Folder structure

@@ -6,6 +6,7 @@
 *.lo
 *.o
 *.obj
+obj/*
 
 # Precompiled Headers
 *.gch
@@ -30,3 +31,4 @@
 *.exe
 *.out
 *.app
+bin/*

+# ------------------------------------------------
+# Generic Makefile
+# ------------------------------------------------
+
+# project name (generate executable with this name)
+TARGET   = motifscan
+
+CC	   = g++
+# compiling flags here
+CFLAGS   = -I. -O3
+CXXFLAGS = -std=c++17 -Wall -Wpedantic -Wextra
+
+LINKER   = g++
+# linking flags here
+LDFLAGS   = -lboost_system -lboost_filesystem -lboost_program_options
+
+# change these to proper directories where each file should be
+SRCDIR   = src
+OBJDIR   = obj
+BINDIR   = bin
+
+SOURCES  := $(wildcard $(SRCDIR)/*.cpp)
+INCLUDES := $(wildcard $(SRCDIR)/*.h)
+OBJECTS  := $(SOURCES:$(SRCDIR)/%.cpp=$(OBJDIR)/%.o)
+rm	   = rm -f
+
+$(BINDIR)/$(TARGET): $(OBJECTS)
+	@mkdir -p $(BINDIR)
+	$(LINKER) $(OBJECTS) $(LDFLAGS) -o $@
+	@echo "\033[00;32mLinking completed.\033[00m"
+
+$(OBJECTS): $(OBJDIR)/%.o : $(SRCDIR)/%.cpp $(INCLUDES)
+	@mkdir -p $(OBJDIR)
+	$(CC) -c $(CFLAGS) $(CXXFLAGS) $< -o $@
+	@echo "\033[00;32mCompiled "$<".\033[00m"
+
+.PHONY: clean
+clean:
+	$(rm) $(OBJECTS)
+	@echo "\033[00;32mCleanup completed.\033[00m"
+
+.PHONY: remove
+remove: clean
+	@$(rm) $(BINDIR)/$(TARGET)
+	@echo "\033[00;32mExecutable removed!\033[00m"
\ No newline at end of file

+#ifndef COMPONENT_H
+#define COMPONENT_H
+
+#include <string>
+
+class Component 
+{
+    public:
+        Component();
+        Component(std::string& cons_seq, uint k);
+    private:
+        std::string     _cons_seq;
+        uint            k;
+};
+
+
+istream& operator>>(istream& is, Component& m);
+ostream& operator<<(ostream& os, const Component& m);
+
+#endif
\ No newline at end of file

+#include "Motif.h"
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+#ifndef MOTIF_H
+#define MOTIF_H
+
+#include <vector>
+#include <string>
+#include "Component.h"
+
+class Motif
+{
+    public:
+        Motif();
+        Motif(std::string filename);
+        ~Motif();
+        std::vector<Component>& getComponents() const;
+        Component& getComponent(uint k) const;
+        std::string name;
+
+    private:
+        std::vector<Component>  _comps;
+
+};
+
+istream& operator>>(istream& is, Motif& m);
+ostream& operator<<(ostream& os, const Motif& m);
+
+#endif
\ No newline at end of file

+#include "RNA.h"
+
+RNA::RNA() {}
+
+RNA::~RNA() {}
+
+RNA::RNA(std::string seq) : _seq(seq) { }

+#ifndef RNA_H
+#define RNA_H
+
+#include <string>
+
+class RNA {
+    public:
+        RNA();
+        RNA(std::string);
+        ~RNA();
+        uint            length() const;
+        std::string     str() const;
+        // char            seq(uint k) const;
+        // bool            isConsensus() const;
+        // bool            containsPseudoBases() const;
+    private:
+        std::string     _seq;
+        // bool            _coding;
+        // bool            _consensus;
+        // bool            _containsPseudoNTs;
+};
+
+inline uint RNA::length() const { return _seq.length(); }
+inline std::string RNA::str() const { return _seq; }
+
+#endif
\ No newline at end of file

+#include "Motif.h"
+#include <cstdlib>
+#include <iostream>
+#include <unistd.h>
+#include <boost/program_options.hpp>
+#include <boost/filesystem.hpp>
+
+#include "RNA.h"
+
+using namespace std;
+namespace bpo = boost::program_options;
+namespace bf = boost::filesystem;
+
+bool checkMotifFolder(bf::path & folder)
+{
+    if (not(bf::is_directory(folder) and bf::exists(folder))) return false;
+    bf::directory_iterator end_itr;
+    uint Ndesc = 0;
+    for (bf::directory_iterator itr(folder); itr != end_itr; ++itr)
+    {
+        if (itr->path().leaf().string().find(string(".desc")) != std::string::npos)
+            Ndesc++;
+    }
+    cout << "Found " << Ndesc << " .desc files in " << folder.string() << endl;
+    if (Ndesc > 0)
+        return true;
+    return false;
+}
+
+int parseMotifs(bf::path & folder)
+{
+    bf::directory_iterator end_itr;
+    for (bf::directory_iterator itr(folder); itr != end_itr; ++itr)
+    {
+        if (itr->path().leaf().string().find(string(".desc")) != std::string::npos)
+        {
+            
+        }
+    }
+
+}
+
+int main(int argc, char** argv)
+{
+    bf::path                    currentFolder(bf::current_path());
+    bf::path                    motifFolderPath(currentFolder); // By default, searching here...
+    bpo::options_description    desc("Options"); 
+    bpo::variables_map          options_map;
+    RNA                         querySequence;
+
+    desc.add_options() 
+      ("help", "Print this help message")
+      ("seq,s", bpo::value<string>()->required(), "RNA sequence to find motives in.")
+      ("motifs,m", bpo::value<bf::path>(), "Path to folder of DESC files describing the motifs to be used") 
+    ;
+    bpo::store(bpo::parse_command_line(argc, argv, desc), options_map);
+    bpo::notify(options_map);
+
+    if (options_map.count("help")) { 
+        cout << desc << endl; 
+        return EXIT_SUCCESS; 
+    } 
+    if (options_map.count("motifs")) {
+        motifFolderPath = options_map["motifs"].as<bf::path>();
+        if (not(checkMotifFolder(motifFolderPath))) { return EXIT_FAILURE; }
+    }
+    if (options_map.count("seq")) {
+        querySequence = RNA(options_map["seq"].as<string>());
+    }
+    cout << "Working with sequence " << querySequence.str() << " (length " << querySequence.length() << ")." << endl;
+
+    return EXIT_SUCCESS;
+}