this and that

src/core/include/global_things.h

@@ -274,6 +274,8 @@ namespace hy_global {
    Global variables (grouped by type, then alphabetically)
    */
 
+  _String* ConstructAnErrorMessage         (_String const&);
+
   extern  _AVLList  _hy_application_globals;
 
   extern  _List     _hy_standard_library_extensions,

src/core/include/likefunc.h

@@ -287,6 +287,18 @@ class   _LikelihoodFunction: public BaseObj {
 
 #endif
 #endif
+
+    void            ComputeDependencyLists  (_List& receptacle, long max_dep = 0x7fffffff) const;
+    /**
+        This function computes a mapping from the index of each independent variable to the list of all dependent variables that it affects.
+                index => {n1,n2,...n3}
+         special cases:
+                index => null (no dependencies)
+                index => {} (all variables, or >max_dep)
+     
+        @param max_dep the maximum number of dependent variables affected by a paritcular independent to generate an explicit list
+    */
+
 
     bool            ProcessPartitionList        (_SimpleList&, _Matrix*) const;
     // given a matrix argument (argument 2; can be nil to include all)
@@ -536,6 +548,12 @@ class   _LikelihoodFunction: public BaseObj {
     void            SetupParameterMapping       (void);
     void            CleanupParameterMapping     (void);
 
+    void            ConvertDependenciesToSimpleFormulas  ();
+    /**
+        Traverse the list of dependent variables and generate simple formulas if they can be created.
+    */
+
+
     _SimpleList     theTrees,
                     theDataFilters,
                     theProbabilities,

src/core/likefunc.cpp

@@ -1932,18 +1932,15 @@ bool      _LikelihoodFunction::SendOffToMPI       (long index) {
 
 //_______________________________________________________________________________________
 
-bool    _LikelihoodFunction::PreCompute         (void)
-{
+bool    _LikelihoodFunction::PreCompute         (void) {
 
     useGlobalUpdateFlag = true;
     // mod 20060125 to only update large globals once
-    unsigned long i = 0UL;
+    unsigned long i;
 
     _SimpleList * arrayToCheck = nonConstantDep?nonConstantDep:&indexDep;
-
 
-
-    for (; i < arrayToCheck->lLength; i++) {
+    for (i = 0UL; i < arrayToCheck->lLength; i++) {
         _Variable* cornholio = LocateVar(arrayToCheck->list_data[i]);
         hyFloat tp = cornholio->Compute()->Value();
          if (!cornholio->IsValueInBounds(tp)){
@@ -4252,6 +4249,7 @@ _Matrix*        _LikelihoodFunction::Optimize (_AssociativeList const * options)
 
     CheckDependentBounds();
 
+
     currentPrecision    = get_optimization_setting (kStartingPrecision, 0.1);
     precision           = get_optimization_setting (kOptimizationPrecision, 0.001);
     maxItersPerVar      = get_optimization_setting (kMaximumIterationsPerVariable, 5000.);

src/mains/unix.cpp

@@ -185,7 +185,8 @@ void            mpiOptimizerLoop (int, int);
 
 #ifdef     __HYPHY_HANDLE_TERM_SIGNAL__
     volatile sig_atomic_t hyphy_sigterm_in_progress = 0;
-
+    volatile sig_atomic_t hyphy_sigstop_in_process = 0;
+
     void    hyphy_sigterm_handler (int sig) {
        if (hyphy_sigterm_in_progress)
            raise (sig);
@@ -202,6 +203,17 @@ void            mpiOptimizerLoop (int, int);
        signal (sig, SIG_DFL);
        raise  (sig);
     }
+
+    void    hyphy_sigstop_handler (int sig) {
+       if (hyphy_sigstop_in_process)
+           raise (sig);
+
+        hyphy_sigstop_in_process = 1;
+        StringToConsole (new _String (ConstructAnErrorMessage ("HyPhy suspended.")));
+
+        signal (sig, SIG_DFL);
+        raise  (sig);
+    }
 
 #endif  
 
@@ -660,8 +672,17 @@ int main (int argc, char* argv[]) {
 #ifdef __HYPHY_HANDLE_TERM_SIGNAL__
     if (signal (SIGTERM, hyphy_sigterm_handler) == SIG_IGN)
          signal (SIGTERM, SIG_IGN);
-     if (signal (SIGINT, hyphy_sigterm_handler) == SIG_IGN)
+
+    if (signal (SIGINT, hyphy_sigterm_handler) == SIG_IGN)
          signal (SIGINT, SIG_IGN);
+
+    if (signal (SIGTSTP, hyphy_sigstop_handler) == SIG_IGN)
+        signal (SIGTSTP, SIG_IGN);
+
+    //if (signal (SIGCONT, hyphy_sigresume_handler) == SIG_IGN)
+    //    signal (SIGCONT, SIG_IGN);
+
+
 #endif
     //printf ("%e\n", mapParameterToInverval (1.322753E-23, 0x2, false));
     //exit (0);