veg · stevenweaver · Nov 6, 2023 · Oct 30, 2023 · Oct 30, 2023 · Oct 30, 2023
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -16,13 +16,15 @@ option(NOSSE4 OFF)
 option(NONEON OFF)
 option(NOZLIB OFF)
 
-
 if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
-  set(NOAVX ON)
-  set(NOSSE4 ON)
-  set(NONEON ON)
-  set(NOZLIB ON)
-endif()
+   set(NOAVX ON)
+   #set(NOSSE4 ON)
+   set(NONEON ON)
+   set(NOZLIB ON)
+   set(LIBRARY_PATH "/hyphy")
+   #set(CMAKE_EXECUTABLE_SUFFIX ".html")
+   add_definitions (-D_USE_EMSCRIPTEN_)
+ endif()
 
 #-------------------------------------------------------------------------------
 # SSE MACROS
@@ -191,12 +193,17 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
     if(NOAVX)
         set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-avx")
         if(NOSSE4)
-            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-sse3")
+	        if(NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
+            	set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-sse3")
+            endif()
         else(NOSSE4)
             PCL_CHECK_FOR_SSE4()
             if(${HAVE_SSE4_EXTENSIONS})
                 add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
                 set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
+                if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
+				 	set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msimd128 ")
+			    endif()
             endif(${HAVE_SSE4_EXTENSIONS})
         endif(NOSSE4)
     else(NOAVX)
@@ -214,6 +221,8 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
             if(${HAVE_SSE4_EXTENSIONS})
                 add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
                 set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
+
+
             endif(${HAVE_SSE4_EXTENSIONS})
         endif(${HAVE_AVX_EXTENSIONS})
     endif(NOAVX)
@@ -222,6 +231,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
 		PCL_CHECK_FOR_NEON()
 		if(${HAVE_NEON_EXTENSIONS})
 			add_definitions (-D_SLKP_USE_ARM_NEON)
+
 		endif(${HAVE_NEON_EXTENSIONS})
 	endif(NOT NONEON)
 
@@ -233,13 +243,18 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2  -std=c++14 -Wall")
     if(NOAVX)
         if(NOSSE4)
-            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-sse3")
-        else(NOSSE4)
+	        if(NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
+            	set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-sse3")
+            endif()
+         else(NOSSE4)
             PCL_CHECK_FOR_SSE4()
-            if(${HAVE_SSE4_EXTENSIONS})
-                add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
-                set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
-            endif(${HAVE_SSE4_EXTENSIONS})
+ 			if("${HAVE_SSE4_EXTENSIONS}" OR ${CMAKE_SYSTEM_NAME} STREQUAL "Emscripten")
+				add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
+				set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
+				if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
+					set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msimd128 ")
+				endif()
+			endif()  
         endif(NOSSE4)
     else(NOAVX)
         PCL_CHECK_FOR_AVX()
@@ -275,7 +290,6 @@ endif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
 
 #set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS}  -fopt-info -fopt-info-vec-missed")
 set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS}")
-MESSAGE ("Set default compiler flags to ${DEFAULT_COMPILE_FLAGS}")
 
 if(NOT DEFINED DEFAULT_COMPILE_FLAGS)
     set(DEFAULT_COMPILE_FLAGS "")
@@ -291,6 +305,11 @@ if(NOT DEFINED DEFAULT_WARNING_FLAGS)
     set(DEFAULT_WARNING_FLAGS "")
 endif(NOT DEFINED DEFAULT_WARNING_FLAGS)
 
+if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
+   set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fwasm-exceptions ")
+endif()
+
+MESSAGE ("Set default compiler flags to ${DEFAULT_COMPILE_FLAGS}")
 
 #-------------------------------------------------------------------------------
 # OpenMP support
@@ -426,7 +445,11 @@ install(
     OPTIONAL
 )
 
+if (NOT DEFINED LIBRARY_PATH)
+    set(LIBRARY_PATH "${CMAKE_INSTALL_PREFIX}/share/hyphy")
+endif()
 
+MESSAGE (${LIBRARY_PATH})
 
 #-------------------------------------------------------------------------------
 # hyphy mpi target
@@ -460,7 +483,7 @@ if(${MPI_FOUND})
     # set definitions here 'cause "s_t_p" below doesn't like lists
     set_property(
         TARGET HYPHYMPI
-        APPEND PROPERTY COMPILE_DEFINITIONS __HYPHYMPI__ __UNIX__ _HYPHY_LIBDIRECTORY_="${CMAKE_INSTALL_PREFIX}/share/hyphy"
+        APPEND PROPERTY COMPILE_DEFINITIONS __HYPHYMPI__ __UNIX__ _HYPHY_LIBDIRECTORY_="${LIBRARY_PATH}"
     )
 
     message ("${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS}")
@@ -592,14 +615,10 @@ set_property(
     APPEND PROPERTY COMPILE_DEFINITIONS __MP__ __MP2__
 )
 
-set_property(
-    TARGET hyphy HYPHYDEBUG
-    APPEND PROPERTY COMPILE_DEFINITIONS _HYPHY_LIBDIRECTORY_="${CMAKE_INSTALL_PREFIX}/share/hyphy"
-)
 
 set_property(
     TARGET hyphy HYPHYDEBUG HYPHYPROFILE
-    APPEND PROPERTY COMPILE_DEFINITIONS _HYPHY_LIBDIRECTORY_="${CMAKE_INSTALL_PREFIX}/share/hyphy"
+    APPEND PROPERTY COMPILE_DEFINITIONS _HYPHY_LIBDIRECTORY_="${LIBRARY_PATH}"
 )
 
 
@@ -631,6 +650,7 @@ makeLink(HYPHYMP hyphy hyphy)
 # TESTS
 #-------------------------------------------------------------------------------
 
+
 add_test (NAME UNIT-TESTS COMMAND bash run_unit_tests.sh)
 add_test (CODON HYPHYMP tests/hbltests/SimpleOptimizations/SmallCodon.bf)
 add_test (PROTEIN HYPHYMP CPU=1 tests/hbltests/SimpleOptimizations/IntermediateProtein.bf)

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/FEL.bf b/res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
@@ -947,12 +947,12 @@ function fel.report.echo (fel.report.site, fel.report.partition, fel.report.row)
      if (fel.report.row [4] < fel.pvalue) {
         if (fel.report.row[0] < fel.report.row[1]) {
             fel.print_row = fel.report.positive_site;
-            fel.color = "\033[0;31m";
+            fel.color = "RED" && 8;
             fel.report.counts[0] += 1;
         } else {
             fel.print_row = fel.report.negative_site;
             fel.report.counts [1] += 1;
-            fel.color = "\033[0;32m";
+            fel.color = "GREEN" && 8;
         }
      }
 
@@ -966,9 +966,7 @@ function fel.report.echo (fel.report.site, fel.report.partition, fel.report.row)
                 fel.table_output_options[terms.table_options.header] = FALSE;
             }
 
-            fprintf (stdout, fel.color, 
-                io.FormatTableRow (fel.print_row,fel.table_output_options),"\033[0m"
-                );
+            fprintf (stdout, io.FormatTableRowDecorators (fel.print_row,fel.table_output_options, fel.color,  "NONE" && 8));
     }
 }
 

diff --git a/res/TemplateBatchFiles/YangNielsenBranchSite2005.bf b/res/TemplateBatchFiles/YangNielsenBranchSite2005.bf
@@ -35,7 +35,7 @@ fprintf (stdout, "\nBase composition:\n\tA: ", Format (baseFreqs[0][0],10,5),","
 /* 5. prompt for the type of model to run */
 
 ChoiceList (modelKind, "Model", 1, SKIP_NONE,
-					   "Alternative", "Fit Model A with 4 rate classes. Class 1: Negative selection in FG and BG. Class 2: Neutral evolution in FG and BG. Class 3: Negative selection in BG, Positive in FG. Class 4: Neutral evolution in BG, Positive in FG",
+					   "Branch-site alternative", "Fit Model A with 4 rate classes. Class 1: Negative selection in FG and BG. Class 2: Neutral evolution in FG and BG. Class 3: Negative selection in BG, Positive in FG. Class 4: Neutral evolution in BG, Positive in FG",
 					   "Null for Test 1", "Fit a model with 2 rate classes. Class 1: Negative selection in FG and BG. Class 2: Neutral evolution in FG and BG.",
 					   "Null for Test 2", "Fit Model A with 3 rate classes. Class 1: Negative selection in FG and BG. Class 2: Neutral evolution in FG and BG. Class 3: Negative selection in BG, Neutral in FG."
 );					   
@@ -54,15 +54,13 @@ global P_0     = 0.5;
 P_0:<1;
 P_0:>0;
 
-if (modelKind == 1)
-{
+if (modelKind == 1) {
 	rateClasses = 2;
 
 	categFreqMatrix = {{P_0,1-P_0}} ;
 	categRateMatrix = {{1,2}};
 }
-else
-{
+else {
 	P_0        = 1/4;
 	global 		P_1_aux = 1/4;
 	global 		P_1     := Min(P_1_aux,1-P_0);

diff --git a/res/TemplateBatchFiles/libv3/IOFunctions.bf b/res/TemplateBatchFiles/libv3/IOFunctions.bf
@@ -344,7 +344,7 @@ lfunction io.format_object(object, options) {
  * @param row
  * @param options
  */
-lfunction io.FormatTableRow(row, options) {
+lfunction io.FormatTableRowDecorators (row, options, prefix, suffix) {
 
     if (None == options) {
         options = {};
@@ -395,7 +395,7 @@ lfunction io.FormatTableRow(row, options) {
             for (k = 0; k < padding$2; k += 1) {
                 row * " ";
             }
-            row * cells[i];
+            row * (prefix + cells[i] + suffix);
             for (k = 0; k < padding - padding$2; k += 1) {
                 row * " ";
             }
@@ -428,7 +428,7 @@ lfunction io.FormatTableRow(row, options) {
             for (k = 0; k < padding$2; k += 1) {
                 row * " ";
             }
-            row * cells[i];
+            row * (prefix + cells[i] + suffix);
             for (k = 0; k < padding - padding$2; k += 1) {
                 row * " ";
             }
@@ -439,6 +439,15 @@ lfunction io.FormatTableRow(row, options) {
     return row;
 }
 
+/**
+ * @name io.FormatTableRow
+ * @param row
+ * @param options
+ */
+lfunction io.FormatTableRow(row, options) {
+    return io.FormatTableRowDecorators (row, options, "", "");
+}
+
 /**
  * @name io.get_a_list_of_files
  * @param filename

diff --git a/res/TemplateBatchFiles/libv3/convenience/regexp.bf b/res/TemplateBatchFiles/libv3/convenience/regexp.bf
@@ -1,13 +1,26 @@
 
 /** @module regexp */
 
+
+namespace terms {
+
+    namespace regexp {
+
+        strings    = "strings";
+        separators = "separators";
+
+    }
+
+}
+
 /**
- * @name regexp.Replace
- * @param {String} string
- * @param {String} re - search for this expression
- * @param {String} repl - replace each occurence of re with repl
- * @returns {Dictionary} a dictionary containing split strings
- */
+* @name regexp.Replace
+* @param {String} string
+* @param {String} re - search for this expression
+* @param {String} repl - replace each occurence of re with repl
+* @returns {Dictionary} a dictionary containing split strings
+*/
+
 lfunction regexp.Replace(string, re, repl) {
     return string ^ {{re,repl}};
 }
@@ -49,6 +62,52 @@ lfunction regexp.Split(string, re) {
     };
 }
 
+/**
+ * @name regexp.SplitWithMatches
+ * @param {String} string
+ * @param {String} re - the regular expression
+ * @returns {Dictionary} a dictionary containing split strings under the key "strings" and separators under the key "separators"
+ */
+lfunction regexp.SplitWithMatches (string, re) {
+    coordinates = string || re;
+    if (coordinates[0] >= 0) {
+        strings = {};
+        separators = {};
+
+        current_end = 0;
+
+        for (i = 0; i < Rows(coordinates); i += 2) {
+            from = coordinates[i];
+            separators + string[coordinates[i]][coordinates[i+1]];
+
+            if (current_end < from) {
+                strings + string[current_end][from - 1];
+            } else {
+                strings + "";
+            }
+            current_end = coordinates[i + 1] + 1;
+        }
+
+        if (current_end < Abs(string)) {
+            strings + string[current_end][Abs(string) - 1];
+        } else {
+            strings + "";
+        }
+
+        return {
+            ^("terms.regexp.strings") :strings,
+            ^("terms.regexp.separators") : separators
+        };
+    }
+    return {
+        ^("terms.regexp.strings") : {
+            "0": string
+        },
+        ^("terms.regexp.separators") : {
+        }
+    };
+}
+
 /**
  * @name regexp.Find
  * @param {String} string

diff --git a/res/TemplateBatchFiles/libv3/tasks/trees.bf b/res/TemplateBatchFiles/libv3/tasks/trees.bf
@@ -363,6 +363,68 @@ lfunction trees.branch_names(tree, respect_case) {
     return result;
 }
 
+/**
+ * @name trees.extract_paml_annotation
+ * @param tree_string {STRING} : PAML (#N $N annotated string)
+ * @param dictionary; tree annotation with PAML_GROUP_N
+ * @returns result
+ */
+
+lfunction trees.extract_paml_annotation (tree_string) {
+
+    pieces = regexp.SplitWithMatches (tree_string, "\$([0-9])");
+    N =  utility.Array1D (pieces[^("terms.regexp.separators")]);
+
+    has_paml_clades = N > 0;
+    sanitized_string = "";
+    if (N > 0) {    
+        for (i,s; in; pieces[^("terms.regexp.strings")]) {
+            sanitized_string += s;
+            if (+i > 0) {
+                sanitized_string += "{" + regexp.Replace ((pieces[^("terms.regexp.separators")])[-1+i], "\$", "PAML_CLADE_") + "}";
+            }
+        }
+    }
+
+    pieces = regexp.SplitWithMatches (sanitized_string, "\#([0-9])");
+    N =  utility.Array1D (pieces[^("terms.regexp.separators")]);
+
+    if (N > 0) {    
+        for (i,s; in; pieces[^("terms.regexp.strings")]) {
+            sanitized_string += s;
+            if (+i > 0) {
+                sanitized_string += "{" + regexp.Replace ((pieces[^("terms.regexp.separators")])[-1+i], "\#", "PAML_GROUP_") + "}";
+            }
+        }
+    }
+
+    if (Abs (sanitized_string) == 0) {
+        sanitized_string = tree_string;
+    } 
+
+    result = trees.ExtractTreeInfo (sanitized_string);
+
+    if (has_paml_clades) {
+        additional_annotation = {};    
+        tree_str = result[^"terms.trees.newick"];
+        Topology T = tree_str;
+        for (b, m; in; result[^"terms.trees.model_map"]) {
+            if (None != regexp.Find (m, "^PAML_CLADE_")) {
+                tag = regexp.Replace (m, "^PAML_CLADE_", "PAML_GROUP_");
+                for (n,foo; in; T[b]) {
+                    additional_annotation[n] = tag;
+                }
+            }
+        }
+        result[^"terms.trees.model_map"] * additional_annotation;
+        result[^"terms.trees.model_list"] = Columns(result[^"terms.trees.model_map"]);
+        result[^"terms.trees.newick_annotated"] = tree.Annotate (&T, result[^"terms.trees.model_map"], "{}", FALSE);
+    }
+
+    return result;
+}
+
+
 
 /**
  * @name trees.KillZeroBranches