Merge pull request #1098 from veg/develop

2.5.6 RC
veg · Feb 29, 2020 · 0e4c12a · 0e4c12a
2 parents 32cd386 + fc220a7
commit 0e4c12a
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Showing 55 changed files with 1,139 additions and 653 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -417,7 +417,7 @@ if(${MPI_FOUND})
         HYPHYMPI
         PROPERTIES
         if(${OPENMP_FOUND})
-            COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} "
+            COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g "
             LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS} -g "
         else(${OPENMP_FOUND})
             COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} "

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf b/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
@@ -490,14 +490,25 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa
      ^"meme.site_mixture_weight" = 0.75;
      if (^"meme.site_alpha" > 0) {
          ^"meme.site_omega_minus" = 1;
+         ^"meme.site_beta_plus"  = ^"meme.site_alpha" * 1.5;
      } else {
          ^"meme.site_omega_minus" = ^"meme.site_beta_plus" / Max (^"meme.site_alpha", 1e-6);
+         ^"meme.site_beta_plus" = 0.1;
          /* avoid 0/0 by making the denominator non-zero*/
      }
-
-    //console.log ("Optimizing MEME for pattern " + pattern_info);
-    //utility.SetEnvVariable ("LF_NEXUS_EXPORT_EXTRA", "Optimize (res,`lf_bsrel`);");
-    //io.SpoolLF (lf_bsrel, "/tmp/meme.debug" + ^"MPI_NODE_ID", "MEME");
+
+
+     /*
+     console.log (pattern_info);
+     console.log (^"meme.site_alpha");
+     console.log (^"meme.site_omega_minus");
+     console.log (^"meme.site_beta_plus");
+
+     console.log ("Optimizing MEME for pattern " + pattern_info);
+     utility.SetEnvVariable ("LF_NEXUS_EXPORT_EXTRA", "Optimize (res,`lf_bsrel`);");
+     io.SpoolLF (lf_bsrel, "/tmp/meme.debug" + (pattern_info['sites'])[0], "MEME");
+     */
+
     Optimize (results, ^lf_bsrel);
     //console.log (results[1][0]);
 

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf b/res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
@@ -86,10 +86,14 @@ function load_file (prefix) {
         name_mapping = {};
         utility.ForEach (alignments.GetSequenceNames (prefix+".codon_data"), "_value_", "`&name_mapping`[_value_] = _value_");
     }
-
+
+    utility.SetEnvVariable(utility.getGlobalValue ("terms.trees.data_for_neighbor_joining"),
+                           codon_data_info[utility.getGlobalValue("terms.data.datafilter")]);
 
     partitions_and_trees = trees.LoadAnnotatedTreeTopology.match_partitions (codon_data_info[utility.getGlobalValue("terms.data.partitions")], name_mapping);
 
+    utility.SetEnvVariable(utility.getGlobalValue ("terms.trees.data_for_neighbor_joining"), None);
+
         /**  this will return a dictionary of partition strings and trees; one set per partition, as in
         {
             "0": {

diff --git a/res/TemplateBatchFiles/libv3/all-terms.bf b/res/TemplateBatchFiles/libv3/all-terms.bf
@@ -484,6 +484,9 @@ namespace terms{
         branches            = "branches";
         meta                = "meta";
         comment             = "comment";
+        neighbor_joining    = "neighbor-joining";
+        data_for_neighbor_joining
+                            = "FILTER_FOR_NEIGHBOR_JOINING";
 
         //node_name = "Name";
         //children = "Children";

diff --git a/res/TemplateBatchFiles/libv3/tasks/ancestral.bf b/res/TemplateBatchFiles/libv3/tasks/ancestral.bf
@@ -198,7 +198,12 @@ lfunction ancestral._buildAncestralCacheInternal(_lfID, _lfComponentID, doSample
     _bacTreeAVLOrder = {};
 
     for (_bacCounter = 1; _bacCounter <= _bacBranchCount; _bacCounter += 1) {
-        _bacTreeAVLOrder[(_bac_tree_avl[_bacCounter])["Name"] && 1] = _bacCounter;
+        _bacNodeName = (_bac_tree_avl[_bacCounter])["Name"];
+
+         if (Abs ((_bac_tree_avl[_bacCounter])["Children"]) == 0) {
+            _bacNodeName = _bacNodeName && 1;
+         }
+        _bacTreeAVLOrder[_bacNodeName] = _bacCounter;
     }
 
 
@@ -207,13 +212,10 @@ lfunction ancestral._buildAncestralCacheInternal(_lfID, _lfComponentID, doSample
         _bacMapTreeNodeToDF[_bacTreeAVLOrder[_bacSequenceNames[_bacCounter] && 1] - 1] = _bacCounter;
     }
 
-
     for (_bacCounter = 0; _bacCounter < Columns(_bacAncestralNames); _bacCounter += 1) {
-        _bacMapTreeNodeToDF[_bacTreeAVLOrder[_bacAncestralNames[_bacCounter] && 1] - 1] = _bacCounter + _bacFilterSequenceCount;
+        _bacMapTreeNodeToDF[_bacTreeAVLOrder[_bacAncestralNames[_bacCounter]] - 1] = _bacCounter + _bacFilterSequenceCount;
     }
 
-
-
     /* make some auxiliary variables */
 
     _bacUnitRow = {

diff --git a/res/TemplateBatchFiles/libv3/tasks/estimators.bf b/res/TemplateBatchFiles/libv3/tasks/estimators.bf
@@ -978,13 +978,14 @@ lfunction estimators.FitCodonModel(codon_data, tree, generator, genetic_code, op
 
     //TODO: Where is data_filter being set?
     if (Type(data_filter) == "String") {
-        return estimators.FitMGREV({
+        return estimators.FitCodonModel({
                 {
                     codon_data__
                 }
             }, {
                 "0": tree
             },
+            generator,
             genetic_code,
             option,
             initial_values)
@@ -1033,7 +1034,7 @@ lfunction estimators.FitCodonModel(codon_data, tree, generator, genetic_code, op
         lf_components[2 * i + 1] = "tree_" + i;
         model.ApplyModelToTree(Eval("&`lf_components[2*i + 1]`"), tree[i], model_assignment, None);
     }
-
+    
 
     partition_omega = {};
 
@@ -1047,7 +1048,7 @@ lfunction estimators.FitCodonModel(codon_data, tree, generator, genetic_code, op
 
 
     if (Abs(partition_omega)) {
-
+    
         /**
             declare the global ratios for each branch set
             and add them to the model parameter set

diff --git a/res/TemplateBatchFiles/libv3/tasks/trees.bf b/res/TemplateBatchFiles/libv3/tasks/trees.bf
@@ -132,11 +132,27 @@ lfunction trees.GetTreeString(look_for_newick_tree) {
 
         if (!utility.GetEnvVariable("IS_TREE_PRESENT_IN_DATA")) {
             SetDialogPrompt("Please select a tree file for the data:");
+            utility.SetEnvVariable ("LAST_FILE_IO_EXCEPTION", None);
+            utility.ToggleEnvVariable ("SOFT_FILE_IO_EXCEPTIONS",TRUE);
             fscanf(PROMPT_FOR_FILE, REWIND, "Raw", treeString);
-            fprintf(stdout, "\n");
-
+
             look_for_newick_tree = utility.getGlobalValue ("LAST_FILE_PATH");
+
+            if (None != utility.GetEnvVariable ("LAST_FILE_IO_EXCEPTION")) {
+                if (utility.getGlobalValue ("LAST_RAW_FILE_PROMPT") ==  utility.getGlobalValue ("terms.trees.neighbor_joining")) {
+                    datafilter_name = utility.GetEnvVariable(utility.getGlobalValue ("terms.trees.data_for_neighbor_joining"));
+                    assert (Type (datafilter_name) == "String", "Expected a string for the datafilter to  build a NJ tree from");
+                    treeString = tree.infer.NJ (datafilter_name, None);
+                } else {
+                    assert (0, utility.GetEnvVariable ("LAST_FILE_IO_EXCEPTION"));
+                }
+                utility.SetEnvVariable ("LAST_FILE_IO_EXCEPTION", None);
+            }
+
+            utility.ToggleEnvVariable ("SOFT_FILE_IO_EXCEPTIONS",None);
+            fprintf(stdout, "\n");
 
+
             if (regexp.Find(treeString, "^#NEXUS")) {
                 ExecuteCommands(treeString);
 
@@ -295,7 +311,7 @@ lfunction trees.LoadAnnotatedTreeTopology.match_partitions(partitions, mapping)
                 utility.getGlobalValue("terms.data.tree"): trees.LoadAnnotatedTopologyAndMap(tree_matrix[i][1], mapping)
             };
         }
-    } else { // no tree matrix; allow if there is a single partition
+    } else { // no tree matrix; apply the same tree to all partitions
 
         tree_info = trees.LoadAnnotatedTopologyAndMap(TRUE, mapping);
 

diff --git a/src/core/associative_list.cpp b/src/core/associative_list.cpp
@@ -110,11 +110,19 @@ bool _AssociativeList::ParseStringRepresentation (_String& serialized_form, _For
                   key = *(_String*)key_value_pair(0);
                 }
 
-                _Formula value      (*(_String*)key_value_pair(1),theP, doErrors?nil :fpc.errMsg());
-                HBLObjectRef   valueC  = compute_keys_values ? value.Compute() : new _MathObject;
-
+                HBLObjectRef   valueC = nil;
+                if (compute_keys_values) {
+                    _Formula value      (*(_String*)key_value_pair(1),theP, doErrors?nil :fpc.errMsg());
+                    valueC  = value.Compute();
+                    if (valueC) {
+                        valueC->AddAReference();
+                    }
+                } else {
+                    valueC  =  new _MathObject;
+                }
+
                 if (valueC) {
-                    MStore (key, valueC, compute_keys_values);
+                    MStore (key, valueC, false);
                 } else {
                     throw (((_String*)key_value_pair(1))->Enquote() & " could not be evaluated");
 

diff --git a/src/core/avllist.cpp b/src/core/avllist.cpp
@@ -279,8 +279,7 @@ bool  _AVLList::IsValidIndex(long index) const {
 
 //______________________________________________________________
 
-long  _AVLList::GetByIndex (const long theIndex)
-{
+long  _AVLList::GetByIndex (const long theIndex) {
     if (theIndex == 0) {
         return First();
     }
@@ -475,7 +474,6 @@ const _List  _AVLList::Keys (void) const {
 
       cn = Traverser (hist,ls,root);
 
-      bool first = true;
       while (cn>=0) {
         keys << Retrieve (cn);
         cn = Traverser (hist,ls);