Additional DecentTree example showing how to plug in

vector classes that *aren't* from Agner Fog's VCL
Vector Class library.
1. Moved example matrix string to example_matrix.cpp
   (example_matrix is declared in example_matrix.h).
2. Added fakevector.h, which declares
   MyFloatVector and MyBoolVector classes, and a
   version of select() that takes a fake boolean
   vector, and two fake float vectors, by reference
   select(a,b,c) returns a float vector, r such that
   r[i] = a[i] !=0 ? b[i] : c[i].
3. Added differentvector.cpp, which builds an example
   that uses MyFloatVector and MyBoolVector.
4. examples/CMakeLists.txt hauls in more stuff (for
   progress bars, and builds differentvector)

Author: James Barbetti

example/CMakeLists.txt

@@ -1,5 +1,14 @@
 add_executable(hod_tree
-    headeronlydecenttree.cpp)
+    headeronlydecenttree.cpp example_matrix.cpp
+    ../utils/progress.cpp         ../utils/progress.h 
+    ../utils/operatingsystem.cpp  ../utils/operatingsystem.h)
 
 add_executable(vectordecenttree
-    vectordecenttree.cpp ../utils/progress.cpp)
+    vectordecenttree.cpp example_matrix.cpp ../utils/progress.cpp
+    ../utils/progress.cpp         ../utils/progress.h 
+    ../utils/operatingsystem.cpp  ../utils/operatingsystem.h)
+
+add_executable(differentvector
+    differentvector.cpp           example_matrix.cpp 
+    ../utils/progress.cpp         ../utils/progress.h 
+    ../utils/operatingsystem.cpp  ../utils/operatingsystem.h)

example/differentvector.cpp

@@ -0,0 +1,26 @@
+#define USE_PROGRESS_DISPLAY    1 //Even though there's not much point on an input this small.
+#define USE_VECTORCLASS_LIBRARY 1 //For an input this small, vectorisation doesn't matter.
+#define DECENT_TREE             1 //Tells shared headers that decenttree, rather than
+                                  //iqtree2, is being built. 
+
+#include "example_matrix.h"
+#include "fakevector.h"
+#include <rapidnj.h>
+
+typedef StartTree::VectorizedBoundingMatrix
+        <double, MyFloatVector, MyBoolVector> 
+        MyVBM;
+
+int main(int argc, char* argv[]) {
+
+    progress_display::setProgressDisplay(true);
+    
+    MyVBM r;
+	std::istringstream input_file(example_matrix);
+	loadDistanceMatrixFromOpenFile(input_file, false, r);
+	r.constructTree();
+
+	int precision = 6;
+	std::string newickTreeFilePath = "STDOUT";
+	r.writeTreeFile(precision, newickTreeFilePath);
+}

example/example_matrix.cpp

@@ -0,0 +1,18 @@
+const char* example_matrix = "17\n"
+		"LngfishAu  0.0000000 0.4394262 0.4253346 0.4739334 0.6469595 0.8072464 0.7697307 0.7867055 0.7850803 0.6959920 0.6336127 0.6997504 0.6793033 0.7120045 0.7344446 0.7318557 0.6820929\n"
+		"LngfishSA  0.4394262 0.0000000 0.3370420 0.6028511 0.7361390 0.8116547 0.7978951 0.7651678 0.6988087 0.7598439 0.7003997 0.7643007 0.7378452 0.7195253 0.8065221 0.7439359 0.6178323\n"
+		"LngfishAf  0.4253346 0.3370420 0.0000000 0.5921847 0.7020407 0.8573580 0.9137406 0.8639154 0.7878422 0.8294442 0.7505365 0.7882964 0.7551778 0.7706974 0.8561868 0.7818997 0.6850401\n"
+		"Frog       0.4739334 0.6028511 0.5921847 0.0000000 0.6268957 0.8150864 0.7705955 0.8145647 0.7573321 0.7166360 0.6626602 0.6762896 0.6809187 0.7005612 0.7136883 0.6974592 0.6449470\n"
+		"Turtle     0.6469595 0.7361390 0.7020407 0.6268957 0.0000000 0.5416702 0.5841215 0.5399763 0.4849490 0.5861821 0.5383720 0.5458270 0.5612534 0.5632785 0.6088667 0.5946969 0.5778748\n"
+		"Sphenodon  0.8072464 0.8116547 0.8573580 0.8150864 0.5416702 0.0000000 0.6723304 0.6249144 0.5897511 0.6946471 0.6787380 0.6565584 0.6772154 0.6833316 0.7476896 0.7240949 0.6518428\n"
+		"Lizard     0.7697307 0.7978951 0.9137406 0.7705955 0.5841215 0.6723304 0.0000000 0.7160903 0.6480652 0.7386573 0.7042574 0.7513723 0.7675040 0.6849374 0.7926459 0.7473559 0.6709445\n"
+		"Crocodile  0.7867055 0.7651678 0.8639154 0.8145647 0.5399763 0.6249144 0.7160903 0.0000000 0.4906657 0.7432287 0.7493887 0.7488493 0.8057593 0.8317762 0.8413625 0.7521970 0.7769550\n"
+		"Bird       0.7850803 0.6988087 0.7878422 0.7573321 0.4849490 0.5897511 0.6480652 0.4906657 0.0000000 0.6755495 0.6691967 0.6860033 0.6905877 0.7565543 0.7504430 0.6842440 0.6705485\n"
+		"Human      0.6959920 0.7598439 0.8294442 0.7166360 0.5861821 0.6946471 0.7386573 0.7432287 0.6755495 0.0000000 0.2750272 0.2814737 0.2961226 0.3590137 0.3757584 0.4477864 0.4220981\n"
+		"Seal       0.6336127 0.7003997 0.7505365 0.6626602 0.5383720 0.6787380 0.7042574 0.7493887 0.6691967 0.2750272 0.0000000 0.1931946 0.2118470 0.2817599 0.3180795 0.3787176 0.3496224\n"
+		"Cow        0.6997504 0.7643007 0.7882964 0.6762896 0.5458270 0.6565584 0.7513723 0.7488493 0.6860033 0.2814737 0.1931946 0.0000000 0.1754464 0.3199376 0.3320971 0.4013694 0.3449257\n"
+		"Whale      0.6793033 0.7378452 0.7551778 0.6809187 0.5612534 0.6772154 0.7675040 0.8057593 0.6905877 0.2961226 0.2118470 0.1754464 0.0000000 0.3251485 0.3558385 0.3925798 0.3595924\n"
+		"Mouse      0.7120045 0.7195253 0.7706974 0.7005612 0.5632785 0.6833316 0.6849374 0.8317762 0.7565543 0.3590137 0.2817599 0.3199376 0.3251485 0.0000000 0.1447365 0.4099219 0.3487804\n"
+		"Rat        0.7344446 0.8065221 0.8561868 0.7136883 0.6088667 0.7476896 0.7926459 0.8413625 0.7504430 0.3757584 0.3180795 0.3320971 0.3558385 0.1447365 0.0000000 0.4419960 0.4050277\n"
+		"Platypus   0.7318557 0.7439359 0.7818997 0.6974592 0.5946969 0.7240949 0.7473559 0.7521970 0.6842440 0.4477864 0.3787176 0.4013694 0.3925798 0.4099219 0.4419960 0.0000000 0.3202751\n"
+		"Opossum    0.6820929 0.6178323 0.6850401 0.6449470 0.5778748 0.6518428 0.6709445 0.7769550 0.6705485 0.4220981 0.3496224 0.3449257 0.3595924 0.3487804 0.4050277 0.3202751 0.0000000\n";

example/example_matrix.h

@@ -0,0 +1 @@
+extern const char* example_matrix;

example/fakevector.h

@@ -0,0 +1,65 @@
+#include <stdint.h>
+
+template<class T, int n> class FakeVector {
+public:
+    T data[n]; //so that operator < can see it
+    FakeVector() {
+        for (int i=0; i<n; ++i) {
+            data[i]=0;
+        }
+    }
+    FakeVector(const FakeVector& r) = default;
+    explicit FakeVector(T v) {
+        for (int i=0; i<n; ++i) {
+            data[i]=v;
+        }
+    }
+    FakeVector& operator= (const FakeVector& rhs) = default;
+
+    int size() { return n; }
+    FakeVector& load(const T* p) {
+        for (int i=0; i<n; ++i) {
+            data[i]=p[i];
+        }
+        return *this;
+    }
+    FakeVector& store(T* p) {
+        for (int i=0; i<n; ++i) {
+            p[i]=data[i];
+        }
+        return *this;
+    }
+
+    FakeVector operator-(const FakeVector& rhs) {
+        FakeVector result;
+        for (int i=0; i<n; ++i) {
+            result.data[i] = data[i] - rhs.data[i];
+        }
+        return result;
+    }
+};
+
+typedef FakeVector<double,  4> MyFloatVector;
+typedef FakeVector<uint64_t, 4> MyBoolVector;
+
+template <class T, int s> 
+    FakeVector<uint64_t,s> operator< 
+    ( const FakeVector<T,s>& left, const FakeVector<T,s>& right ) {
+    FakeVector<uint64_t,s> result;
+    for (int i=0; i<s; ++i) {
+        result.data[i] = ( left.data[i] < right.data[i] ) ? -1 : 0;
+    }
+    return result;
+}
+
+template <class T, int s, class B> 
+    FakeVector<T,s> select ( const FakeVector<B,s>& isLess,
+                             const FakeVector<T,s>& left,
+                             const FakeVector<T,s>& right ) {
+    FakeVector<T,s> result;
+    for (int i=0; i<s; ++i) {
+        result.data[i] = (isLess.data[i]==-1) 
+                       ? left.data[i] : right.data[i];
+    }
+    return result;
+}

example/headeronlydecenttree.cpp

@@ -13,32 +13,12 @@
 #include <distancematrix.h>	//for loadDistanceMatrixFromOpenFile
 #include <rapidnj.h>		//for RapidNJ
 #include <sstream>          //for std::istringstream
+#include "example_matrix.h" //for example_matrix string
 
 void example_1() {
 	StartTree::RapidNJ r;
 
-	const char* input_string =
-		"17\n"
-		"LngfishAu  0.0000000 0.4394262 0.4253346 0.4739334 0.6469595 0.8072464 0.7697307 0.7867055 0.7850803 0.6959920 0.6336127 0.6997504 0.6793033 0.7120045 0.7344446 0.7318557 0.6820929\n"
-		"LngfishSA  0.4394262 0.0000000 0.3370420 0.6028511 0.7361390 0.8116547 0.7978951 0.7651678 0.6988087 0.7598439 0.7003997 0.7643007 0.7378452 0.7195253 0.8065221 0.7439359 0.6178323\n"
-		"LngfishAf  0.4253346 0.3370420 0.0000000 0.5921847 0.7020407 0.8573580 0.9137406 0.8639154 0.7878422 0.8294442 0.7505365 0.7882964 0.7551778 0.7706974 0.8561868 0.7818997 0.6850401\n"
-		"Frog       0.4739334 0.6028511 0.5921847 0.0000000 0.6268957 0.8150864 0.7705955 0.8145647 0.7573321 0.7166360 0.6626602 0.6762896 0.6809187 0.7005612 0.7136883 0.6974592 0.6449470\n"
-		"Turtle     0.6469595 0.7361390 0.7020407 0.6268957 0.0000000 0.5416702 0.5841215 0.5399763 0.4849490 0.5861821 0.5383720 0.5458270 0.5612534 0.5632785 0.6088667 0.5946969 0.5778748\n"
-		"Sphenodon  0.8072464 0.8116547 0.8573580 0.8150864 0.5416702 0.0000000 0.6723304 0.6249144 0.5897511 0.6946471 0.6787380 0.6565584 0.6772154 0.6833316 0.7476896 0.7240949 0.6518428\n"
-		"Lizard     0.7697307 0.7978951 0.9137406 0.7705955 0.5841215 0.6723304 0.0000000 0.7160903 0.6480652 0.7386573 0.7042574 0.7513723 0.7675040 0.6849374 0.7926459 0.7473559 0.6709445\n"
-		"Crocodile  0.7867055 0.7651678 0.8639154 0.8145647 0.5399763 0.6249144 0.7160903 0.0000000 0.4906657 0.7432287 0.7493887 0.7488493 0.8057593 0.8317762 0.8413625 0.7521970 0.7769550\n"
-		"Bird       0.7850803 0.6988087 0.7878422 0.7573321 0.4849490 0.5897511 0.6480652 0.4906657 0.0000000 0.6755495 0.6691967 0.6860033 0.6905877 0.7565543 0.7504430 0.6842440 0.6705485\n"
-		"Human      0.6959920 0.7598439 0.8294442 0.7166360 0.5861821 0.6946471 0.7386573 0.7432287 0.6755495 0.0000000 0.2750272 0.2814737 0.2961226 0.3590137 0.3757584 0.4477864 0.4220981\n"
-		"Seal       0.6336127 0.7003997 0.7505365 0.6626602 0.5383720 0.6787380 0.7042574 0.7493887 0.6691967 0.2750272 0.0000000 0.1931946 0.2118470 0.2817599 0.3180795 0.3787176 0.3496224\n"
-		"Cow        0.6997504 0.7643007 0.7882964 0.6762896 0.5458270 0.6565584 0.7513723 0.7488493 0.6860033 0.2814737 0.1931946 0.0000000 0.1754464 0.3199376 0.3320971 0.4013694 0.3449257\n"
-		"Whale      0.6793033 0.7378452 0.7551778 0.6809187 0.5612534 0.6772154 0.7675040 0.8057593 0.6905877 0.2961226 0.2118470 0.1754464 0.0000000 0.3251485 0.3558385 0.3925798 0.3595924\n"
-		"Mouse      0.7120045 0.7195253 0.7706974 0.7005612 0.5632785 0.6833316 0.6849374 0.8317762 0.7565543 0.3590137 0.2817599 0.3199376 0.3251485 0.0000000 0.1447365 0.4099219 0.3487804\n"
-		"Rat        0.7344446 0.8065221 0.8561868 0.7136883 0.6088667 0.7476896 0.7926459 0.8413625 0.7504430 0.3757584 0.3180795 0.3320971 0.3558385 0.1447365 0.0000000 0.4419960 0.4050277\n"
-		"Platypus   0.7318557 0.7439359 0.7818997 0.6974592 0.5946969 0.7240949 0.7473559 0.7521970 0.6842440 0.4477864 0.3787176 0.4013694 0.3925798 0.4099219 0.4419960 0.0000000 0.3202751\n"
-		"Opossum    0.6820929 0.6178323 0.6850401 0.6449470 0.5778748 0.6518428 0.6709445 0.7769550 0.6705485 0.4220981 0.3496224 0.3449257 0.3595924 0.3487804 0.4050277 0.3202751 0.0000000\n";
-
-	std::istringstream input_file(input_string);
-
+	std::istringstream input_file(example_matrix);
 	loadDistanceMatrixFromOpenFile(input_file, false, r);
 	r.constructTree();
 

example/vectordecenttree.cpp

@@ -15,6 +15,7 @@
 #include <distancematrix.h>	//for loadDistanceMatrixFromOpenFile
 #include <rapidnj.h>		//for RapidNJ
 #include <sstream>          //for std::istringstream
+#include "example_matrix.h" //for example_matrix string
 
 template <class T> void testMatrix
     (const std::string &infile_name, bool silent, T& r) {
@@ -23,32 +24,11 @@ template <class T> void testMatrix
 }
 
 void example_2() {
-
-    const char* input_string =
-		"17\n"
-		"LngfishAu  0.0000000 0.4394262 0.4253346 0.4739334 0.6469595 0.8072464 0.7697307 0.7867055 0.7850803 0.6959920 0.6336127 0.6997504 0.6793033 0.7120045 0.7344446 0.7318557 0.6820929\n"
-		"LngfishSA  0.4394262 0.0000000 0.3370420 0.6028511 0.7361390 0.8116547 0.7978951 0.7651678 0.6988087 0.7598439 0.7003997 0.7643007 0.7378452 0.7195253 0.8065221 0.7439359 0.6178323\n"
-		"LngfishAf  0.4253346 0.3370420 0.0000000 0.5921847 0.7020407 0.8573580 0.9137406 0.8639154 0.7878422 0.8294442 0.7505365 0.7882964 0.7551778 0.7706974 0.8561868 0.7818997 0.6850401\n"
-		"Frog       0.4739334 0.6028511 0.5921847 0.0000000 0.6268957 0.8150864 0.7705955 0.8145647 0.7573321 0.7166360 0.6626602 0.6762896 0.6809187 0.7005612 0.7136883 0.6974592 0.6449470\n"
-		"Turtle     0.6469595 0.7361390 0.7020407 0.6268957 0.0000000 0.5416702 0.5841215 0.5399763 0.4849490 0.5861821 0.5383720 0.5458270 0.5612534 0.5632785 0.6088667 0.5946969 0.5778748\n"
-		"Sphenodon  0.8072464 0.8116547 0.8573580 0.8150864 0.5416702 0.0000000 0.6723304 0.6249144 0.5897511 0.6946471 0.6787380 0.6565584 0.6772154 0.6833316 0.7476896 0.7240949 0.6518428\n"
-		"Lizard     0.7697307 0.7978951 0.9137406 0.7705955 0.5841215 0.6723304 0.0000000 0.7160903 0.6480652 0.7386573 0.7042574 0.7513723 0.7675040 0.6849374 0.7926459 0.7473559 0.6709445\n"
-		"Crocodile  0.7867055 0.7651678 0.8639154 0.8145647 0.5399763 0.6249144 0.7160903 0.0000000 0.4906657 0.7432287 0.7493887 0.7488493 0.8057593 0.8317762 0.8413625 0.7521970 0.7769550\n"
-		"Bird       0.7850803 0.6988087 0.7878422 0.7573321 0.4849490 0.5897511 0.6480652 0.4906657 0.0000000 0.6755495 0.6691967 0.6860033 0.6905877 0.7565543 0.7504430 0.6842440 0.6705485\n"
-		"Human      0.6959920 0.7598439 0.8294442 0.7166360 0.5861821 0.6946471 0.7386573 0.7432287 0.6755495 0.0000000 0.2750272 0.2814737 0.2961226 0.3590137 0.3757584 0.4477864 0.4220981\n"
-		"Seal       0.6336127 0.7003997 0.7505365 0.6626602 0.5383720 0.6787380 0.7042574 0.7493887 0.6691967 0.2750272 0.0000000 0.1931946 0.2118470 0.2817599 0.3180795 0.3787176 0.3496224\n"
-		"Cow        0.6997504 0.7643007 0.7882964 0.6762896 0.5458270 0.6565584 0.7513723 0.7488493 0.6860033 0.2814737 0.1931946 0.0000000 0.1754464 0.3199376 0.3320971 0.4013694 0.3449257\n"
-		"Whale      0.6793033 0.7378452 0.7551778 0.6809187 0.5612534 0.6772154 0.7675040 0.8057593 0.6905877 0.2961226 0.2118470 0.1754464 0.0000000 0.3251485 0.3558385 0.3925798 0.3595924\n"
-		"Mouse      0.7120045 0.7195253 0.7706974 0.7005612 0.5632785 0.6833316 0.6849374 0.8317762 0.7565543 0.3590137 0.2817599 0.3199376 0.3251485 0.0000000 0.1447365 0.4099219 0.3487804\n"
-		"Rat        0.7344446 0.8065221 0.8561868 0.7136883 0.6088667 0.7476896 0.7926459 0.8413625 0.7504430 0.3757584 0.3180795 0.3320971 0.3558385 0.1447365 0.0000000 0.4419960 0.4050277\n"
-		"Platypus   0.7318557 0.7439359 0.7818997 0.6974592 0.5946969 0.7240949 0.7473559 0.7521970 0.6842440 0.4477864 0.3787176 0.4013694 0.3925798 0.4099219 0.4419960 0.0000000 0.3202751\n"
-		"Opossum    0.6820929 0.6178323 0.6850401 0.6449470 0.5778748 0.6518428 0.6709445 0.7769550 0.6705485 0.4220981 0.3496224 0.3449257 0.3595924 0.3487804 0.4050277 0.3202751 0.0000000\n";
-
 	const std::string input_file("./example.dist");
 
     std::ofstream dist;
     dist.open(input_file.c_str(), std::ios_base::out);
-    dist << input_string;
+    dist << example_matrix;
     dist.close();
 
 	StartTree::NJMatrix<NJFloat> r1;