2.5.64

CMakeLists.txt

@@ -7,6 +7,7 @@ enable_testing()
 
 set(CMAKE_CONFIGURATION_TYPES Release)
 
+
 #-------------------------------------------------------------------------------
 # OPTIONS
 #-------------------------------------------------------------------------------
@@ -170,12 +171,14 @@ set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPIL
 
 set(DEFAULT_WARNING_FLAGS " -w -Weffc++ -Wextra -Wall ")
 set(DEFAULT_DEBUG_WARNING_FLAGS "-Wall -Wno-int-to-pointer-cast -Wno-conversion-null -Wno-sign-compare")
-set(ADDITIONAL_FLAGS "")
+set(ADDITIONAL_FLAGS "-g")
 
 if (DEBUGFLAGS)
 	set(ADDITIONAL_FLAGS "-g")
 endif()
 
+#include_directories("/Library/Developer/CommandLineTools/SDKs/MacOSX15.2.sdk/usr/include/c++/v1")
+
 
 if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
      execute_process(
@@ -371,6 +374,7 @@ endif(NOT NOZLIB)
 
 
 
+
 #-------------------------------------------------------------------------------
 # uninstall target
 #-------------------------------------------------------------------------------

README.md

@@ -86,6 +86,27 @@ And then run make install to install the software
 +   libhyphy_mp.(so/dylib/dll) will be installed at `/location/of/choice/lib`
 +   HyPhy's standard library of batchfiles will go into `/location/of/choice/lib/hyphy`
 
+#### Building HyPhy for Web Assembly
+
+Use [Emscripten](https://emscripten.org/docs/compiling/Building-Projects.html) to produce web assembly files, which can be run entirely within a modern browser. See https://observablehq.com/@spond/hyphy-biowasm for an example. 
+
+```
+emcmake cmake -DCMAKE_EXE_LINKER_FLAGS="-sTOTAL_STACK=2097152 -02 -sASSERTIONS=1 -sMODULARIZE=1 -sALLOW_MEMORY_GROWTH -sFORCE_FILESYSTEM=1 -sEXIT_RUNTIME=0 -s EXPORTED_RUNTIME_METHODS=["callMain","FS","PROXYFS","WORKERFS","UTF8ToString","getValue","AsciiToString"] -lworkerfs.js -lproxyfs.js -s INVOKE_RUN=0 -s ENVIRONMENT="web,worker" ${EM_FLAGS//-s /-s} -fwasm-exceptions --preload-file res@/hyphy --preload-file tests/hbltests@/tests"
+``` 
+
+```
+emmake make -j hyphy 
+```
+
+This creates 
+
+```
+hyphy.js
+hyphy.wasm
+hyphy.data
+```
+
+Which should be served from the same directory.
 
 #### Testing
 

res/TemplateBatchFiles/F_ST.bf

@@ -242,42 +242,32 @@ if (distanceChoice == "Full likelihood") {
 	{
 		for (j = 0; j<=i; j = j+1)
 		{
-			if (dataType)
-			{
+			if (dataType == "Codon") {
 				DataSetFilter twoSpecFilter = CreateFilter (filteredData,3,"",(speciesIndex==i+1)||(speciesIndex==j),GeneticCodeExclusions);
 			}
-			else
-			{
+			else {
 				DataSetFilter twoSpecFilter = CreateFilter (filteredData,1,"",(speciesIndex==i+1)||(speciesIndex==j));
 			}
-			if (FREQUENCY_SENSITIVE)
-			{
-				if (USE_POSITION_SPECIFIC_FREQS)
-				{
+			if (FREQUENCY_SENSITIVE) {
+				if (USE_POSITION_SPECIFIC_FREQS) {
 					HarvestFrequencies (vectorOfFrequencies,filteredData,3,1,1);
 				}
-				else
-				{
+				else {
 					HarvestFrequencies (vectorOfFrequencies,twoSpecFilter,1,1,0);
 				}
 			}
-			if (FREQUENCY_SENSITIVE)
-			{
+			if (FREQUENCY_SENSITIVE) {
 				MULTIPLY_BY_FREQS = PopulateModelMatrix ("modelMatrix",vectorOfFrequencies);
-				if (dataType)
-				{
+				if (dataType == "Codon") {
 					codonFrequencies = BuildCodonFrequencies (vectorOfFrequencies);
 					Model pairModel = (modelMatrix, codonFrequencies, MULTIPLY_BY_FREQS);
 				}
-				else
-				{
+				else {
 					Model pairModel = (modelMatrix, vectorOfFrequencies, MULTIPLY_BY_FREQS);
 				}
 			}
-			else
-			{
-				if (i+j==0)
-				{
+			else {
+				if (i+j==0) {
 					MULTIPLY_BY_FREQS = PopulateModelMatrix ("modelMatrix",equalFreqs);
 					Model pairModel = (modelMatrix, equalFreqs, MULTIPLY_BY_FREQS);
 				}

res/TemplateBatchFiles/libv3/models/codon/MG_GTR.bf

@@ -0,0 +1,114 @@
+RequireVersion ("2.5.60");
+
+LoadFunctionLibrary("../codon.bf");
+LoadFunctionLibrary("../DNA.bf");
+LoadFunctionLibrary("../parameters.bf");
+LoadFunctionLibrary("../frequencies.bf");
+LoadFunctionLibrary("../../UtilityFunctions.bf");
+LoadFunctionLibrary("MG_REV.bf");
+LoadFunctionLibrary("../protein.bf");
+
+/** @module models.codon.GTR */
+//----------------------------------------------------------------------------------------------------------------
+
+
+lfunction model.codon.MG_GTR.prompt_and_define (type, code) {
+     console.log (type);
+     return models.codon.MG_GTR.ModelDescription(type, code);
+}
+
+lfunction models.codon.MG_GTR.ModelDescription(type, code) {
+
+
+    io.CheckAssertion ("`&type` == '`^'terms.global'`'", "MG_GTR only supports `^'terms.global'` type");
+
+    // piggyback on the standard MG_REV model for most of the code
+
+    mg_base = models.codon.MG_REV.ModelDescription (type, code);
+    mg_base[utility.getGlobalValue("terms.description")] = "The Muse-Gaut 94 codon-substitution model coupled with the general time reversible (GTR) model of nucleotide substitution, which defines a separate dN/dS ratio for each pair of amino-acids";
+    mg_base[utility.getGlobalValue("terms.model.q_ij")] = "models.codon.MG_GTR._GenerateRate";
+    mg_base[utility.getGlobalValue("terms.model.post_definition")] = "models.codon.MG_GTR.post_definition";
+    return mg_base;
+}
+
+lfunction models.codon.MG_GTR._GenerateRate(fromChar, toChar, namespace, model_type, model) {
+
+    return models.codon.MG_GTR._GenerateRate_generic (fromChar, toChar, namespace, model_type,
+        model[utility.getGlobalValue("terms.translation_table")],
+        "alpha", utility.getGlobalValue("terms.parameters.synonymous_rate"),
+        "omega",  utility.getGlobalValue("terms.parameters.omega_ratio"),
+    );
+}
+
+/**
+ * @name models.codon.MG_GTR._GenerateRate
+ * @param {Number} fromChar
+ * @param {Number} toChar
+ * @param {String} namespace
+ * @param {String} model_type
+ * @param {Matrix} _tt - translation table
+ */
+
+
+lfunction models.codon.MG_GTR._GenerateRate_generic (fromChar, toChar, namespace, model_type, _tt, alpha, alpha_term, omega, omega_term) {
+
+    _GenerateRate.p = {};
+    _GenerateRate.diff = models.codon.diff.complete(fromChar, toChar);
+    diff_count = utility.Array1D (_GenerateRate.diff);
+
+    if (diff_count == 1) {
+
+        _GenerateRate.p[model_type] = {};
+        _GenerateRate.p[utility.getGlobalValue("terms.global")] = {};
+
+        nuc_rate = "";
+
+        for (i = 0; i < diff_count; i += 1) {
+            if ((_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")] > (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")]) {
+                nuc_p = "theta_" + (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")] + (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")];
+            } else {
+                nuc_p = "theta_" + (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")] +(_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")];
+            }
+            nuc_p = parameters.ApplyNameSpace(nuc_p, namespace);
+            (_GenerateRate.p[utility.getGlobalValue("terms.global")])[terms.nucleotideRateReversible((_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")], (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")])] = nuc_p;
+
+            nuc_rate = parameters.AppendMultiplicativeTerm (nuc_rate, nuc_p);
+       }
+
+        rate_entry = nuc_rate;
+
+        if (_tt[fromChar] != _tt[toChar]) {
+
+            if (_tt[fromChar] < _tt[toChar]) {
+                aa_pair = _tt[fromChar] + " and " + _tt[toChar];
+                aa_tag = "_" + _tt[fromChar] + _tt[toChar];
+            } else {
+                aa_pair = _tt[toChar] + " and " + _tt[fromChar];
+                aa_tag = "_" + _tt[toChar] + _tt[fromChar];
+            }
+
+            omega_p = parameters.ApplyNameSpace (omega + aa_tag , namespace);
+            (_GenerateRate.p[model_type]) [^"terms.parameters.omega_ratio" + " for " + aa_pair] = omega_p;
+
+            rate_entry = parameters.AppendMultiplicativeTerm (rate_entry, omega_p);
+        } else {
+            _GenerateRate.p[utility.getGlobalValue("terms.model.rate_entry")] = nuc_rate;
+        }
+
+        _GenerateRate.p[utility.getGlobalValue("terms.model.rate_entry")] = rate_entry;
+    }
+    return _GenerateRate.p;
+}
+
+lfunction  models.codon.MG_GTR.post_definition (model) {
+
+    for (id; in ; model.GetParameters_RegExp (model,  ^"terms.parameters.omega_ratio")) {
+        parameters.SetValue(id, 0.25);
+    }
+
+    models.generic.post.definition (model);
+}
+
+lfunction models.codon.MG_GTR.set_branch_length(model, value, parameter) {
+    return models.codon.MG_REV.set_branch_length(model,value,parameter);
+}