output format cleanup and polish

Author: bhaller

VERSIONS

@@ -130,6 +130,7 @@ development head (in the master branch):
 			Species method outputFull(): allow multi-chromosome output with a new sectioned format, for both text and binary
 			Species method readFromPopulationFile(): support reading multi-chromosome output, for both text and binary
 			policy change: readFromPopulationFile() breaks backward compatibility with old file formats, for both text and binary; too much has changed
+		change file format codes for class Haplosome from GS/GM/GV to HS/HM/HV, matching the rename from Genome to Haplosome
 
 
 version 4.3 (Eidos version 3.3):

core/haplosome.cpp

@@ -1343,8 +1343,6 @@ void Haplosome::PrintHaplosomes_SLiM(std::ostream &p_out, std::vector<Haplosome
 		else
 			p_out << "p" << p_source_subpop_id << ":" << j;
 
-		p_out << " " << p_chromosome.Symbol();	// all haplosomes must be associated with p_chromosome
-		
 		for (int run_index = 0; run_index < haplosome.mutrun_count_; ++run_index)
 		{
 			const MutationRun *mutrun = haplosome.mutruns_[run_index];
@@ -3069,7 +3067,8 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_outputX(EidosGlobalStringID p_metho
 		// BCH 2/2/2025: added the cycle count here after the tick; it was already documented as being here!
 		// BCH 2/2/2025: added the chromosome symbol in the header; it is redundant for SLiM-format output,
 		// but useful for MS and VCF; I decided to put it in all three for consistency across formats
-		output_stream << "#OUT: " << community.Tick() << " " << species->Cycle() << " G";
+		// BCH 2/7/2025: changed GS/GM/GV to HS/HM/HV, for the genome -> haplosome transition
+		output_stream << "#OUT: " << community.Tick() << " " << species->Cycle() << " H";
 
 		if (p_method_id == gID_output)
 			output_stream << "S";
@@ -3081,7 +3080,10 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_outputX(EidosGlobalStringID p_metho
 		output_stream << " " << sample_size;
 
 		if (chromosomes.size() > 1)
-			output_stream << " " << chromosome->Symbol();			// chromosome symbol, with >1 chromosome
+		{
+			output_stream << " " << chromosome->Type();						// chromosome type, with >1 chromosome
+			output_stream << " \"" << chromosome->Symbol() << "\"";			// chromosome symbol, with >1 chromosome
+		}
 
 		output_stream << std::endl;
 
@@ -3111,10 +3113,14 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_outputX(EidosGlobalStringID p_metho
 					// BCH 2/2/2025: added the cycle count here after the tick; it was already documented as being here!
 					// BCH 2/2/2025: added the chromosome symbol in the header; it is redundant for SLiM-format output,
 					// but useful for MS and VCF; I decided to put it in all three for consistency across formats
-					outfile << "#OUT: " << community.Tick() << " " << species->Cycle() << " GS " << sample_size;
+					// BCH 2/7/2025: changed GS/GM/GV to HS/HM/HV, for the genome -> haplosome transition
+					outfile << "#OUT: " << community.Tick() << " " << species->Cycle() << " HS " << sample_size;
 
 					if (chromosomes.size() > 1)
-						outfile << " " << chromosome->Symbol();			// chromosome symbol, with >1 chromosome
+					{
+						outfile << " " << chromosome->Type();						// chromosome type, with >1 chromosome
+						outfile << " \"" << chromosome->Symbol() << "\"";			// chromosome symbol, with >1 chromosome
+					}
 
 					outfile << " " << outfile_path << std::endl;
 

core/polymorphism.cpp

@@ -73,7 +73,7 @@ void Polymorphism::Print_NoID(std::ostream &p_out) const
 	{
 		Chromosome *chromosome = chromosomes[mutation_ptr_->chromosome_index_];
 
-		p_out << " " << chromosome->Symbol();
+		p_out << " \"" << chromosome->Symbol() << "\"";
 	}
 
 	// and then the remainder of the output line

core/population.cpp

@@ -7666,9 +7666,9 @@ void Population::PrintAll(std::ostream &p_out, bool p_output_spatial_positions,
 				p_out << " " << individual.PedigreeID();
 
 			if (subpop->sex_enabled_)
-				p_out << ((i < first_male_index) ? " F " : " M ");		// sex: SEX ONLY
+				p_out << ((i < first_male_index) ? " F" : " M");		// sex: SEX ONLY
 			else
-				p_out << " H ";											// hermaphrodite
+				p_out << " H";											// hermaphrodite
 
 			// BCH 2/5/2025: Before version 8, we emitted haplosome identifiers here, like "p1:16" and
 			// "p1:17", but now that we have multiple chromosomes that really isn't helpful; removing
@@ -7727,7 +7727,7 @@ void Population::PrintAll(std::ostream &p_out, bool p_output_spatial_positions,
 		// write information about the chromosome; note that we write the chromosome symbol, but PrintAllBinary() does not
 		slim_chromosome_index_t chromosome_index = chromosome->Index();
 
-		p_out << "Chromosome: " << (uint32_t)chromosome_index << " " << chromosome->Type() << " " << chromosome->ID() << " " << chromosome->last_position_ << " " << chromosome->Symbol()  << std::endl;
+		p_out << "Chromosome: " << (uint32_t)chromosome_index << " " << chromosome->Type() << " " << chromosome->ID() << " " << chromosome->last_position_ << " \"" << chromosome->Symbol() << "\"" << std::endl;
 
 		int first_haplosome_index = species_.FirstHaplosomeIndices()[chromosome_index];
 		int last_haplosome_index = species_.LastHaplosomeIndices()[chromosome_index];
@@ -7811,8 +7811,7 @@ void Population::PrintAll(std::ostream &p_out, bool p_output_spatial_positions,
 
 					// i used to be the haplosome index, now it is the individual index; we will have one or
 					// two lines with this individual index, depending on the intrinsic ploidy of the chromosome
-					// symbol is redundant but kinda nice for orientation
-					p_out << "p" << subpop_id << ":" << individual_index << " " << chromosome->Symbol();
+					p_out << "p" << subpop_id << ":" << individual_index;
 
 					if (haplosome->IsNull())
 					{

core/slim_globals.cpp

@@ -2428,7 +2428,7 @@ void WriteProfileResults(std::string profile_output_path, std::string model_name
 
 		for (Chromosome *focal_chromosome : chromosomes)
 		{
-			fout << "<p><i>Chromosome " << focal_chromosome->Symbol() << ":</i></p>\n";
+			fout << "<p><i>Chromosome \"" << focal_chromosome->Symbol() << "\":</i></p>\n";
 
 			{
 				int64_t power_tallies[20];	// we only go up to 1024 mutruns right now, but this gives us some headroom

core/species.cpp

@@ -1123,8 +1123,9 @@ slim_tick_t Species::_InitializePopulationFromTextFile(const char *p_file, Eidos
 
 		// chromosome symbol
 		chrom_iss >> sub;
+		std::string quoted_symbol = '\"' + chromosome->Symbol() + '\"';
 
-		if (sub != chromosome->Symbol())
+		if (sub != quoted_symbol)
 			EIDOS_TERMINATION << "ERROR (Species::_InitializePopulationFromTextFile): chromosome symbol " << sub << " does not match expected symbol " << chromosome->Symbol() << "." << EidosTerminate();
 
 		GetInputLine(infile, line);
@@ -1287,12 +1288,6 @@ slim_tick_t Species::_InitializePopulationFromTextFile(const char *p_file, Eidos
 			int haplosome_index = first_haplosome_index + is_individual_index_repeat;
 			Haplosome &haplosome = *(ind->haplosomes_[haplosome_index]);
 
-			// Now we should have a chromosome symbol, which should match the one we read
-			iss >> sub;
-			
-			if (sub != chromosome->Symbol())
-				EIDOS_TERMINATION << "ERROR (Species::_InitializePopulationFromTextFile): haplosome is specified with chromosome symbol '" << sub << "', in the Chromosome section for symbol '" << chromosome->Symbol() << "'." << EidosTerminate();
-			
 			if (iss >> sub)
 			{
 				// BCH 2/5/2025: We instantiate null haplosomes only where expect them to be, based upon

core/subpopulation.cpp

@@ -11153,7 +11153,10 @@ EidosValue_SP Subpopulation::ExecuteMethod_outputXSample(EidosGlobalStringID p_m
 			out << " " << requested_sex;
 
 		if (chromosomes.size() > 1)
-			output_stream << " " << chromosome->Symbol();			// chromosome symbol, with >1 chromosome
+		{
+			output_stream << " " << chromosome->Type();						// chromosome type, with >1 chromosome
+			output_stream << " \"" << chromosome->Symbol() << "\"";			// chromosome symbol, with >1 chromosome
+		}
 
 		if (has_file)
 			out << " " << outfile_path;

core/substitution.cpp

@@ -60,7 +60,7 @@ void Substitution::PrintForSLiMOutput(std::ostream &p_out) const
 	{
 		Chromosome *chromosome = chromosomes[chromosome_index_];
 
-		p_out << " " << chromosome->Symbol();
+		p_out << " \"" << chromosome->Symbol() << "\"";
 	}
 
 	// and then the remainder of the output line