diff --git a/.ycm_extra_conf.py b/.ycm_extra_conf.py
index ea97fe481c903d1e5319bf4a9e0174069c75ddc5..0157edd8b889d01de253f8545b06cbf91b9b8416 100644
--- a/.ycm_extra_conf.py
+++ b/.ycm_extra_conf.py
@@ -45,6 +45,8 @@ flags = [
'/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1'
'-isystem',
'/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1/bits'
+ '-I',
+ 'src',
# '-I',
# '/usr/include/c++/4.9.2',
# '-isystem',
diff --git a/src/tree.hpp b/src/tree.hpp
index 04f8ccd4d35b207a5567906d3eb84c47058340c2..6b53aa6f329490a3c431817445f9b2be4dda25b1 100644
--- a/src/tree.hpp
+++ b/src/tree.hpp
@@ -128,13 +128,13 @@ class tree {
return branch_index;
}
- int num_children() const {
+ size_t num_children() const {
return children_.size();
}
- int num_children(int b) const {
+ size_t num_children(size_t b) const {
return child_index_[b+1] - child_index_[b];
}
- int num_nodes() const {
+ size_t num_nodes() const {
return child_index_.size() - 1;
}
@@ -149,7 +149,7 @@ class tree {
}
/// return the list of all children of branch b
- const index_view children(int b) const {
+ const index_view children(size_t b) const {
return children_(child_index_[b], child_index_[b+1]);
}
@@ -159,10 +159,10 @@ class tree {
}
/// return the parent of branch b
- int_type parent(int b) const {
+ int_type parent(size_t b) const {
return parents_[b];
}
- int_type& parent(int b) {
+ int_type& parent(size_t b) {
return parents_[b];
}
@@ -171,7 +171,7 @@ class tree {
return sizeof(int_type)*data_.size() + sizeof(tree);
}
- index_type change_root(int b) {
+ index_type change_root(size_t b) {
assert(b<num_nodes());
// no need to rebalance if the root node has been requested
@@ -222,16 +222,16 @@ class tree {
auto nchild = nnode - 1;
// data_ is partitioned as follows:
// data_ = [children_[nchild], child_index_[nnode+1], parents_[nnode]]
- assert(data_.size() == nchild + (nnode+1) + nnode);
+ assert(data_.size() == unsigned(nchild + (nnode+1) + nnode));
children_ = data_(0, nchild);
child_index_ = data_(nchild, nchild+nnode+1);
parents_ = data_(nchild+nnode+1, memory::end);
// check that arrays have appropriate size
// this should be moved into a unit test
- assert(children_.size() == nchild);
- assert(child_index_.size() == nnode+1);
- assert(parents_.size() == nnode);
+ assert(children_.size() == unsigned(nchild));
+ assert(child_index_.size() == unsigned(nnode+1));
+ assert(parents_.size() == unsigned(nnode));
}
/// Renumber the sub-tree with old_node as its root with new_node as
diff --git a/tests/test_tree.cpp b/tests/test_tree.cpp
index 3bd26796147d8d906fd88ae9b57c8708ef61e2e7..a0bd0742cdcf6041b80847bd1c5fd2b064a44d52 100644
--- a/tests/test_tree.cpp
+++ b/tests/test_tree.cpp
@@ -5,7 +5,7 @@
#include "gtest.h"
-#include "cell_tree.hpp"
+#include "../src/cell_tree.hpp"
#include "json/src/json.hpp"
using json = nlohmann::json;
@@ -18,112 +18,112 @@ TEST(cell_tree, from_parent_index) {
{
std::vector<int> parent_index = {0};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 1);
- EXPECT_EQ(tree.num_children(0), 0);
+ EXPECT_EQ(tree.num_segments(), 1u);
+ EXPECT_EQ(tree.num_children(0), 0u);
}
// CASE 2 : empty parent_index
{
std::vector<int> parent_index;
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 1);
- EXPECT_EQ(tree.num_children(0), 0);
+ EXPECT_EQ(tree.num_segments(), 1u);
+ EXPECT_EQ(tree.num_children(0), 0u);
}
// tree with two segments off the root node
{
std::vector<int> parent_index =
{0, 0, 1, 2, 0, 4};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 3);
+ EXPECT_EQ(tree.num_segments(), 3u);
// the root has 2 children
- EXPECT_EQ(tree.num_children(0), 2);
+ EXPECT_EQ(tree.num_children(0), 2u);
// the children are leaves
- EXPECT_EQ(tree.num_children(1), 0);
- EXPECT_EQ(tree.num_children(2), 0);
+ EXPECT_EQ(tree.num_children(1), 0u);
+ EXPECT_EQ(tree.num_children(2), 0u);
}
{
// tree with three segments off the root node
std::vector<int> parent_index =
{0, 0, 1, 2, 0, 4, 0, 6, 7, 8};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 4);
+ EXPECT_EQ(tree.num_segments(), 4u);
// the root has 3 children
- EXPECT_EQ(tree.num_children(0), 3);
+ EXPECT_EQ(tree.num_children(0), 3u);
// the children are leaves
- EXPECT_EQ(tree.num_children(1), 0);
- EXPECT_EQ(tree.num_children(2), 0);
- EXPECT_EQ(tree.num_children(3), 0);
+ EXPECT_EQ(tree.num_children(1), 0u);
+ EXPECT_EQ(tree.num_children(2), 0u);
+ EXPECT_EQ(tree.num_children(3), 0u);
}
{
// tree with three segments off the root node, and another 2 segments off of the third branch from the root node
std::vector<int> parent_index =
{0, 0, 1, 2, 0, 4, 0, 6, 7, 8, 9, 8, 11, 12};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 6);
+ EXPECT_EQ(tree.num_segments(), 6u);
// the root has 3 children
- EXPECT_EQ(tree.num_children(0), 3);
+ EXPECT_EQ(tree.num_children(0), 3u);
// one of the chilren has 2 children ...
- EXPECT_EQ(tree.num_children(3), 2);
+ EXPECT_EQ(tree.num_children(3), 2u);
// the rest are leaves
- EXPECT_EQ(tree.num_children(1), 0);
- EXPECT_EQ(tree.num_children(2), 0);
- EXPECT_EQ(tree.num_children(4), 0);
- EXPECT_EQ(tree.num_children(5), 0);
+ EXPECT_EQ(tree.num_children(1), 0u);
+ EXPECT_EQ(tree.num_children(2), 0u);
+ EXPECT_EQ(tree.num_children(4), 0u);
+ EXPECT_EQ(tree.num_children(5), 0u);
}
{
//
// 0
// /
// 1
- // / \
+ // / \.
// 2 3
std::vector<int> parent_index = {0,0,1,1};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 4);
+ EXPECT_EQ(tree.num_segments(), 4u);
- EXPECT_EQ(tree.num_children(0), 1);
- EXPECT_EQ(tree.num_children(1), 2);
- EXPECT_EQ(tree.num_children(2), 0);
- EXPECT_EQ(tree.num_children(3), 0);
+ EXPECT_EQ(tree.num_children(0), 1u);
+ EXPECT_EQ(tree.num_children(1), 2u);
+ EXPECT_EQ(tree.num_children(2), 0u);
+ EXPECT_EQ(tree.num_children(3), 0u);
}
{
//
// 0
- // / \
+ // / \.
// 1 2
- // / \
+ // / \.
// 3 4
std::vector<int> parent_index = {0,0,0,1,1};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 5);
+ EXPECT_EQ(tree.num_segments(), 5u);
- EXPECT_EQ(tree.num_children(0), 2);
- EXPECT_EQ(tree.num_children(1), 2);
- EXPECT_EQ(tree.num_children(2), 0);
- EXPECT_EQ(tree.num_children(3), 0);
- EXPECT_EQ(tree.num_children(4), 0);
+ EXPECT_EQ(tree.num_children(0), 2u);
+ EXPECT_EQ(tree.num_children(1), 2u);
+ EXPECT_EQ(tree.num_children(2), 0u);
+ EXPECT_EQ(tree.num_children(3), 0u);
+ EXPECT_EQ(tree.num_children(4), 0u);
}
{
// 0
- // / \
+ // / \.
// 1 2
- // / \
+ // / \.
// 3 4
- // / \
+ // / \.
// 5 6
std::vector<int> parent_index = {0,0,0,1,1,4,4};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 7);
+ EXPECT_EQ(tree.num_segments(), 7u);
- EXPECT_EQ(tree.num_children(0), 2);
- EXPECT_EQ(tree.num_children(1), 2);
- EXPECT_EQ(tree.num_children(2), 0);
- EXPECT_EQ(tree.num_children(3), 0);
- EXPECT_EQ(tree.num_children(4), 2);
- EXPECT_EQ(tree.num_children(5), 0);
- EXPECT_EQ(tree.num_children(6), 0);
+ EXPECT_EQ(tree.num_children(0), 2u);
+ EXPECT_EQ(tree.num_children(1), 2u);
+ EXPECT_EQ(tree.num_children(2), 0u);
+ EXPECT_EQ(tree.num_children(3), 0u);
+ EXPECT_EQ(tree.num_children(4), 2u);
+ EXPECT_EQ(tree.num_children(5), 0u);
+ EXPECT_EQ(tree.num_children(6), 0u);
}
}
@@ -141,32 +141,32 @@ TEST(tree, change_root) {
t.init_from_parent_index(parent_index);
t.change_root(1);
- EXPECT_EQ(t.num_nodes(), 3);
+ EXPECT_EQ(t.num_nodes(), 3u);
- EXPECT_EQ(t.num_children(0), 1);
- EXPECT_EQ(t.num_children(1), 1);
- EXPECT_EQ(t.num_children(2), 0);
+ EXPECT_EQ(t.num_children(0), 1u);
+ EXPECT_EQ(t.num_children(1), 1u);
+ EXPECT_EQ(t.num_children(2), 0u);
}
{
// a cell with the following structure
// make 1 the new root
// 0 0
- // / \ /|\
+ // / \ /|\.
// 1 2 -> 1 2 3
// / \ |
// 3 4 4
std::vector<int> parent_index = {0,0,0,1,1};
tree t;
t.init_from_parent_index(parent_index);
- t.change_root(1);
+ t.change_root(1u);
- EXPECT_EQ(t.num_nodes(), 5);
+ EXPECT_EQ(t.num_nodes(), 5u);
- EXPECT_EQ(t.num_children(0), 3);
- EXPECT_EQ(t.num_children(1), 0);
- EXPECT_EQ(t.num_children(2), 0);
- EXPECT_EQ(t.num_children(3), 1);
- EXPECT_EQ(t.num_children(4), 0);
+ EXPECT_EQ(t.num_children(0), 3u);
+ EXPECT_EQ(t.num_children(1), 0u);
+ EXPECT_EQ(t.num_children(2), 0u);
+ EXPECT_EQ(t.num_children(3), 1u);
+ EXPECT_EQ(t.num_children(4), 0u);
}
{
// a cell with the following structure
@@ -174,11 +174,11 @@ TEST(tree, change_root) {
// unlike earlier tests, this decreases the depth
// of the tree
// 0 0
- // / \ /|\
+ // / \ /|\.
// 1 2 -> 1 2 5
- // / \ / \ \
+ // / \ / \ \.
// 3 4 3 4 6
- // / \
+ // / \.
// 5 6
std::vector<int> parent_index = {0,0,0,1,1,4,4};
tree t;
@@ -186,15 +186,15 @@ TEST(tree, change_root) {
t.change_root(1);
- EXPECT_EQ(t.num_nodes(), 7);
+ EXPECT_EQ(t.num_nodes(), 7u);
- EXPECT_EQ(t.num_children(0), 3);
- EXPECT_EQ(t.num_children(1), 0);
- EXPECT_EQ(t.num_children(2), 2);
- EXPECT_EQ(t.num_children(3), 0);
- EXPECT_EQ(t.num_children(4), 0);
- EXPECT_EQ(t.num_children(5), 1);
- EXPECT_EQ(t.num_children(6), 0);
+ EXPECT_EQ(t.num_children(0), 3u);
+ EXPECT_EQ(t.num_children(1), 0u);
+ EXPECT_EQ(t.num_children(2), 2u);
+ EXPECT_EQ(t.num_children(3), 0u);
+ EXPECT_EQ(t.num_children(4), 0u);
+ EXPECT_EQ(t.num_children(5), 1u);
+ EXPECT_EQ(t.num_children(6), 0u);
}
}
@@ -203,11 +203,11 @@ TEST(cell_tree, balance) {
// a cell with the following structure
// will balance around 1
// 0 0
- // / \ /|\
+ // / \ /|\.
// 1 2 -> 1 2 5
- // / \ / \ \
+ // / \ / \ \.
// 3 4 3 4 6
- // / \
+ // / \.
// 5 6
std::vector<int> parent_index = {0,0,0,1,1,4,4};
cell_tree t(parent_index);
@@ -217,14 +217,14 @@ TEST(cell_tree, balance) {
// the soma (original root) has moved to 5 in the new tree
EXPECT_EQ(t.soma(), 5);
- EXPECT_EQ(t.num_segments(), 7);
- EXPECT_EQ(t.num_children(0),3);
- EXPECT_EQ(t.num_children(1),0);
- EXPECT_EQ(t.num_children(2),2);
- EXPECT_EQ(t.num_children(3),0);
- EXPECT_EQ(t.num_children(4),0);
- EXPECT_EQ(t.num_children(5),1);
- EXPECT_EQ(t.num_children(6),0);
+ EXPECT_EQ(t.num_segments(), 7u);
+ EXPECT_EQ(t.num_children(0),3u);
+ EXPECT_EQ(t.num_children(1),0u);
+ EXPECT_EQ(t.num_children(2),2u);
+ EXPECT_EQ(t.num_children(3),0u);
+ EXPECT_EQ(t.num_children(4),0u);
+ EXPECT_EQ(t.num_children(5),1u);
+ EXPECT_EQ(t.num_children(6),0u);
EXPECT_EQ(t.parent(0),-1);
EXPECT_EQ(t.parent(1), 0);
EXPECT_EQ(t.parent(2), 0);
diff --git a/vector b/vector
index 79ad5236b219a7618a8cda8caad6cd3de1f9e122..a8dfadd460262ebbc1bc22b159efe9e33ad1d359 160000
--- a/vector
+++ b/vector
@@ -1 +1 @@
-Subproject commit 79ad5236b219a7618a8cda8caad6cd3de1f9e122
+Subproject commit a8dfadd460262ebbc1bc22b159efe9e33ad1d359