EvryRNA / C-RCPred

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guillaume
c5ec7954 1 parent 54344319

remove dlib dependency

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Showing 5 changed files with 2 additions and 105 deletions
......@@ -68,8 +68,6 @@ RUN cd /tmp && \
make && \
make install
# Install Dlib
RUN cd /tmp && tar -xjf dlib-19.17.tar.bz2 -C /opt
RUN rm -rf /tmp/*
# ----------------
......
####### Compiler, tools and options
CXX = g++
CXXFLAGS = -pipe -std=c++17 -O2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Wall -W -D_REENTRANT -fPIC
INCPATH = -I./src -I. -I/opt/ibm/ILOG/CPLEX_Studio221/cplex/include -I/opt/dlib-19.17 -I/usr/local/include
INCPATH = -I./src -I. -I/opt/ibm/ILOG/CPLEX_Studio221/cplex/include -I/usr/local/include
DEL_FILE = rm -f
LINK = g++
LFLAGS = -Wl,-O1 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now
LIBS = -L/opt/ibm/ILOG/CPLEX_Studio221/cplex/lib/x86-64_linux/static_pic/ -lcplex -L/usr/local/lib/ -lRNA -lnupackconc -lnupackpfunc -lnupackutils -L/usr/lib/x86_64-linux-gnu/ -lpthread -lX11 -ldl
####### Files
OBJECTS = source.o \
graph.o \
OBJECTS = graph.o \
main.o \
rna.o \
structure.o \
......@@ -46,9 +45,6 @@ C-RCPred: /opt/ibm/ILOG/CPLEX_Studio221/cplex/lib/x86-64_linux/static_pic/libcpl
all: Makefile C-RCPred
####### Compile
source.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o source.o /opt/dlib-19.17/dlib/all/source.cpp
graph.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o graph.o ./src/graph.cpp
......
This file is too large to display.
#include "utils.h"
#include <dlib/clustering.h>
#include <sys/stat.h>
#include <boost/algorithm/string.hpp>
......@@ -146,97 +145,6 @@ int dominate(std::vector < float > c1, std::vector < float > c2) {
return dominate;
}
void readFeatureVector(std::vector < dlib::matrix < float > > &features){
std::vector < std::vector < int > > featureIds;
std::vector < std::vector < float > > featureValues;
std::vector < int > commonFeatureIds, intersec;
int nline = 0;
std::string name = "graphNSPDK.txt.feature", line = "";
std::vector < std::string > elements, elements2;
struct stat buf;
if( (stat(name.c_str(), &buf) == 0)) {
std::ifstream ifs(name);
while (std::getline(ifs, line)) {
if (line[0] != '\n' and line != "") {
featureIds.push_back(std::vector < int >());
featureValues.push_back(std::vector < float >());
boost::split( elements, line, boost::is_any_of(" \t"), boost::token_compress_on );
uint count = 0;
for(size_t i = 0, size = elements.size(); i != size; i++) {
if (elements[i] != "") {
boost::split(elements2, elements[i], boost::is_any_of(":"), boost::token_compress_on);
featureIds[nline].push_back(std::stoi(elements2[0]));
featureValues[nline].push_back(std::stof(elements2[1]));
count++;
}
}
std::cout << " count = " << count << std::endl;
}
nline++;
}
ifs.close();
}
// Intersection of all the feature ids
commonFeatureIds = featureIds[0];
for (size_t i = 1, size = featureIds.size(); i != size; i++) {
std::set_intersection(commonFeatureIds.begin(), commonFeatureIds.end(),
featureIds[i].begin(), featureIds[i].end(),
std::back_inserter(intersec));
commonFeatureIds = intersec;
intersec.clear();
}
std::cout << "commonFeatureIds.size = " << commonFeatureIds.size() << std::endl;
// Recover only the common features
for(size_t i = 0, size = featureIds.size(); i != size; i++) {
for (size_t j = 0, size2 = featureIds[i].size(); j != size2; j++) {
if (featureIds[i][j] != commonFeatureIds[j]) {
featureIds[i].erase(featureIds[i].begin() + j);
featureValues[i].erase(featureValues[i].begin() + j);
size2--;
j--;
}
}
}
// Put into the common features into a matrix
dlib::matrix<float> feature;
feature.set_size(uint(featureIds[0].size()), 1); // nrow = x and only one column
for(size_t i = 0, size = featureValues.size(); i != size; i++) {
for (size_t j = 0, size2 = featureValues[i].size(); j != size2; j++) {
feature(long(j)) = featureValues[i][j];
}
features.push_back(feature);
}
}
void readKernelMatrix(dlib::matrix < double > &K, uint length) {
K.set_size(length, length);
std::string name = "graphNSPDK.txt.kernel", line = "";
std::vector < std::string > elements;
struct stat buf;
int nline = 0;
if( (stat(name.c_str(), &buf) == 0)) {
std::ifstream ifs(name);
while (std::getline(ifs, line)) {
if (line[0] != '\n' and line != "") {
boost::split( elements, line, boost::is_any_of(" \t"), boost::token_compress_on );
for(size_t i = 0, size = elements.size(); i != size; i++) {
if (elements[i] != "")
K(nline,i) = double(std::stof(elements[i]));
}
}
nline++;
}
ifs.close();
}
}
std::string join(const std::vector < std::string >& v, std::string d) {
size_t size;
std::string s = "";
......
......@@ -4,7 +4,6 @@
#include <vector>
#include <utility>
#include <string>
#include <dlib/clustering.h>
static const float PRECISION = 0.00001;
......@@ -31,10 +30,6 @@ bool checkIC(std::string ic);
int dominate(std::vector < float > c1, std::vector < float > c2);
void readFeatureVector(std::vector < dlib::matrix < float > > &features);
void readKernelMatrix(dlib::matrix < double > &K, uint length);
std::string join(const std::vector < std::string >& v, std::string d);
#endif
......