Merge pull request #1519 from veg/develop

2.5.42rc

res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf

@@ -161,7 +161,7 @@ busted.multi_hit = io.SelectAnOption ({
 
 if (busted.do_srv) {
     KeywordArgument ("syn-rates", "The number alpha rate classes to include in the model [1-10, default 3]", busted.synonymous_rate_classes);
-    busted.synonymous_rate_classes = io.PromptUser ("The number omega rate classes to include in the model", busted.synonymous_rate_classes, 1, 10, TRUE);
+    busted.synonymous_rate_classes = io.PromptUser ("The number alpha rate classes to include in the model [1-10, default 3]", busted.synonymous_rate_classes, 1, 10, TRUE);
 }
 
 KeywordArgument ("grid-size", "The number of points in the initial distributional guess for likelihood fitting", 250);

src/core/classes.cp

@@ -205,7 +205,7 @@ template <class node_data> node<node_data>* node<node_data>::duplicate_tree(void
 
   //-------------------------------------------------------------
 
-template <class node_data> void node_count_descendants (node<node_data>* source, node<node_data>* n) {
+template <class node_data> void node_count_descendants (node<node_data>* , node<node_data>* n) {
     if (n->get_num_nodes() == 0) {
         n->in_object = 1L;
     } else {
@@ -314,15 +314,13 @@ template <class node_data> int node<node_data>::tree_depth(void)
 template <class node_data>
 node<node_data>* NodeTraverser  (node<node_data>* root)
 {
-  static int  going_up;
   static node<node_data>* laststep;
   node<node_data>* curstep, *crashdummy;
 
   if (root)
   {
     laststep = root;
     while ((crashdummy = laststep->go_down(1))) laststep = crashdummy;
-    going_up = false;
     return laststep;
   }
 
@@ -332,11 +330,9 @@ node<node_data>* NodeTraverser  (node<node_data>* root)
   {
     curstep=crashdummy;
     while ((crashdummy = curstep->go_down(1))) curstep = crashdummy;
-    going_up = false;
     return laststep = curstep;
   }
   curstep=curstep->get_parent();
-  going_up = true;
   laststep = curstep;
   return curstep;
 }
@@ -363,7 +359,6 @@ template <class node_data> void node<node_data>::replace_node(node<node_data>* e
 
   //-----------------------------------Set Number 1----------------
 template <class node_data> int node<node_data>::get_child_num() {
-    int num_siblings;
     if (parent) {
         if (this == parent->one) return 1;
         if (this == parent->two) return 2;

src/core/global_things.cpp

@@ -122,7 +122,7 @@ 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 ("2.5.41"),
+                     kHyPhyVersion  = _String ("2.5.42"),
 
                     kNoneToken = "None",
                     kNullToken = "null",

src/core/include/batchlan.h

@@ -125,8 +125,8 @@ class   _ExecutionList: public _List // a sequence of commands to be executed
     _String*    FetchFromStdinRedirect     (_String const * dialog_tag = nil, bool handle_multi_choice = false, bool do_echo = false);
 
     _ElementaryCommand* FetchLastCommand (void) {
-        if (currentCommand - 1 < lLength && currentCommand > 0) {
-            return (_ElementaryCommand*)(*this)(currentCommand - 1);
+        if (currentCommand - 1L < (long)lLength && currentCommand > 0L) {
+            return (_ElementaryCommand*)(*this)(currentCommand - 1L);
         }
         return nil;
     }
@@ -135,7 +135,7 @@ class   _ExecutionList: public _List // a sequence of commands to be executed
     }
 
     void        GoToLastInstruction         (void) {
-        currentCommand = MAX(currentCommand,lLength-1);
+        currentCommand = MAX(currentCommand,(long)lLength-1L);
     }
 
     _StringBuffer const GenerateHelpMessage         (_AVLList * scanned_functions = nil) const;

src/core/include/dataset.h

@@ -145,7 +145,7 @@ class _DataSet : public _List // a complete data set
   _String *GetSequenceCharacters(long seqID) const;
 
   bool SetSequenceName(long index, _String *new_name) {
-    if (index >= 0L && index < theNames.lLength) {
+    if (index >= 0L && index < (long)theNames.lLength) {
       theNames.Replace(index, new_name, false);
       return true;
     }

src/core/include/hy_strings.h

@@ -362,7 +362,7 @@ class _String : public BaseObj {
    - SLKP 20170517 reviewed while porting from v3 branch
    */
   virtual char get_char(long index) const {
-    if (index >= 0L && index < s_length) {
+    if (index >= 0L && index < (long)s_length) {
       return s_data[index];
     }
     return _String::default_return;
@@ -1130,7 +1130,7 @@ class _String : public BaseObj {
     bool   do_escape = false;
     char   quote_state = '\0';
 
-    while (current_position < s_length) {
+    while (current_position < (long)s_length) {
       char this_char = s_data[current_position];
       if (do_escape) {
         do_escape = false;

src/core/include/likefunc.h

@@ -701,7 +701,7 @@ class   _CustomFunction: public _LikelihoodFunction {
     _CustomFunction         (const _String& , _VariableContainer const * context = nil);
 
     virtual     hyFloat     Compute                 (void);
-    virtual     void        RescanAllVariables      (bool obtain_variable_mapping = false) {}
+    virtual     void        RescanAllVariables      (bool = false) {}
     virtual void            SerializeLF             (_StringBuffer& res, char=0, _SimpleList* = nil, _SimpleList* = nil) {
                res.AppendNewInstance ((_String*)myBody.toStr(kFormulaStringConversionNormal));
     }
@@ -774,7 +774,7 @@ FindLikeFuncByName           (_String&);
 
 template <typename ACTION>
 void DoForEachLikelihoodFunction (ACTION cb) {
-    for (long i = 0; i < likeFuncNamesList.lLength; i++) {
+    for (unsigned long i = 0UL; i < likeFuncNamesList.lLength; i++) {
         if (((_String*)likeFuncNamesList.GetItem(i))->nonempty()) {
             cb ((_LikelihoodFunction*)likeFuncList.GetItem (i), i);
         }

src/core/include/list.h

@@ -141,10 +141,10 @@ class _List:public _SimpleList {
             _List result;
             if (endAt < 0) {
                 endAt = lLength;
-            } else if (endAt > lLength) {
+            } else if (endAt > (long)lLength) {
                 endAt = lLength;
             }
-            for (unsigned long i = startAt; i<endAt; i++) {
+            for (long i = startAt; i<endAt; i++) {
                 result < mapper ( ((BaseRef*)(list_data))[i], i );
             }
             return result;

src/core/include/matrix.h

@@ -441,7 +441,7 @@ class       _Matrix: public _MathObject {
         return hDim;
     }
 
-    bool     check_dimension                         (unsigned long rows, unsigned long columns) const {
+    bool     check_dimension                         (long rows, long columns) const {
         return hDim == rows && vDim == columns;
     }
 

src/core/include/parser.h

@@ -122,7 +122,7 @@ void        DeleteTreeVariable (long, _SimpleList&, _String * prefix = nil, bool
 
 template <typename ACTION>
 void DoForEachVariable(ACTION do_this) {
-    for (long i = 0; i < variablePtrs.lLength; i++) {
+    for (unsigned long i = 0; i < variablePtrs.lLength; i++) {
         _Variable * ith_var = (_Variable *)variablePtrs.GetItem (i);
         if (ith_var) {
             do_this (ith_var, i);

src/core/include/vector.h

@@ -56,7 +56,7 @@ class   _Vector: public _Matrix
     virtual     BaseRef     makeDynamic (void) const; // duplicate this object into a dynamic copy
     virtual     void        Duplicate   (BaseRefConst); // duplicate an object from reference
 
-    virtual     void        Clear (void);
+    virtual     void        Clear (bool complete = true);
 
     virtual     unsigned long        GetHDim                     (void) const {
         if (is_column) {

src/core/likefunc.cpp

@@ -4401,6 +4401,7 @@ _Matrix*        _LikelihoodFunction::Optimize (_AssociativeList const * options)
             }
             ConjugateGradientDescent(precision, bestSoFar, true);
         }
+        //_TerminateAndDump("CHECK ME");
 #if !defined __UNIX__ || defined __HEADLESS__
 #ifdef __HYPHYMPI__
         if (hy_mpi_node_rank == 0) {
@@ -4934,6 +4935,7 @@ _Matrix*        _LikelihoodFunction::Optimize (_AssociativeList const * options)
                     BufferToConsole (buffer);
                     StringToConsole (*GetIthIndependentVar(current_index)->GetName());
                     BufferToConsole (CheckEqual(GetIthIndependentBound (current_index, true), cj)? ("[Lower bound]") : (CheckEqual(GetIthIndependentBound (current_index, false),cj) ? "[Upper bound]" : ""));
+
                 }
 #if defined __UNIX__ && ! defined __HEADLESS__ && !defined __HYPHYQT__ && !defined __HYPHY_GTK__
                 else if (verbosity_level==1) {
@@ -8424,7 +8426,12 @@ bool    _LikelihoodFunction::HasPartitionChanged (long index) {
                         //return LocateVar(value)->HasChanged();
                         return (LocateVar(value)->varFlags & HY_VARIABLE_CHANGED);
                        }
-                    );
+                    ) || ListAny (*(_SimpleList*)depVarsByPartition(index),
+                                  [] (const long value, const unsigned long index) -> bool {
+                                      //return LocateVar(value)->HasChanged();
+                                      return (LocateVar(value)->HasChanged());
+                                     }
+                                  );
 
 }
 

src/core/vector.cpp

@@ -121,8 +121,8 @@ void        _Vector::operator << (const _SimpleList& list) {
 
 /*--------------------------------------------------------------------------------------------------------------------------------*/
 
-void        _Vector::Clear (void) {
-    _Matrix::Clear();
+void        _Vector::Clear (bool complete_clear) {
+    _Matrix::Clear(complete_clear);
     ZeroUsed();
     vDim = 1UL;
 }

src/mains/unix.cpp

@@ -104,20 +104,7 @@ const char hy_help_message [] =
 "Run a custom analysis and pass it some arguments \n\thyphy path/to/hyphy.script argument1 'argument 2' \n"
 ;
 
-const char hy_available_cli_analyses [] =
-"Available standard analyses and their [standard analysis name] are listed below:\n\n"
-"        [meme] Test for episodic site-level selection using MEME (Mixed Effects Model of Evolution).\n"
-"        [contrast-fel] Use a FEL method to test which sites in a gene may be associated with adaptation to a different environment.\n"
-"        [fel] Test for pervasive site-level selection using FEL (Fixed Effects Likelihood).\n"
-"        [fubar] Test for pervasive site-level selection using FUBAR (Fast Unconstrained Bayesian AppRoximation for inferring selection).\n"
-"        [fade] Test a protein alignment for directional selection towards specific amino acids along a specified set of test branches using FADE (a FUBAR Approach to Directional Evolution).\n"
-"        [slac] Test for pervasive site-level selection using SLAC (Single Likelihood Ancestor Counting).\n"
-"        [busted] Test for episodic gene-wide selection using BUSTED (Branch-site Unrestricted Statistical Test of Episodic Diversification).\n"
-"        [bgm] Apply Bayesian Graphical Model inference to substitution histories at individual sites.\n"
-"        [absrel] Test for lineage-specific evolution using the branch-site method aBS-REL (Adaptive Branch-Site Random Effects Likelihood).\n"
-"        [relax] Test for relaxation of selection pressure along a specified set of test branches using RELAX (a random effects test of selection relaxation).\n"
-"        [gard] Screen an alignment for recombination using GARD (Genetic Algorithm for Recombination Detection).\n\n"
-;
+
 
 
 #ifdef _MINGW32_MEGA_
@@ -567,7 +554,7 @@ void    ProcessKWStr (_String const & conf, _String const & conf2, _AssociativeL
                 (*(_AssociativeList*)existing_value) < _associative_list_key_value {nil, new _FString (conf2)};
             } else {
                 _AssociativeList * replacement_list = new _AssociativeList;
-                (*replacement_list) << _associative_list_key_value {nil, existing_value} < _associative_list_key_value {nil, new _FString (conf2)};
+                ((*replacement_list) << _associative_list_key_value {nil, existing_value}) < _associative_list_key_value {nil, new _FString (conf2)};
                 kwargs.MStore(key, replacement_list, false);
             }
         } else {