diff --git a/app/src/App.cpp b/app/src/App.cpp
index 3835dba..cb1dda1 100644
--- a/app/src/App.cpp
+++ b/app/src/App.cpp
@@ -74,7 +74,7 @@ void App::init(int screenWidth, int screenHeight)
}
DnaStore::load(&manager);
- simil = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
+ simil = Similarity::calc_similarity(manager.vector);
upTex(Liked::tbd);
while (!canvas.tick(canvasTexure[TOP]))
{
@@ -128,7 +128,7 @@ void App::upTex(Liked liked)
DnaStore::saveGen(&manager);
DnaManager::newGen(&manager);
DnaStore::saveVec(&manager);
- simil = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
+ simil = Similarity::calc_similarity(manager.vector);
}
DnaStore::saveData(&manager);
}
diff --git a/shared/inc/values/Similarity.hpp b/shared/inc/values/Similarity.hpp
index b0c0edb..ed01179 100644
--- a/shared/inc/values/Similarity.hpp
+++ b/shared/inc/values/Similarity.hpp
@@ -5,13 +5,14 @@ namespace Similarity
{
// float euclidean_distance(Dna *d1, Dna *d2); direct distance betwen vector. wont give 0 and 1
// float dot_product(Dna *d1, Dna *d2); doent return betwen 0 to 1
- float cosine_similarity(Dna *d1, Dna *d2);
- float cosine_similarity_int(Dna *d1, Dna *d2);
+ // float cosine_similarity(Dna *d1, Dna *d2);
+ // float cosine_similarity_int(Dna *d1, Dna *d2);
float hamming_distance(Dna *d1, Dna *d2);
+ float hamming_distance_without_seeds(Dna *d1, Dna *d2);
// float jaccard_index(Dna *d1, Dna *d2); // primerja unio genov naprimer gleda ce je gen za nebo isti z genom za barvo za liste, to nerabimo
// float levenshtein_distance(Dna *d1, Dna *d2); // odstranjen ker mi vrne iste podatke kot hamming distance ki je bolj enostaven za izracun
// float needleman_wunsch(Dna *d1, Dna *d2); used for bioinformatics and aligment. Dont need its aligned alredy
typedef float(simil_func)(Dna *d1, Dna *d2);
- float calc_similarity(std::vector<Dna> &vec, simil_func f);
+ float calc_similarity(std::vector<Dna> &vec, simil_func f = hamming_distance_without_seeds);
}
\ No newline at end of file
diff --git a/shared/src/values/Similarity.cpp b/shared/src/values/Similarity.cpp
index b36bd98..fcb5a05 100644
--- a/shared/src/values/Similarity.cpp
+++ b/shared/src/values/Similarity.cpp
@@ -7,50 +7,50 @@ namespace Similarity
// 0 -> -128
// 255 -> 127
// int8_t = uint8_t - 128
- float cosine_similarity(Dna *d1, Dna *d2)
- {
- uint8_t *d1a = (uint8_t *)d1;
- uint8_t *d2a = (uint8_t *)d2;
+ // float cosine_similarity(Dna *d1, Dna *d2)
+ // {
+ // uint8_t *d1a = (uint8_t *)d1;
+ // uint8_t *d2a = (uint8_t *)d2;
- float mag1 = 0.0f;
- float mag2 = 0.0f;
- float dot_prod = 0.0f;
- for (size_t i = 0; i < sizeof(Dna); i++)
- {
- dot_prod += d1a[i] * d2a[i];
- mag1 += d1a[i] * d1a[i];
- mag2 += d2a[i] * d2a[i];
- }
- mag1 = sqrt(mag1);
- mag2 = sqrt(mag2);
+ // float mag1 = 0.0f;
+ // float mag2 = 0.0f;
+ // float dot_prod = 0.0f;
+ // for (size_t i = 0; i < sizeof(Dna); i++)
+ // {
+ // dot_prod += d1a[i] * d2a[i];
+ // mag1 += d1a[i] * d1a[i];
+ // mag2 += d2a[i] * d2a[i];
+ // }
+ // mag1 = sqrt(mag1);
+ // mag2 = sqrt(mag2);
- return dot_prod / (mag1 * mag2);
- }
+ // return dot_prod / (mag1 * mag2);
+ // }
- float cosine_similarity_int(Dna *d1, Dna *d2)
- {
- auto map = [](uint8_t a) -> int8_t
- { return a - 128; };
+ // float cosine_similarity_int(Dna *d1, Dna *d2)
+ // {
+ // auto map = [](uint8_t a) -> int8_t
+ // { return a - 128; };
- uint8_t *d1a = (uint8_t *)d1;
- uint8_t *d2a = (uint8_t *)d2;
+ // uint8_t *d1a = (uint8_t *)d1;
+ // uint8_t *d2a = (uint8_t *)d2;
- float mag1 = 0.0f;
- float mag2 = 0.0f;
- float dot_prod = 0.0f;
- for (size_t i = 0; i < sizeof(Dna); i++)
- {
- int8_t a = map(d1a[i]);
- int8_t b = map(d2a[i]);
- dot_prod += a * b;
- mag1 += a * a;
- mag2 += b * b;
- }
- mag1 = sqrt(mag1);
- mag2 = sqrt(mag2);
+ // float mag1 = 0.0f;
+ // float mag2 = 0.0f;
+ // float dot_prod = 0.0f;
+ // for (size_t i = 0; i < sizeof(Dna); i++)
+ // {
+ // int8_t a = map(d1a[i]);
+ // int8_t b = map(d2a[i]);
+ // dot_prod += a * b;
+ // mag1 += a * a;
+ // mag2 += b * b;
+ // }
+ // mag1 = sqrt(mag1);
+ // mag2 = sqrt(mag2);
- return dot_prod / (mag1 * mag2);
- }
+ // return dot_prod / (mag1 * mag2);
+ // }
float hamming_distance(Dna *d1, Dna *d2)
{
@@ -67,6 +67,23 @@ namespace Similarity
return 1 - (distance / sizeof(Dna));
}
+ float hamming_distance_without_seeds(Dna *d1, Dna *d2)
+ {
+ constexpr size_t start = sizeof(uint128) * 3;
+ constexpr size_t end = sizeof(Dna);
+ uint8_t *d1a = (uint8_t *)d1;
+ uint8_t *d2a = (uint8_t *)d2;
+ float distance = 0;
+ for (size_t i = start; i < end; i++)
+ {
+ if (d1a[i] != d2a[i])
+ {
+ distance++;
+ }
+ }
+ return 1 - (distance / (end - start));
+ }
+
float calc_similarity(std::vector<Dna> &vec, simil_func f)
{
size_t num_pairs = (vec.size() * (vec.size() - 1)) / 2;
diff --git a/view/inc/Vapp.hpp b/view/inc/Vapp.hpp
index fe6b20d..5f9873d 100644
--- a/view/inc/Vapp.hpp
+++ b/view/inc/Vapp.hpp
@@ -14,6 +14,8 @@ enum DrawingStage
done,
};
+constexpr int numberOfFunc = 2;
+
class Vapp
{
public:
@@ -45,9 +47,9 @@ private:
int drawX = 0;
int drawY = 0;
void setUpManager();
-
- std::array<float, 3> simil;
- std::vector<std::array<float, 3>> similTable;
+
+ std::array<float, numberOfFunc> simil;
+ std::vector<std::array<float, numberOfFunc>> similTable;
void setUpTable();
};
\ No newline at end of file
diff --git a/view/src/Vapp.cpp b/view/src/Vapp.cpp
index 996d049..6551095 100644
--- a/view/src/Vapp.cpp
+++ b/view/src/Vapp.cpp
@@ -100,9 +100,8 @@ void Vapp::update()
break;
case DrawingStage::calSim:
- simil[0] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity);
- simil[1] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
- simil[2] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity_int);
+ simil[0] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
+ simil[1] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance_without_seeds);
stageOfDrawing = DrawingStage::done;
break;
@@ -174,12 +173,11 @@ void Vapp::draw()
if (showStats)
{
ImGui::Begin("Status", &showStats);
- ImGui::LabelText("##sim1", "cosine_similarity: %f", simil[0]);
- ImGui::LabelText("##sim2", "hamming_distance: %f", simil[1]);
- ImGui::LabelText("##sim3", "cosine_similarity_int: %f", simil[2]);
+ ImGui::LabelText("##sim1", "hamming_distance: %f", simil[0]);
+ ImGui::LabelText("##sim2", "hamming_distance_without_seeds: %f", simil[1]);
const ImGuiTableFlags flags = ImGuiTableFlags_NoHostExtendX | ImGuiTableFlags_SizingFixedFit | ImGuiTableFlags_Resizable | ImGuiTableFlags_BordersOuter | ImGuiTableFlags_BordersV | ImGuiTableFlags_ContextMenuInBody;
- const int columns = 4;
+ const int columns = numberOfFunc + 1;
if (ImGui::BeginTable("table1", columns, flags))
{
for (int row = 0; row < similTable.size(); row++)
@@ -292,9 +290,8 @@ void Vapp::setUpTable()
{
similTable.emplace_back();
int s = similTable.size() - 1;
- similTable[s][0] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity);
- similTable[s][1] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
- similTable[s][2] = Similarity::calc_similarity(manager.vector, Similarity::cosine_similarity_int);
+ similTable[s][0] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance);
+ similTable[s][1] = Similarity::calc_similarity(manager.vector, Similarity::hamming_distance_without_seeds);
DnaManager::newGen(&manager);
}