New upstream version 1.6.5+dfsg (a1731c9c) · Commits · Debian Med / iqtree

CMakeLists.txt

+4 −2

Original line number	Diff line number	Diff line
		@@ -51,7 +51,7 @@ add_definitions(-DIQ_TREE)
		# The version number.
		set (iqtree_VERSION_MAJOR 1)
		set (iqtree_VERSION_MINOR 6)
		set (iqtree_VERSION_PATCH "3")
		set (iqtree_VERSION_PATCH "5")

		set(BUILD_SHARED_LIBS OFF)

		@@ -71,6 +71,7 @@ endif()

		if (CMAKE_GENERATOR MATCHES "Xcode")
		set(CMAKE_XCODE_ATTRIBUTE_DEBUG_INFORMATION_FORMAT "dwarf-with-dsym")
		set(CMAKE_XCODE_ATTRIBUTE_COMPILER_INDEX_STORE_ENABLE "No")
		endif()

		include_directories("${PROJECT_SOURCE_DIR}")
		@@ -278,6 +279,7 @@ if (NOT IQTREE_FLAGS MATCHES "single")
		elseif (CLANG)
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp=libomp -pthread")
		set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fopenmp=libomp")
		endif()
		else()
		message("OpenMP : NONE")

alignment/alignment.cpp

+53 −8

Original line number	Diff line number	Diff line
		@@ -123,7 +123,7 @@ int Alignment::checkAbsentStates(string msg) {
		rare_states += ", ";
		rare_states += convertStateBackStr(i);
		}
		if (count >= num_states-1)
		if (count >= num_states-1 && Params::getInstance().fixed_branch_length != BRLEN_FIX)
		outError("Only one state is observed in " + msg);
		if (!absent_states.empty())
		cout << "NOTE: State(s) " << absent_states << " not present in " << msg << " and thus removed from Markov process to prevent numerical problems" << endl;
		@@ -138,12 +138,7 @@ void Alignment::checkSeqName() {
		StrVector::iterator it;
		for (it = seq_names.begin(); it != seq_names.end(); it++) {
		string orig_name = (*it);
		for (string::iterator i = it->begin(); i != it->end(); i++) {
		if (!isalnum(i) && (i) != '_' && (i) != '-' && (i) != '.') {
		(*i) = '_';
		}
		}
		if (orig_name != (*it))
		if (renameString(*it))
		warn_str << orig_name << " -> " << (*it) << endl;
		}
		if (warn_str.str() != "") {
		@@ -394,7 +389,12 @@ void Alignment::checkGappySeq(bool force_error) {
		}
		}

		Alignment::Alignment(char filename, char sequence_type, InputType &intype) : vector<Pattern>() {
		Alignment::Alignment(char filename, char sequence_type, InputType &intype, string model) : vector<Pattern>() {
		name = "Noname";
		this->model_name = model;
		if (sequence_type)
		this->sequence_type = sequence_type;
		aln_file = filename;
		num_states = 0;
		frac_const_sites = 0.0;
		frac_invariant_sites = 0.0;
		@@ -2636,6 +2636,11 @@ void Alignment::extractSubAlignment(Alignment *aln, IntVector &seq_id, int min_t
		ASSERT(it >= 0 && it < aln->getNSeq());
		seq_names.push_back(aln->getSeqName(*it));
		}
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		num_states = aln->num_states;
		seq_type = aln->seq_type;
		STATE_UNKNOWN = aln->STATE_UNKNOWN;
		@@ -2684,6 +2689,11 @@ void Alignment::extractPatterns(Alignment *aln, IntVector &ptn_id) {
		for (i = 0; i < aln->getNSeq(); i++) {
		seq_names.push_back(aln->getSeqName(i));
		}
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		num_states = aln->num_states;
		seq_type = aln->seq_type;
		STATE_UNKNOWN = aln->STATE_UNKNOWN;
		@@ -2720,6 +2730,11 @@ void Alignment::extractPatternFreqs(Alignment *aln, IntVector &ptn_freq) {
		for (i = 0; i < aln->getNSeq(); i++) {
		seq_names.push_back(aln->getSeqName(i));
		}
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		num_states = aln->num_states;
		seq_type = aln->seq_type;
		genetic_code = aln->genetic_code;
		@@ -2756,6 +2771,11 @@ void Alignment::extractSites(Alignment *aln, IntVector &site_id) {
		for (i = 0; i < aln->getNSeq(); i++) {
		seq_names.push_back(aln->getSeqName(i));
		}
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		num_states = aln->num_states;
		seq_type = aln->seq_type;
		STATE_UNKNOWN = aln->STATE_UNKNOWN;
		@@ -2799,6 +2819,11 @@ void Alignment::convertToCodonOrAA(Alignment aln, char gene_code_id, bool nt2a
		for (i = 0; i < aln->getNSeq(); i++) {
		seq_names.push_back(aln->getSeqName(i));
		}
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		// num_states = aln->num_states;
		seq_type = SEQ_CODON;
		initCodon(gene_code_id);
		@@ -2971,6 +2996,11 @@ void Alignment::extractSites(Alignment aln, const char spec) {

		void Alignment::createBootstrapAlignment(Alignment aln, IntVector pattern_freq, const char *spec) {
		if (aln->isSuperAlignment()) outError("Internal error: ", __func__);
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		int site, nsite = aln->getNSite();
		seq_names.insert(seq_names.begin(), aln->seq_names.begin(), aln->seq_names.end());
		num_states = aln->num_states;
		@@ -3235,6 +3265,11 @@ void Alignment::createBootstrapAlignment(int pattern_freq, const char spec, in
		void Alignment::buildFromPatternFreq(Alignment & aln, IntVector new_pattern_freqs){
		int nsite = aln.getNSite();
		seq_names.insert(seq_names.begin(), aln.seq_names.begin(), aln.seq_names.end());
		name = aln.name;
		model_name = aln.model_name;
		sequence_type = aln.sequence_type;
		position_spec = aln.position_spec;
		aln_file = aln.aln_file;
		num_states = aln.num_states;
		seq_type = aln.seq_type;

		@@ -3274,6 +3309,11 @@ void Alignment::createGapMaskedAlignment(Alignment masked_aln, Alignment aln)

		int site, nsite = aln->getNSite(), nseq = aln->getNSeq();
		seq_names.insert(seq_names.begin(), aln->seq_names.begin(), aln->seq_names.end());
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		num_states = aln->num_states;
		seq_type = aln->seq_type;
		genetic_code = aln->genetic_code;
		@@ -3343,6 +3383,11 @@ void Alignment::concatenateAlignment(Alignment *aln) {
		void Alignment::copyAlignment(Alignment *aln) {
		int site, nsite = aln->getNSite();
		seq_names.insert(seq_names.begin(), aln->seq_names.begin(), aln->seq_names.end());
		name = aln->name;
		model_name = aln->model_name;
		sequence_type = aln->sequence_type;
		position_spec = aln->position_spec;
		aln_file = aln->aln_file;
		num_states = aln->num_states;
		seq_type = aln->seq_type;
		genetic_code = aln->genetic_code;

alignment/alignment.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -65,7 +65,7 @@ Multiple Sequence Alignment. Stored by a vector of site-patterns

		@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>
		*/
		class Alignment : public vector<Pattern> {
		class Alignment : public vector<Pattern>, public CharSet {
		friend class SuperAlignment;

		public:
		@@ -81,7 +81,7 @@ public:
		@param sequence_type type of the sequence, either "BIN", "DNA", "AA", or NULL
		@param intype (OUT) input format of the file
		*/
		Alignment(char filename, char sequence_type, InputType &intype);
		Alignment(char filename, char sequence_type, InputType &intype, string model);

		/**
		destructor

alignment/maalignment.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -34,7 +34,7 @@ class MaAlignment : public Alignment
		public:
		MaAlignment() : Alignment() {};

		MaAlignment(char filename, char sequence_type, InputType &intype) : Alignment(filename, sequence_type, intype){};
		MaAlignment(char filename, char sequence_type, InputType &intype, string model) : Alignment(filename, sequence_type, intype, model){};

		MaAlignment(Alignment &align) : Alignment(align){};

alignment/superalignment.cpp

+513 −14

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