void SodController::postscript(f_parameter& par)
{
QString dviewer;
if(!par.param("viewer", dviewer)){
warn("Specify viewer to be used viewer=(..)");
return;
}
if(!distanceViewers.count(dviewer)){
warn("Unknown viewer specified");
return;
}
DistanceViewer* viewer = distanceViewers[dviewer];
QString error;
QTextStream qts(&error);
float w, h;
QString fname;
if(!par.param("fname", fname))
qts << "Specify postscript output file name fname=...\n";
if(!par.param("w", w))
qts << "Specify width (in points) of plot w=..\n";
if(!par.param("h", h))
qts << "Specify height (in points) of plot h=..\n";
if(error.length()){
warn(error);
return;
}
bool stress = par.defined("stress");
if(!par.defined("svg")){
viewer->postscript(fname, w, h, stress);
}else{
viewer->svg(fname, (int)w, (int)h);
}
}
bool GetInfo_Devices (QListView *lbox)
{
QFile *f = new QFile("/var/run/dmesg.boot");
if (f->open(IO_ReadOnly)) {
QTextStream qts(f);
QDict<QListViewItem> lv_items;
Device *dev;
QString line, controller;
lbox->setRootIsDecorated(true);
lbox->addColumn("Device");
lbox->addColumn("Description");
while ( !(line=qts.readLine()).isNull() ) {
controller = GetController(line);
if (controller.isNull())
continue;
dev=GetDevice(line);
if (!dev)
continue;
// Ewww assuing motherboard is the only toplevel controller is rather gross
if (controller == "motherboard") {
if (!lv_items[dev->name]) {
lv_items.insert(dev->name, new QListViewItem(lbox, dev->name, dev->description) );
}
} else {
QListViewItem *parent=lv_items[controller];
if (parent && !lv_items[dev->name]) {
lv_items.insert(dev->name, new QListViewItem(parent, dev->name, dev->description) );
}
}
}
return true;
}
return false;
}
void SodController::read_annotation(f_parameter& par)
{
QString error;
QTextStream qts(&error);
QString filename;
QString dist_name;
if(!par.param("file", filename))
qts << "read_annotation: no file specified, (file=..)\n";
if(!par.param("dist", dist_name))
qts << "read_annotation: no dist mapper specified (dist=..)\n";
if(!distanceViewers.count(dist_name))
qts << "read_annotation: unknown dist mapper: " << dist_name << "\n";
if(error.length()){
warn(error);
return;
}
node_set ns = read_node_set(filename, true);
if(!ns.n_size()){
warn("read_annotation obtained empty node_set");
return;
}
if(!distances.count(dist_name)){
warn("read_annotation: unknown distance set");
return;
}
if(distances[dist_name].n_size() != ns.n_size() ){
warn("read_annotation: specified node set has a different size to the annotation node_set");
return;
}
Annotation annot(ns);
distanceViewers[dist_name]->setAnnotation(annot);
}
void SodController::make_gaussian_background(f_parameter& par)
{
QString error;
QTextStream qts(&error);
QString dviewer;
float var;
std::vector<unsigned int> dims;
std::vector<unsigned int> alpha;
std::vector<unsigned int> red;
std::vector<unsigned int> green;
std::vector<unsigned int> blue;
if(!par.param("viewer", dviewer))
qts << "Specify viewer (viewer=..)\n";
if(!dviewer.isEmpty() && !distanceViewers.count(dviewer))
qts << "Unknown viewer " << dviewer << "\n";
if(!par.param("dims", ',', dims))
qts << "Specify dimensions to use (dims=a,b,c)\n";
if(!par.param("a", ',', alpha) || !par.param("r", ',', red) ||
!par.param("g", ',', green) || !par.param("b", ',', blue))
qts << "Specify argb components (a=a,b,c r=a,b,c) one value (0-255) for each dim\n";
if(!par.param("var", var))
qts << "Specify the variance to use (radius will be 2xvar) (var=..)\n";
if(error.length()){
warn(error);
return;
}
// there should be a viewer, but also there should be a positions of the same name
if(!positions.count(dviewer)){
qts << "No positions set for viewer " << dviewer << " aborting";
warn(error);
return;
}
// check that colours have been specified for all dimensions and that no value is
// larger than 255
if(dims.size() != alpha.size() || dims.size() != red.size() ||
dims.size() != green.size() || dims.size() != blue.size()){
warn("Colors not same size as specified by dim\n");
}
// check that none of the dimensions is too large..
for(unsigned int i=0; i < dims.size(); ++i){
if(dims[i] >= positions[dviewer].n_dim()){
warn("dimension specified too large");
return;
}
if(alpha[i] > 255 || red[i] > 255 || green[i] > 255 || blue[i] > 255){
warn("Illegal color specified (value larger than 255)");
return;
}
}
// if that's ok..
unsigned char* color_matrix = new unsigned char[4 * dims.size()];
for(unsigned int i=0; i < dims.size(); ++i){
color_matrix[i * 4 + 0] = alpha[i];
color_matrix[i * 4 + 1] = red[i];
color_matrix[i * 4 + 2] = green[i];
color_matrix[i * 4 + 3] = blue[i];
}
// then make a function in the viewer..
distanceViewers[dviewer]->set_simple_gaussian_background(dims, color_matrix, var);
}
//-------------------------------------------------------------------------
QString buildLine(QVector<aln::s_hap> vT, QString &f_genotype, int &i, int &j, QVector<s_res> &vRes)
{
//build line of data in tab 6
//uses makeFreq & makeSZ
QString str;
QTextStream ts(&str);
QString qstr;
QTextStream qts(&qstr);
int nrS = 0;
int nrZ = 0;
QString colum23;
QString colum45;
float dprob;
qts << vT[i].a << vT[i].b << vT[j].a << vT[j].b;
colum23 = aln::makeSZ(f_genotype, qstr, nrS, nrZ);
ts << qstr << " " << vT[i].a << " " << vT[i].b << " " << vT[j].a << " " << vT[j].b << " " << colum23;
dprob = (vT[i].dprob * vT[j].dprob);
colum45 = aln::makeFreq(nrS, nrZ, dprob, vRes);
ts << " " << colum45;
return(str);
}
std::ostream& operator<<(std::ostream& os, const RulesetObject& rulesetObject)
{
QString str;
QTextStream qts(&str);
rulesetObject.toXml().save(qts, 2);
os << str.toStdString();
return os;
}
std::ostream& operator<<(std::ostream& os, const BCLFileReference& file)
{
QDomDocument doc;
QDomElement element = doc.createElement(QString("File"));
doc.appendChild(element);
file.writeValues(doc, element);
QString str;
QTextStream qts(&str);
doc.save(qts, 2);
os << str.toStdString();
return os;
}
// The file should contain rows and columns (more than 2).
// The first column identifies the node and the
// following columns contain it's coordinates. (These
// can indicate all against all distances as well as
// spatial coordinates)..
// All columns except the first should contain values that can be assigned as floats
node_set SodController::read_node_set(QString fileName, bool has_col_header)
{
node_set ns;
QString error;
QTextStream qts(&error);
QFile file(fileName);
if(!file.open(QIODevice::ReadOnly | QIODevice::Text)){
qts << "Unable to open file : " << fileName;
warn(error);
return(ns);
}
QTextStream in(&file);
QString line;
bool ok;
/// A little bit messy, but what the hell..
std::vector<QString> col_header;
if(has_col_header){
line = in.readLine();
QStringList words = line.split(QRegExp("\\s+"), QString::SkipEmptyParts);
for(int i=0; i < words.size(); ++i)
col_header.push_back(words[i]);
}
while(!in.atEnd()){
line = in.readLine();
QStringList words = line.split(QRegExp("\\s+"), QString::SkipEmptyParts);
if(words.size() < 2){
warn("read_node_set skipping line");
continue;
}
QString label = words[0];
std::vector<float> coords;
for(int i=1; i < words.size(); ++i){
float f = words[i].toFloat(&ok);
if(!ok)
continue;
coords.push_back(f);
}
if(!ns.push_node(label, coords))
warn("read_node_set failed to push node");
}
if(has_col_header){
if(!ns.set_col_header(col_header))
warn("read_node_set failed to set column header");
}
return(ns);
}
void SodController::read_positions(f_parameter& par)
{
QString error;
QTextStream qts(&error);
QString filename;
QString pos_name;
unsigned int grid_points = 0;
if(!par.param("file", filename))
qts << "read_positions: no position file specified (file=..)\n";
if(!par.param("pos", pos_name) || pos_name.isEmpty())
qts << "specify a name for the position set (pos=..)\n";
if(error.length()){
warn(error);
return;
}
par.param("grid", grid_points);
node_set ns = read_node_set(filename);
if(!ns.n_size()){
warn("read_positions obtained empty node_set");
return;
}
positions[pos_name] = ns;
bool set_mapper = true;
par.param("set_mapper", set_mapper);
if(set_mapper && !distanceViewers.count(pos_name)){
distances[pos_name] = positions[pos_name].distances();
std::vector<int> memberInts = int_range(distances[pos_name].n_size());
bool trackCoordinates = true;
par.param("coords", trackCoordinates);
if(!par.defined("gpu")){
distanceViewers[ pos_name ] = new DistanceViewer(memberInts, distances[pos_name].Nodes(), pos_name, trackCoordinates);
distanceViewers[ pos_name ]->show();
distanceViewers[ pos_name ]->raise();
}else{ // set up a gpu
if(ocl_mappers.count(pos_name))
delete(ocl_mappers[pos_name]);
ocl_mappers[pos_name] = new OCL_DistanceMapperManager(&positions[pos_name], &distances[pos_name]);
ocl_mappers[pos_name]->print_pointers();
}
}
if(set_mapper && distanceViewers.count(pos_name)){
distanceViewers[pos_name]->set_starting_dimensionality(ns.n_dim());
distanceViewers[pos_name]->setPositions(ns.Nodes(), grid_points);
}
}
void MainWindow::loadFile(const QString &fileName)
{
//if is empty
if(fileName.isEmpty())
{
//set the file name
this->setFileName(QString ());
ui->AppOutput->append("No file is open");
return;
}
// create a QFile Object with the fileName variable
QFile *qfo=new QFile(fileName);
//if
if(!(qfo->open(QIODevice::Text|QIODevice::ReadOnly)))
{
ui->AppOutput->append("The file "+fileName+" cannot be opened");
QMessageBox::warning(this,"Error","The file cannot be opened",QMessageBox::Ok,QMessageBox::Ok);
setFileName(QString());
return;
}
else
{
ui->AppOutput->append("The file at "+fileName+" is opened");
QTextStream qts(qfo);
//codigo de parseo.
int count_lines=0;
while(!qts.atEnd())
{
//se lee la linea
QString line=qts.readLine();
//se muestra en la pantalla
ui->textEdit->appendPlainText(line);
//se envia a parsearla
lineParser(line);
//se cuenta la cantidad de lineas
count_lines++;
}
ui->AppOutput->append("Lines: "+QString::number(count_lines));
qfo->close();
setFileName(fileName);
setWindowModified(false);
}
}
void SodController::read_distances(f_parameter& par)
{
QString error;
QTextStream qts(&error);
QString fileName;
QString disName;
// std::string filename;
if(!par.param("file", fileName))
qts << "read_distances: no distance file specified\n";
if(!par.param("dist", disName))
qts << "read_distances: specify name for distances (dist=..)";
if(error.length()){
warn(error);
return;
}
node_set ns = read_node_set(fileName);
if(!ns.n_size()){
warn("read_distances obtained empty node_set");
return;
}
if(ns.n_size() != ns.n_dim()){
qts << "read_distances node_set is not square: " << ns.n_size() << "*" << ns.n_dim();
warn(error);
return;
}
distances[disName] = ns;
std::vector<int> memberInts(ns.n_size());
for(unsigned int i=0; i < memberInts.size(); ++i)
memberInts[i] = i;
bool trackCoordinates = true;
par.param("coords", trackCoordinates);
par.param("comps", trackCoordinates);
DistanceViewer* viewer = new DistanceViewer(memberInts, ns.Nodes(), fileName, trackCoordinates);
if(distanceViewers.count(disName))
delete distanceViewers[disName];
distanceViewers[disName] = viewer;
viewer->show();
viewer->raise();
}
void SodController::titrate(f_parameter& par)
{
QString dviewer;
if(!par.param("viewer", dviewer)){
warn("Specify viewer to be used viewer=(..)");
return;
}
if(!distanceViewers.count(dviewer)){
warn("Unknown viewer specified");
return;
}
DistanceViewer* viewer = distanceViewers[dviewer];
unsigned int rep=10;
std::vector<unsigned int> iter;
std::vector<unsigned int> dim_no;
QString error;
QTextStream qts(&error);
par.param("rep", rep);
if(!par.param("iter", ',', iter))
qts << "Please specify iteration numbers: iter=300,500, etc..\n";
if(!par.param("dim_no", ',', dim_no))
qts << "Please specify starting dimensionalities dim_no=6,4,2 or something\n";
if(error.length()){
warn(error);
return;
}
std::vector<std::vector<float> > minStresses ;
for(unsigned int i=0; i < dim_no.size(); ++i){
for(unsigned int j=0; j < iter.size(); ++j)
minStresses.push_back( viewer->runMultiple(rep, iter[j], dim_no[i]));
}
// and then let's try to print out a simple table..
std::string out_file;
std::ofstream out;
if(par.param("ofile", out_file))
out.open(out_file.c_str());
for(unsigned int d=0; d < dim_no.size(); ++d){
for(unsigned int it=0; it < iter.size(); ++it){
std::cout << "\t" << dim_no[d] << "," << iter[it];
if(out.is_open())
out << "\t" << dim_no[d] << "," << iter[it];
}
}
std::cout << std::endl;
if(out.is_open())
out << std::endl;
for(unsigned int i=0; i < rep; ++i){
std::cout << i;
if(out.is_open())
out << i;
for(unsigned int d=0; d < dim_no.size(); ++d){
for(unsigned int it=0; it < iter.size(); ++it){
unsigned int j = d * iter.size() + it;
std::cout << "\t" << minStresses[j][i];
if(out.is_open())
out << "\t" << minStresses[j][i];
}
}
std::cout << std::endl;
if(out.is_open())
out << std::endl;
}
}
