[med-svn] [Git][med-team/hyphy][upstream] New upstream version 2.5.42+dfsg
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Sep 22 08:20:59 BST 2022
Andreas Tille pushed to branch upstream at Debian Med / hyphy
Commits:
13b2fc15 by Andreas Tille at 2022-09-22T09:13:22+02:00
New upstream version 2.5.42+dfsg
- - - - -
14 changed files:
- res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
- src/core/classes.cp
- src/core/global_things.cpp
- src/core/include/batchlan.h
- src/core/include/dataset.h
- src/core/include/hy_strings.h
- src/core/include/likefunc.h
- src/core/include/list.h
- src/core/include/matrix.h
- src/core/include/parser.h
- src/core/include/vector.h
- src/core/likefunc.cpp
- src/core/vector.cpp
- src/mains/unix.cpp
Changes:
=====================================
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 {
@@ -314,7 +314,6 @@ 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;
@@ -322,7 +321,6 @@ node<node_data>* NodeTraverser (node<node_data>* 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 @@ public:
_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 @@ public:
}
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 @@ public:
_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 @@ public:
- 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 @@ public:
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 @@ public:
_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 @@ public:
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 @@ public:
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 {
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/commit/13b2fc159fb346d7d77cfd2c4671a78071665f11
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/commit/13b2fc159fb346d7d77cfd2c4671a78071665f11
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