647844038979) -87 (0.9855377532726842) +26 (0.9073875948114321) +28 (0.9992025678347832) +66 (0.9984914617477231) +87 (0.9856775436206967) ------------------------------------------------ Sites with dN/dS<=1 (Posterior cutoff = 0.9) -1 (0.50564337965482) -2 (0.0004635313656910933) -3 (0.005952924670428214) -4 (9.765520936665395e-05) -5 (0.03185639802201144) -6 (0.0001527036074198602) -7 (0.006988328973977571) -8 (0.05691838485498499) -9 (0.722460409856472) -10 (0.09688440510634511) -11 (0.0009287285296281832) -12 (0.01069736214711896) -13 (0.0004973370958702279) -14 (0.04005882941786322) -15 (0.0002246784862725794) -16 (0.0002246784862725794) -17 (0.0004635313656910933) -18 (0.4332343157975523) -19 (0.01167949265469138) -20 (0.03384753927105891) -21 (0.2479756329867343) -22 (0.7982428690533777) 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------------------------------------------------ @@ -256,95 +256,95 @@ Import the following part into a data processing program for further analysis -Rate/Site Rate=0.05908673874612212 Rate=1 Rate=3.631785964259932 -1 2.209886404949519e-05 0.4943345214811306 0.50564337965482 -2 0.8460161268297731 0.1535203418045359 0.0004635313656910933 -3 0.7178875037617195 0.2761595715678524 0.005952924670428214 -4 0.9027019402600399 0.09720040453059345 9.765520936665395e-05 -5 0.5835979970977249 0.3845456048802637 0.03185639802201144 -6 0.8879088189467084 0.1119384774458718 0.0001527036074198602 -7 0.7019780057351419 0.2910336652908806 0.006988328973977571 -8 0.5264685329089774 0.4166130822360376 0.05691838485498499 -9 0.001076642261722848 0.2764629478818052 0.722460409856472 -10 0.101532339047803 0.801583255845852 0.09688440510634511 -11 0.8199723700816371 0.1790989013887346 0.0009287285296281832 -12 0.6724953262661715 0.3168073115867096 0.01069736214711896 -13 0.8650858518136233 0.1344168110905064 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0.7005893332391919 0.2924459969608693 0.006964669799938786 +33 0.8188562475908056 0.1802196488220434 0.0009241035871510441 +34 0.294227312852384 0.7012397409940583 0.004532946153557716 +35 0.3538810428818183 0.6440586639893733 0.00206029312880844 +36 0.001285582575667415 0.8933043209742497 0.1054100964500828 +37 0.01165718682986431 0.9021673106901632 0.08617550247997249 +38 0.2922703773213358 0.7023110021631068 0.005418620515557353 +39 0.0001414258245998662 0.3552897640117538 0.6445688101636463 +40 0.0002480343083803734 0.5431706918246311 0.4565812738669887 +41 0.2106126640808448 0.7774907500550804 0.01189658586407484 +42 0.6999813936613979 0.2931385631454202 0.006880043193181909 +43 0.4833675933746905 0.4327946482058024 0.08383775841950711 +44 0.02972267732322751 0.9584116611571429 0.01186566151962948 +45 0.1879863406307251 0.794443770881722 0.01756988848755292 +46 0.003315641843239341 0.5668519937359566 0.4298323644208041 +47 0.629338958900993 0.3522332182779525 0.01842782282105454 +48 0.02177628572232749 0.9528189772586725 0.0254047370190001 +49 0.01338501370939216 0.915333710519133 0.07128127577147472 +50 0.2225629558216143 0.7667647912328456 0.01067225294554009 +51 2.404895779791487e-08 0.1134753865484972 0.8865245894025451 +52 0.8817912341059508 0.1179853011844181 0.0002234647096312131 +53 0.8205811797770941 0.1786469342675719 0.0007718859553339688 +54 0.01085855589549476 0.8905891540512085 0.09855229005329673 +55 0.2815509463068884 0.7120872890472977 0.00636176464581387 +56 0.9051318930548866 0.09478819305605581 7.991388905762001e-05 +57 0.006954013156504206 0.7876756439325455 0.2053703429109503 +58 0.8234877428822261 0.1757814841469247 0.0007307729708490679 +59 0.004520728063547726 0.6636065872613631 0.3318726846750891 +60 0.5888994883965843 0.3816206737079166 0.02947983789549902 +61 0.1070261395717946 0.8108154871611706 0.0821583732670348 +62 0.06809611425332979 0.7379419931303244 0.1939618926163459 +63 0.01226409761551406 0.9103218310480462 0.07741407133643979 +64 0.02359148881874123 0.9548765284644904 0.02153198271676823 +65 0.02123541489639974 0.9512565153910327 0.02750806971256748 +66 2.559895392744628e-12 0.001508538249717034 0.9984914617477231 +67 0.4288250311729814 0.4447869689660212 0.1263879998609974 +68 3.01456183745524e-05 0.3937817218281177 0.6061881325535077 +69 4.111620173592685e-07 0.1660196412401442 0.8339799475978384 +70 0.1279534450655496 0.8165676068857958 0.0554789480486545 +71 0.08847995007210885 0.7885234456361478 0.1229966042917432 +72 0.02465882951134361 0.9541836247192624 0.02115754576939405 +73 0.05258851663773368 0.6693965224781443 0.278014960884122 +74 0.8449518403304845 0.1545867259269795 0.0004614337425358581 +75 0.004915006811497326 0.6872810504563897 0.3078039427321129 +76 1.240382580633888e-06 0.3235963721964268 0.6764023874209926 +77 0.8879460304650322 0.1118225238196982 0.0002314457152695367 +78 0.6478242029579393 0.3371411102281834 0.01503468681387728 +79 0.3301507890571248 0.6666092401145077 0.003239970828367461 +80 0.8870461607667295 0.1128019335691497 0.0001519056641208466 +81 0.7186677176876294 0.276142911204988 0.005189371107382598 +82 0.6312241344251047 0.3509574274447219 0.01781843813017348 +83 9.192174161540158e-07 0.1852362904254418 0.8147627903571421 +84 9.770691779303996e-05 0.7216475052636109 0.2782547878185961 +85 0.8803206278886949 0.119482029072152 0.0001973430391530894 +86 0.8817912341059508 0.1179853011844181 0.0002234647096312131 +87 1.491742663992061e-08 0.0143224414618767 0.9856775436206967 +88 0.6312241344251047 0.3509574274447219 0.01781843813017348 +89 0.8111749800816118 0.1876472293909075 0.001177790527480832 +90 0.007386259819672177 0.8059058058601724 0.1867079343201554 +91 0.4751049150380716 0.4364379828463839 0.08845710211554457 diff --git a/tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex b/tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex index 2569fc463..a7bcdeb77 100644 --- a/tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex +++ b/tests/hbltests/Results/HIVSweden.out_MODEL_-1.nex @@ -37,8 +37,8 @@ END; BEGIN HYPHY; -global c=0.911942160103597; -global kappa=0.4054809128706205; +global c=0.9061405978972703; +global kappa=0.4052126959574972; modelMatrix={61,61}; modelMatrix[0][1]:=kappa*c*t; modelMatrix[0][2]:=t; @@ -638,31 +638,31 @@ ACCEPT_ROOTED_TREES=0; UseModel (theModel); Tree givenTree=((((U68496,U68497)Node4)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node16,U68505)Node15,U68507)Node14,U68508)Node13)Node11)Node9)Node7)Node2,U68498,(U68499,U68500)Node6); -givenTree.U68496.t=0.192121483894935; -givenTree.U68497.t=0.6392494100253431; -givenTree.Node4.t=0.4462505878848448; -givenTree.Node3.t=0.7884830206774067; -givenTree.U68501.t=1.064822202007258; -givenTree.U68502.t=1.54361895190365; -givenTree.U68503.t=1.564178047414112; -givenTree.U68504.t=0.1535209341229616; -givenTree.U68506.t=0.5682858444575011; -givenTree.Node16.t=0.4495915518878103; -givenTree.U68505.t=0.2449210887709239; -givenTree.Node15.t=0.296433362542081; -givenTree.U68507.t=0.4937996785015182; -givenTree.Node14.t=0.2814901272462195; -givenTree.U68508.t=1.603901882326408; -givenTree.Node13.t=0.4087267713543258; -givenTree.Node11.t=0.5166989104912423; -givenTree.Node9.t=0.2722019890411134; -givenTree.Node7.t=0.3889706412703413; -givenTree.Node2.t=0.1910629239730626; -givenTree.U68498.t=0.4076006171477853; -givenTree.U68499.t=0.2294111927752583; -givenTree.U68500.t=0.8077872067298961; -givenTree.Node6.t=0.6740793127558758; -givenTree.Node1.t=0.0006724153807641; +givenTree.U68496.t=0.1929875274492814; +givenTree.U68497.t=0.6431584321767878; +givenTree.Node4.t=1.056200341428187; +givenTree.Node3.t=0.1857001773835679; +givenTree.U68501.t=1.069902923546889; +givenTree.U68502.t=1.551998803483345; +givenTree.U68503.t=1.570292931943806; +givenTree.U68504.t=0.1542144074729374; +givenTree.U68506.t=0.5714940266175258; +givenTree.Node16.t=0.45175746072273; +givenTree.U68505.t=0.2461779332005472; +givenTree.Node15.t=0.2981291901629515; +givenTree.U68507.t=0.4970559051826392; +givenTree.Node14.t=0.2829053736537681; +givenTree.U68508.t=1.613730629930154; +givenTree.Node13.t=0.4111958814809425; +givenTree.Node11.t=0.5206528566898802; +givenTree.Node9.t=0.2738622103302701; +givenTree.Node7.t=0.3908052088043463; +givenTree.Node2.t=0.1920787122566935; +givenTree.U68498.t=0.4096240880956289; +givenTree.U68499.t=0.2307264134110747; +givenTree.U68500.t=0.8126540684833774; +givenTree.Node6.t=0.6782916664732664; +givenTree.Node1.t=0.0004136765506309006; DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA); DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0,1,5-8,10,9,11,12,2-4","TAA,TAG,TGA"); ASSUME_REVERSIBLE_MODELS=0; diff --git a/tests/hbltests/Results/HIVSweden.out_MODEL_0.nex b/tests/hbltests/Results/HIVSweden.out_MODEL_0.nex index 31cc3ec9b..c4598e335 100644 --- a/tests/hbltests/Results/HIVSweden.out_MODEL_0.nex +++ b/tests/hbltests/Results/HIVSweden.out_MODEL_0.nex @@ -37,11 +37,11 @@ END; BEGIN HYPHY; -global W=0.07861747394474425; +global W=0.07848009442627751; W:<1; -global P=0.4832764870262197; +global P=0.4830084511575133; P:<1; -global kappa=0.3862518235736528; +global kappa=0.3863359609620791; c.weights={1,2}; c.weights[0][0]:=P; @@ -654,31 +654,31 @@ ACCEPT_ROOTED_TREES=0; UseModel (theModel); Tree givenTree=((((U68496,U68497)Node4)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node16,U68505)Node15,U68507)Node14,U68508)Node13)Node11)Node9)Node7)Node2,U68498,(U68499,U68500)Node6); -givenTree.U68496.t=0.3015729502329249; -givenTree.U68497.t=1.058257102031187; -givenTree.Node4.t=1.15318474939162; -givenTree.Node3.t=0.9309921194099001; -givenTree.U68501.t=1.765169045625969; -givenTree.U68502.t=2.672360864363262; -givenTree.U68503.t=2.709162795696727; -givenTree.U68504.t=0.24325406993288; -givenTree.U68506.t=0.9044931073442913; -givenTree.Node16.t=0.7151085459517377; -givenTree.U68505.t=0.3954674837568525; -givenTree.Node15.t=0.4999222691606283; -givenTree.U68507.t=0.774494812266955; -givenTree.Node14.t=0.2768696155089731; -givenTree.U68508.t=2.85524014204128; -givenTree.Node13.t=0.7481759723267783; -givenTree.Node11.t=0.8226165012238955; -givenTree.Node9.t=0.3105248433782432; -givenTree.Node7.t=0.6406594119850229; -givenTree.Node2.t=0.3045529344681134; -givenTree.U68498.t=0.639065007964962; -givenTree.U68499.t=0.3595232565084895; -givenTree.U68500.t=1.322198597699191; -givenTree.Node6.t=1.136724122974329; -givenTree.Node1.t=0.0533314624311028; +givenTree.U68496.t=0.3017425916763694; +givenTree.U68497.t=1.058296701011468; +givenTree.Node4.t=0.977021241682638; +givenTree.Node3.t=1.105252498178708; +givenTree.U68501.t=1.768634707578611; +givenTree.U68502.t=2.676825802233908; +givenTree.U68503.t=2.703337691942369; +givenTree.U68504.t=0.2431762666473008; +givenTree.U68506.t=0.9045418574338289; +givenTree.Node16.t=0.7161050133725773; +givenTree.U68505.t=0.3958176949239906; +givenTree.Node15.t=0.4999771832173105; +givenTree.U68507.t=0.7736824283984889; +givenTree.Node14.t=0.2768797826282548; +givenTree.U68508.t=2.850443848076719; +givenTree.Node13.t=0.7469931505884494; +givenTree.Node11.t=0.8222248334521901; +givenTree.Node9.t=0.3095325845376597; +givenTree.Node7.t=0.6412236945161859; +givenTree.Node2.t=0.3043214554856749; +givenTree.U68498.t=0.6388583725281214; +givenTree.U68499.t=0.3593040916729295; +givenTree.U68500.t=1.320153241531879; +givenTree.Node6.t=1.138223365002844; +givenTree.Node1.t=0.04590557833973997; DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA); DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0,1,5-8,10,9,11,12,2-4","TAA,TAG,TGA"); ASSUME_REVERSIBLE_MODELS=0; diff --git a/tests/hbltests/Results/HIVSweden.out_MODEL_1.nex b/tests/hbltests/Results/HIVSweden.out_MODEL_1.nex index 28c4591c1..b9301a791 100644 --- a/tests/hbltests/Results/HIVSweden.out_MODEL_1.nex +++ b/tests/hbltests/Results/HIVSweden.out_MODEL_1.nex @@ -37,15 +37,15 @@ END; BEGIN HYPHY; -global P2=0.7075930251249289; +global P2=0.7080333137100422; P2:<1; -global W_1=0.05908673874612212; +global W_1=0.0582725649744682; W_1:<1; -global W_2=3.631785964259932; +global W_2=3.642753519065559; W_2:>1; -global P1=0.375270533842653; +global P1=0.3740950248051497; P1:<1; -global kappa=0.3595771504468483; +global kappa=0.3598067834570357; c.weights={1,3}; c.weights[0][0]:=P1; @@ -660,31 +660,31 @@ ACCEPT_ROOTED_TREES=0; UseModel (theModel); Tree givenTree=((((U68496,U68497)Node4)Node3,(U68501,(U68502,(U68503,((((U68504,U68506)Node16,U68505)Node15,U68507)Node14,U68508)Node13)Node11)Node9)Node7)Node2,U68498,(U68499,U68500)Node6); -givenTree.U68496.t=0.1823362090160219; -givenTree.U68497.t=0.6319005932006931; -givenTree.Node4.t=0.7186608573956341; -givenTree.Node3.t=0.5266760584930447; -givenTree.U68501.t=1.055244295651116; -givenTree.U68502.t=1.749088321204769; -givenTree.U68503.t=1.77644065923493; -givenTree.U68504.t=0.1465075775527527; -givenTree.U68506.t=0.5207162468101293; -givenTree.Node16.t=0.4175230702755034; -givenTree.U68505.t=0.2414636650897602; -givenTree.Node15.t=0.2762765131975846; -givenTree.U68507.t=0.4780905520756796; -givenTree.Node14.t=0.006622253494086367; -givenTree.U68508.t=1.945288305463255; -givenTree.Node13.t=0.5084351480256487; -givenTree.Node11.t=0.5079487549393463; -givenTree.Node9.t=0.1809457716846473; -givenTree.Node7.t=0.3944024554603371; -givenTree.Node2.t=0.1898471467430669; -givenTree.U68498.t=0.3345594207692562; -givenTree.U68499.t=0.1879923629015026; -givenTree.U68500.t=0.8015647611761196; -givenTree.Node6.t=0.7495558244484987; -givenTree.Node1.t=0.07436824582250151; +givenTree.U68496.t=0.1815990811136892; +givenTree.U68497.t=0.6304763514852175; +givenTree.Node4.t=0.795880282613745; +givenTree.Node3.t=0.4459198799278273; +givenTree.U68501.t=1.05221356540879; +givenTree.U68502.t=1.746188236136285; +givenTree.U68503.t=1.773172618325882; +givenTree.U68504.t=0.1461964572143971; +givenTree.U68506.t=0.5195029362303628; +givenTree.Node16.t=0.4166424843260762; +givenTree.U68505.t=0.2408766408879654; +givenTree.Node15.t=0.2753611582743126; +givenTree.U68507.t=0.4769154872414726; +givenTree.Node14.t=0.007204791848271492; +givenTree.U68508.t=1.938020474598267; +givenTree.Node13.t=0.5069704229342387; +givenTree.Node11.t=0.5065281308370582; +givenTree.Node9.t=0.1807128135103633; +givenTree.Node7.t=0.3939750335388774; +givenTree.Node2.t=0.1895637791752665; +givenTree.U68498.t=0.3336535328315168; +givenTree.U68499.t=0.1875446659620321; +givenTree.U68500.t=0.7993837470120337; +givenTree.Node6.t=0.7477437763727508; +givenTree.Node1.t=0.07414324758015953; DataSet ds = ReadDataFile(USE_NEXUS_FILE_DATA); DataSetFilter filteredData = CreateFilter(ds,3,"0-272","0,1,5-8,10,9,11,12,2-4","TAA,TAG,TGA"); ASSUME_REVERSIBLE_MODELS=0; diff --git a/tests/hbltests/libv3/data/partitioned.nex.slac.json b/tests/hbltests/libv3/data/partitioned.nex.slac.json deleted file mode 100644 index c818e6e4b..000000000 --- a/tests/hbltests/libv3/data/partitioned.nex.slac.json +++ /dev/null @@ -1,9835 +0,0 @@ -{ - "MLE":{ - "content":{ - "0":{ - "by-branch":{ - "AVERAGED": [ -[177.2214650696752, 389.3074719377043, 1, 0, 0.3128197934704379, 0.005642657336157598, 0, -0.1977486184010424, 1, 0.312819793470438, 0.00179017202270015], - [0, 0, 0, 0, null, null, null, null, 1, 1, 0], - [177.1544340150171, 389.346589839098, 2, 0, 0.312716882327538, 0.01128958476890543, 0, -0.3956468836175571, 1, 0.09779184849265521, 0.003590507139306545], - [177.1931719507896, 389.3318000374899, 2, 0, 0.3127720413257537, 0.01128711664214377, 0, -0.3955603873750811, 0.9999999999999999, 0.0978263498350791, 0.003596148785609333], - [177.0874029603591, 389.413620893756, 0, 1, 0.3125985576434942, 0, 0.002567963590243369, 0.08999505407156334, 0.6874014423565058, 1, 0.001796474080375715], - [177.1015495198019, 389.3994743343133, 1, 1, 0.3126235294596907, 0.005646477982329506, 0.00256805688222749, -0.1078841905747062, 0.902266528828166, 0.5275135877475472, 0.003589039869745379], - [177.0814203820047, 389.4196034721105, 2, 1, 0.3125879970653089, 0.01129423965363248, 0.002567924139113398, -0.3058163439537867, 0.9694566342245758, 0.2320470361770557, 0.005380736593463641], - [177.5122013863345, 389.016735621045, 1, 2, 0.3133329822904037, 0.005633415574761631, 0.005141166990687699, -0.01725099923873363, 0.7669918605802887, 0.6762285404748578, 0.008791418395720877], - [0, 0, 0, 0, null, null, null, null, 1, 1, 0], - [0, 0, 0, 0, null, null, null, null, 1, 1, 0] - ], - "NAMES": [ -["Node3"], - ["Node6"], - ["Node2"], - ["Node11"], - ["Node9"], - ["Node1"], - ["Node17"], - ["Node20"], - ["Node16"], - ["Node15"] - ], - "RESOLVED": [ -[177.2214650696752, 389.3074719377043, 1, 0, 0.3128197934704379, 0.005642657336157598, 0, -0.1977486184010424, 1, 0.312819793470438, 0.00179017202270015], - [0, 0, 0, 0, null, null, null, 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0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.02997099514929494] - ] - } - } - }, - "headers": [ -["ES", "Expected synonymous sites"], - ["EN", "Expected non-synonymous sites"], - ["S", "Inferred synonymous substitutions"], - ["N", "Inferred non-synonymous substitutions"], - ["P[S]", "Expected proportion of synonymous sites"], - ["dS", "Inferred synonymous susbsitution rate"], - ["dN", "Inferred non-synonymous susbsitution rate"], - ["dN-dS", "Scaled by the length of the tested branches"], - ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"], - ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"], - ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] - ] - }, - "analysis":{ - "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", - "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", - "contact":"spond@temple.edu", - "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", - "requirements":"in-frame codon alignment and a phylogenetic tree", - "version":"2.00" - }, - "branch attributes":{ - "0":{ - "AF082576":{ - "Global MG94xREV":0.001856367375488537, - "Nucleotide GTR":0.001707224253909208, - "amino-acid": [ -["E", "T", "D", "C", "W", "T", "K", "K", "S", "L", "D", "I", "D", "C", "I", "G", "P", "M", "L", "D", "I", "G", "S", "C", "T", "N", "K", "N", "T", "R", "S", "Y", "D", "A", "E", "A", "Q", "K", "L", "V", "S", "Q", "S", "K", "I", "S", "Q", "L", "D", "A", "D", "Q", "A", "S", "L", "L", "G", "N", "S", "I", "D", "S", "A", "I", "K", "A", "I", "R", "A", "Q", "K", "T", "Y", "P", "T", "M", "H", "L", "L", "E", "T", "I", "F", "L", "M", "K", "N", "C", "D", "Y", "Y", "T", "S", "F", "N", "H", "N", "S", "G", "Y", "S", "Q", "A", "K", "W", "R", "L", "I", "A", "K", "T", "G", "H", "F", "D", "I", "C", "S", "R", "H", "S", "T", "H", "H", "F", "C", "Q", "C", "I", "N", "D", "G", "T", "K", "C", "Q", "N", "G", "D", "W", "D", "F", "A", "G", "E", "M", "N", "E", "T", "Y", "N", "S", "K", "N", "D", "F", "Y", "S", "H", "D", "L", "N", "L", "F", "Y", "T", "I", "F", "E", "N", "A", "F", "P", "G", "T", "T", "E", "S", "L", "F", "Y", "Q", "L", "I", "Q", "K", "K", "N", "T", "T", "G", "A", "S", "K", "V", "L"] - 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