minor cleanup

.gitignore

@@ -14,3 +14,5 @@ experiments/data/markdowns/
 !experiments/data/markdowns/*topSeparators.Rmd
 experiments/data/htmls/*files
 experiments/logs/
+*.vscode
+*ipynb*

CTC_SCITE/CTC_treeScoring.cpp

@@ -17,8 +17,6 @@
 #include <stdio.h>
 #include <string.h>
 #include <vector>
-//#include "binTree_output.h"
-//#include "beta_distr.h"
 
 #include "CTC_treeScoring.h"
 #include "binTree_output.h"

CTC_SCITE/makefile

@@ -0,0 +1,56 @@
+CXX	= g++
+CXXFLAGS = -std=c++11 -O2
+
+
+CTC-SCITE: findBestTrees.o CTC_treeScoring.o binTree_output.o doublets.o enum.o matrices.o mcmc.o mcmcBinTreeMove.o output.o rand.o recMut.o scoreBinTree.o scoreTree.o treelist.o trees.o
+	${CXX} ${CXXFLAGS} -o CTC-SCITE findBestTrees.o CTC_treeScoring.o binTree_output.o doublets.o enum.o matrices.o mcmc.o mcmcBinTreeMove.o output.o rand.o recMut.o scoreBinTree.o scoreTree.o treelist.o trees.o
+
+
+
+findBestTrees.o: doublets.h matrices.h treelist.h trees.h output.h mcmc.h rand.h scoreTree.h binTree_output.h CTC_treeScoring.h
+	${CXX} ${CXXFLAGS} -c findBestTrees.cpp
+
+CTC_treeScoring.o: binTree_output.h scoreTree.h matrices.h rand.h trees.h matrices.h mcmcBinTreeMove.h mcmc.h CTC_treeScoring.h
+	${CXX} ${CXXFLAGS} -c CTC_treeScoring.cpp
+
+binTree_output.o: output.h scoreTree.h matrices.h trees.h binTree_output.h
+	${CXX} ${CXXFLAGS} -c binTree_output.cpp
+
+doublets.o: matrices.h treeList.h trees.h mcmc.h scoreTree.h scoreBinTree.h rand.h output.h mcmcBinTreeMove.h mcmcTreeMove.h recMut.h doublets.h
+	${CXX} ${CXXFLAGS} -c doublets.cpp
+
+enum.o: treelist.h trees.h matrices.h rand.h scoreTree.h enum.h
+	${CXX} ${CXXFLAGS} -c enum.cpp
+
+matrices.o: matrices.h
+	${CXX} ${CXXFLAGS} -c matrices.cpp
+
+mcmc.o: matrices.h treelist.h trees.h mcmc.h scoreTree.h scoreBinTree.h rand.h output.h mcmcBinTreeMove.h mcmcTreeMove.h
+	${CXX} ${CXXFLAGS} -c mcmc.cpp
+
+mcmcBinTreeMove.o: matrices.h treelist.h trees.h scoreTree.h rand.h output.h mcmcBinTreeMove.h
+	${CXX} ${CXXFLAGS} -c mcmcBinTreeMove.cpp
+
+output.o: output.h scoreTree.h trees.h recMut.h matrices.h
+	${CXX} ${CXXFLAGS} -c output.cpp
+
+rand.o: rand.h matrices.h
+	${CXX} ${CXXFLAGS} -c rand.cpp
+
+recMut.o: matrices.h trees.h scoreTree.o recMut.h
+	${CXX} ${CXXFLAGS} -c recMut.cpp
+
+scoreBinTree.o: scoreBinTree.h matrices.h trees.h
+	${CXX} ${CXXFLAGS} -c scoreBinTree.cpp
+
+scoreTree.o: scoreTree.h matrices.h treelist.h trees.h
+	${CXX} ${CXXFLAGS} -c scoreTree.cpp
+
+treelist.o: matrices.h rand.h treelist.h
+	${CXX} ${CXXFLAGS} -c treelist.cpp	
+
+trees.o: matrices.h treeList.o trees.h rand.h output.h
+	${CXX} ${CXXFLAGS} -c trees.cpp
+
+clean:
+	rm *.o

CTC_SCITE/rand.cpp

@@ -5,8 +5,6 @@
  *      Author: jahnka
  */
 
-//#include <string>
-//#include <random>
 #include <iostream>
 #include <random>
 #include <stdlib.h>

CTC_SCITE/rand.h

@@ -9,7 +9,6 @@
 #define RAND_H
 
 #include <vector>
-//#include <string>
 
 void initRand();
 bool changeBeta(double prob);

CTC_SCITE/treelist.h

@@ -6,8 +6,6 @@
  */
 
 #include <string>
-//#include <iostream>
-//#include <sstream>
 
 #ifndef TREELIST_H
 #define TREELIST_H