NSGA-II Optimizer

.gitignore

@@ -4,8 +4,18 @@ modules.h
 # Ignore xcode project file:
 mabe.xcodeproj
 
+# Ignore vs project files:
+mabe.vcxproj
+mabe.vcxproj.user
+
 # Ingore intermediate objects:
 objectFiles/
 
 # Ignore python's cache:
 __pycache__/
+
+x64/
+.vs/
+Debug/
+*.csv
+*.out

.vscode/settings.json

@@ -0,0 +1,72 @@
+{
+    "files.associations": {
+        "ostream": "cpp",
+        "algorithm": "cpp",
+        "array": "cpp",
+        "bitset": "cpp",
+        "cctype": "cpp",
+        "chrono": "cpp",
+        "cmath": "cpp",
+        "csignal": "cpp",
+        "cstddef": "cpp",
+        "cstdint": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "deque": "cpp",
+        "exception": "cpp",
+        "fstream": "cpp",
+        "functional": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "ios": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "iterator": "cpp",
+        "limits": "cpp",
+        "list": "cpp",
+        "locale": "cpp",
+        "map": "cpp",
+        "memory": "cpp",
+        "new": "cpp",
+        "numeric": "cpp",
+        "random": "cpp",
+        "ratio": "cpp",
+        "regex": "cpp",
+        "set": "cpp",
+        "sstream": "cpp",
+        "stack": "cpp",
+        "stdexcept": "cpp",
+        "streambuf": "cpp",
+        "string": "cpp",
+        "system_error": "cpp",
+        "thread": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "typeinfo": "cpp",
+        "unordered_map": "cpp",
+        "unordered_set": "cpp",
+        "utility": "cpp",
+        "vector": "cpp",
+        "xfacet": "cpp",
+        "xhash": "cpp",
+        "xiosbase": "cpp",
+        "xlocale": "cpp",
+        "xlocbuf": "cpp",
+        "xlocinfo": "cpp",
+        "xlocmes": "cpp",
+        "xlocmon": "cpp",
+        "xlocnum": "cpp",
+        "xloctime": "cpp",
+        "xmemory": "cpp",
+        "xstddef": "cpp",
+        "xstring": "cpp",
+        "xtr1common": "cpp",
+        "xtree": "cpp",
+        "xutility": "cpp"
+    }
+}

DAG_settings.cfg

@@ -0,0 +1,4 @@
+node_weights_filename=canon_nw
+edge_weights_filename=canon_ew
+bandwidth_filename=canon_bw
+graph_size=10

Genome/AbstractGenome.h

@@ -156,6 +156,7 @@ class AbstractGenome {
   virtual void copyFrom(std::shared_ptr<AbstractGenome> from) = 0;
 
   virtual void fillRandom() = 0;
+  virtual void fillConstant(int value) = 0;
 
   //// gets data about genome which can be added to a data map
   //// data is in pairs of strings (key, value)

Genome/CircularGenome/CircularGenome.cpp

@@ -17,24 +17,24 @@
 std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::sizeInitialPL = Parameters::register_parameter("GENOME_CIRCULAR-sizeInitial", 5000, "starting size for genome");
 std::shared_ptr<ParameterLink<double>> CircularGenomeParameters::mutationPointRatePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationPointRate", 0.005, "per site point mutation rate");
 std::shared_ptr<ParameterLink<double>> CircularGenomeParameters::mutationCopyRatePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationCopyRate", 0.00002, "per site insertion rate");
-std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationCopyMinSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationCopyMinSize", 128, "minimum size of insertion mutation");
-std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationCopyMaxSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationCopyMaxSize", 512, "maximum size of insertion mutation");
+std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationCopyMinSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationCopyMinSize", 1, "minimum size of insertion mutation");
+std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationCopyMaxSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationCopyMaxSize", 10, "maximum size of insertion mutation");
 std::shared_ptr<ParameterLink<double>> CircularGenomeParameters::mutationDeleteRatePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationDeleteRate", 0.00002, "per site deletion rate");
-std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationDeleteMinSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationDeleteMinSize", 128, "minimum size of insertion mutation");
-std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationDeleteMaxSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationDeleteMaxSize", 512, "maximum size of insertion mutation");
+std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationDeleteMinSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationDeleteMinSize", 1, "minimum size of insertion mutation");
+std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationDeleteMaxSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationDeleteMaxSize", 10, "maximum size of insertion mutation");
 std::shared_ptr<ParameterLink<double>> CircularGenomeParameters::mutationIndelRatePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationIndelRate", 0.0, "per site insertion+deletion (indel) rate. This mutation copies a segment of the genome and deletes a segment of the same size so genome size remains fixed).");
-std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationIndelMinSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationIndelMinSize", 128, "minimum size of insertion-deletion mutation");
-std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationIndelMaxSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationIndelMaxSize", 512, "maximum size of insertion-deletion mutation");
+std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationIndelMinSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationIndelMinSize", 1, "minimum size of insertion-deletion mutation");
+std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationIndelMaxSizePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationIndelMaxSize", 10, "maximum size of insertion-deletion mutation");
 std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationIndelInsertMethodPL = Parameters::register_parameter("GENOME_CIRCULAR-mutationIndelInsertMethod", 0, "where is copied material inserted?\n0 = place random, 1 = replace deleted sites, 2 = insert just before copied material");
 std::shared_ptr<ParameterLink<bool>> CircularGenomeParameters::mutationIndelCopyFirstPL = Parameters::register_parameter("GENOME_CIRCULAR-mutationIndelCopyFirst", true, "whether copy or deletion happens first (0 = delete first, 1 = copy first)");
 std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::sizeMinPL = Parameters::register_parameter("GENOME_CIRCULAR-sizeMin", 2000, "if genome is smaller then this, mutations will only increase chromosome size");
 std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::sizeMaxPL = Parameters::register_parameter("GENOME_CIRCULAR-sizeMax", 20000, "if genome is larger then this, mutations will only decrease chromosome size");
 std::shared_ptr<ParameterLink<int>> CircularGenomeParameters::mutationCrossCountPL = Parameters::register_parameter("GENOME_CIRCULAR-mutationCrossCount", 3, "number of crosses when performing crossover (including during recombination)");
 
 
-std::shared_ptr<ParameterLink<double>> CircularGenomeParameters::mutationPointOffsetRatePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationPointOffsetRate", 0.0, "per site point offset mutation rate (site changes in range (+/-)mutationPointOffsetRange)");
+std::shared_ptr<ParameterLink<double>> CircularGenomeParameters::mutationPointOffsetRatePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationPointOffsetRate", 0.0, "per site point offset mutation rate (site changes in range (+/-)mutationPointOffsetRange)");
 std::shared_ptr<ParameterLink<double>> CircularGenomeParameters::mutationPointOffsetRangePL = Parameters::register_parameter("GENOME_CIRCULAR-mutationPointOffsetRange", 1.0, "range of PointOffset mutation");
-
+
 
 // constructor
 template<class T>
@@ -353,6 +353,8 @@ std::vector<std::vector<int>> CircularGenome<T>::Handler::readTable(std::pair<in
 template<class T>
 void CircularGenome<T>::setupCircularGenome(int _size, double _alphabetSize) {
 	sites.resize(_size);
+
+
 	alphabetSize = _alphabetSize;
 	// define columns to be written to genome files
 	genomeFileColumns.clear();

Genome/CircularGenome/CircularGenome.h

@@ -12,7 +12,7 @@
 
 #include <cstdlib>
 #include <vector>
-#include <limits>
+#include <limits>
 
 #include <fstream>
 #include <iostream>
@@ -42,11 +42,11 @@ class CircularGenomeParameters {
 	static std::shared_ptr<ParameterLink<int>> sizeMinPL;
 	static std::shared_ptr<ParameterLink<int>> mutationCrossCountPL;  // number of crosses to make when performing crossover
 
-	static std::shared_ptr<ParameterLink<double>> mutationIndelRatePL;
-	static std::shared_ptr<ParameterLink<int>> mutationIndelMinSizePL;
-	static std::shared_ptr<ParameterLink<int>> mutationIndelMaxSizePL;
-	static std::shared_ptr<ParameterLink<int>> mutationIndelInsertMethodPL;
-	static std::shared_ptr<ParameterLink<bool>> mutationIndelCopyFirstPL;
+	static std::shared_ptr<ParameterLink<double>> mutationIndelRatePL;
+	static std::shared_ptr<ParameterLink<int>> mutationIndelMinSizePL;
+	static std::shared_ptr<ParameterLink<int>> mutationIndelMaxSizePL;
+	static std::shared_ptr<ParameterLink<int>> mutationIndelInsertMethodPL;
+	static std::shared_ptr<ParameterLink<bool>> mutationIndelCopyFirstPL;
 
 };
 
@@ -107,6 +107,7 @@ class CircularGenome : public AbstractGenome {
 		virtual std::vector<std::vector<int>> readTable(std::pair<int, int> tableSize, std::pair<int, int> tableMaxSize, std::pair<int, int> valueRange, int code = -1, int CodingRegionIndex = 0) override;
 
 	};
+
 
 	std::vector<T> sites;
 	double alphabetSize;
@@ -174,7 +175,7 @@ class CircularGenome : public AbstractGenome {
 	virtual int incrementPoint();
 	virtual int incrementPointOffset();
 	virtual int incrementDelete();
-	virtual int incrementIndel();
+	virtual int incrementIndel();
 
 	// apply mutations to this genome
 	virtual void mutate() override;

Genome/MultiGenome/MultiGenome.cpp

@@ -361,6 +361,13 @@ void MultiGenome::fillRandom() {
 	}
 }
 
+void MultiGenome::fillConstant(int value)
+{
+	for (auto chromosome : chromosomes) {
+		chromosome->fillConstant(value);
+	}
+}
+
 // fill all sites of this genome with ascending values
 // This function is to make testing easy.
 void MultiGenome::fillAcending() {

Genome/MultiGenome/MultiGenome.h

@@ -115,7 +115,7 @@ class MultiGenome : public AbstractGenome {
                              double valueMax) override;
 
     virtual std::shared_ptr<AbstractGenome::Handler> makeCopy() override;
-
+	
     // copy contents of this handler to "to"
     virtual void copyTo(std::shared_ptr<AbstractGenome::Handler> to) override;
     // true if handler is within length sites from end of a chromosome
@@ -156,6 +156,7 @@ class MultiGenome : public AbstractGenome {
 
   // randomize this genomes contents
   virtual void fillRandom() override;
+  virtual void fillConstant(int value) override;
 
   // fill all sites of this genome with ascending values
   // This function is to make testing easy.