/*******************************************************************************
* fill_and_save - fill in missing genotypes and save the result
*
* INPUTS: snp_t *snps - array of snp_t structs
* em_params_t *em_params - input parameters for hmm_em()
* em_out_t *em_out - output of hmm_em()
* int path_option - which path algorithm was used
* int sort_option - state sorting option (for path output)
* double threshold - confidence threshold for filtered output
* int num_emission_types - 2 or 3 depending if missing is a valid emission type
* int chromosome - which chromosome was processed
* int smooth_out - boolean value to instruct maxSmthPath to write out
* the smoothness information
* double **fill_probability_matrix - pointer to memory to store filling probabilities
*
*
* RETURNS:
* funciton returns void, filling probabilities returned via parameter
*
* ASSUMES:
*
* EFFECTS: modifies contents of fill_probability_matrix, writes filled file and path file
*
* ERROR CONDITIONS:
*
* COMMENTS:
*
******************************************************************************/
void fill_and_save(snp_t *snps, em_params_t *em_params, em_out_t *em_out,
int path_option, int sort_option, double threshold,
int num_emission_types, int chromosome, int smooth_out,
double **fill_probability_matrix)
{
clock_t tStart;
clock_t tEnd;
int **path_matrix;
double **log_prob_matrix = NULL;
assert(path_option == PATH_VITERBI || path_option == PATH_MAXSMTH);
path_matrix = allocate2Di(em_params->num_snps, em_params->num_strains);
tStart = clock();
if (path_option == PATH_VITERBI)
{
printf("Calculating Viterbi path...");
log_prob_matrix = allocate2Dd(em_params->num_snps, em_params->num_strains);
viterbiPath(em_params, em_out, path_matrix, log_prob_matrix,
fill_probability_matrix);
}
else
{
printf("Calculating max smooth path...");
maxSmthPath(em_params, em_out, em_params->file_prefix, smooth_out,
path_matrix, fill_probability_matrix);
}
tEnd = clock();
printf("Done (%.2fs)\n", ((double)(tEnd - tStart)) / CLOCKS_PER_SEC);
/* write the path to a file */
writePath(snps, path_matrix, em_params->num_snps,
em_params->num_strains, em_params->file_prefix,
path_option, chromosome, sort_option,
em_out->last_emission_matrix);
/* if random missing then fill in using path */
if ( em_params->miss_option > 0)
{
fillin(em_params->snps, path_matrix, em_out->last_emission_matrix,
em_params->num_snps, em_params->num_strains, num_emission_types,
fill_probability_matrix);
writeFilledData(snps, chromosome, fill_probability_matrix,
em_params->file_prefix, path_option, sort_option,
threshold, em_params->num_snps);
}
free2Di(path_matrix, em_params->num_snps);
if (path_option == PATH_VITERBI)
{
free2Dd(log_prob_matrix, em_params->num_snps);
}
}
int PathPlanner::runRRT(){
this->RRT();
calcPathLength();
writePath();
writeMetadata();
cout<<"Estimated path length: "<<this->pathLength<<"\n";
return 0;
}
void LowLevelGraphicsPostScriptRenderer::clipToPath (const Path& path, const AffineTransform& transform)
{
writeClip();
Path p (path);
p.applyTransform (transform.translated ((float) stateStack.getLast()->xOffset, (float) stateStack.getLast()->yOffset));
writePath (p);
out << "clip\n";
}
int PathPlanner::runSquareSpiral(){
Points spiralpath = this->getSpiralPath();
this->setPath(spiralpath);
calcPathLength();
writePath();
writeMetadata();
cout<<"Estimated path length: "<<this->pathLength<<"\n";
return 0;
}
//In a perfect world these would have some kind of error checking. I like to live dangerously....
int PathPlanner::runTrace(){
vector<Polygon_2> all = this->linearShrink();
this->setPath(all);
calcPathLength();
writePath();
writeMetadata();
cout<<"Estimated path length: "<<this->pathLength<<"\n";
return 0;
}
//==============================================================================
void LowLevelGraphicsPostScriptRenderer::fillPath (const Path& path, const AffineTransform& t)
{
if (stateStack.getLast()->fillType.isColour())
{
writeClip();
Path p (path);
p.applyTransform (t.translated ((float) stateStack.getLast()->xOffset,
(float) stateStack.getLast()->yOffset));
writePath (p);
writeColour (stateStack.getLast()->fillType.colour);
out << "fill\n";
}
else if (stateStack.getLast()->fillType.isGradient())
{
// this doesn't work correctly yet - it could be improved to handle solid gradients, but
// postscript can't do semi-transparent ones.
notPossibleInPostscriptAssert // you can disable this warning by setting the WARN_ABOUT_NON_POSTSCRIPT_OPERATIONS flag at the top of this file
writeClip();
out << "gsave ";
{
Path p (path);
p.applyTransform (t.translated ((float) stateStack.getLast()->xOffset, (float) stateStack.getLast()->yOffset));
writePath (p);
out << "clip\n";
}
const Rectangle<int> bounds (stateStack.getLast()->clip.getBounds());
// ideally this would draw lots of lines or ellipses to approximate the gradient, but for the
// time-being, this just fills it with the average colour..
writeColour (stateStack.getLast()->fillType.gradient->getColourAtPosition (0.5f));
out << bounds.getX() << ' ' << -bounds.getBottom() << ' ' << bounds.getWidth() << ' ' << bounds.getHeight() << " rectfill\n";
out << "grestore\n";
}
}
bool side::enter()
{
if (filesPath.size() < 2 && !(_stricmp(files[indexFile].name, "..")))
return false;
else if (!(_stricmp(files[indexFile].name, ".."))) //..
{
string tName(filesPath.back());
filesPath.pop_back();
makePath();
if (!fillFiles())
throw string("Can't read the directory: " + path);
indexFile = getIndexByNameInCurrent(tName);
if (indexFile >= side::countFiles) // не вміщається в першу (значить хз :) десь посерединці поставимо :))
{
indexRow = 10;
upIndexFile = indexFile - 10;
}
else // ваміщається в перший комлект
{
upIndexFile = 0;
indexRow = indexFile;
}
show();
writePath();
return true;
}
else if ((_stricmp(files[indexFile].name, "..")) && !(files[indexFile].attrib & _A_SUBDIR))
return false;
else // not .. but folder
{
filesPath.emplace_back(files[indexFile].name);
makePath();
if (!fillFiles())
throw string("Can't read the directory: " + path);
clearIndex();
show();
writePath();
return true;
}
}
bool QgsProject::write()
{
clearError();
// if we have problems creating or otherwise writing to the project file,
// let's find out up front before we go through all the hand-waving
// necessary to create all the Dom objects
if ( !imp_->file.open( QIODevice::WriteOnly | QIODevice::Text | QIODevice::Truncate ) )
{
imp_->file.close(); // even though we got an error, let's make
// sure it's closed anyway
setError( tr( "Unable to save to file %1" ).arg( imp_->file.fileName() ) );
return false;
}
QFileInfo myFileInfo( imp_->file );
if ( !myFileInfo.isWritable() )
{
// even though we got an error, let's make
// sure it's closed anyway
imp_->file.close();
setError( tr( "%1 is not writable. Please adjust permissions (if possible) and try again." )
.arg( imp_->file.fileName() ) );
return false;
}
QDomImplementation DomImplementation;
QDomDocumentType documentType =
DomImplementation.createDocumentType( "qgis", "http://mrcc.com/qgis.dtd",
"SYSTEM" );
std::auto_ptr < QDomDocument > doc =
std::auto_ptr < QDomDocument > ( new QDomDocument( documentType ) );
QDomElement qgisNode = doc->createElement( "qgis" );
qgisNode.setAttribute( "projectname", title() );
qgisNode.setAttribute( "version", QString( "%1" ).arg( QGis::QGIS_VERSION ) );
doc->appendChild( qgisNode );
// title
QDomElement titleNode = doc->createElement( "title" );
qgisNode.appendChild( titleNode );
QDomText titleText = doc->createTextNode( title() ); // XXX why have title TWICE?
titleNode.appendChild( titleText );
// let map canvas and legend write their information
emit writeProject( *doc );
// within top level node save list of layers
QMap<QString, QgsMapLayer*> & layers = QgsMapLayerRegistry::instance()->mapLayers();
// Iterate over layers in zOrder
// Call writeXML() on each
QDomElement projectLayersNode = doc->createElement( "projectlayers" );
projectLayersNode.setAttribute( "layercount", qulonglong( layers.size() ) );
QMap<QString, QgsMapLayer*>::iterator li = layers.begin();
while ( li != layers.end() )
{
//QgsMapLayer *ml = QgsMapLayerRegistry::instance()->mapLayer(*li);
QgsMapLayer* ml = li.value();
if ( ml )
{
QString externalProjectFile = layerIsEmbedded( ml->id() );
QHash< QString, QPair< QString, bool> >::const_iterator emIt = mEmbeddedLayers.find( ml->id() );
if ( emIt == mEmbeddedLayers.constEnd() )
{
ml->writeXML( projectLayersNode, *doc );
}
else //layer defined in an external project file
{
//only save embedded layer if not managed by a legend group
if ( emIt.value().second )
{
QDomElement mapLayerElem = doc->createElement( "maplayer" );
mapLayerElem.setAttribute( "embedded", 1 );
mapLayerElem.setAttribute( "project", writePath( emIt.value().first ) );
mapLayerElem.setAttribute( "id", ml->id() );
projectLayersNode.appendChild( mapLayerElem );
}
}
}
li++;
}
qgisNode.appendChild( projectLayersNode );
// now add the optional extra properties
dump_( imp_->properties_ );
QgsDebugMsg( QString( "there are %1 property scopes" ).arg( static_cast<int>( imp_->properties_.count() ) ) );
if ( !imp_->properties_.isEmpty() ) // only worry about properties if we
// actually have any properties
{
imp_->properties_.writeXML( "properties", qgisNode, *doc );
}
// now wrap it up and ship it to the project file
doc->normalize(); // XXX I'm not entirely sure what this does
//QString xml = doc->toString(4); // write to string with indentation of four characters
// (yes, four is arbitrary)
// const char * xmlString = xml; // debugger probe point
// qDebug( "project file output:\n\n" + xml );
QTextStream projectFileStream( &imp_->file );
//projectFileStream << xml << endl;
doc->save( projectFileStream, 4 ); // save as utf-8
imp_->file.close();
// check if the text stream had no error - if it does
// the user will get a message so they can try to resolve the
// situation e.g. by saving project to a volume with more space
//
if ( projectFileStream.pos() == -1 || imp_->file.error() != QFile::NoError )
{
setError( tr( "Unable to save to file %1. Your project "
"may be corrupted on disk. Try clearing some space on the volume and "
"check file permissions before pressing save again." )
.arg( imp_->file.fileName() ) );
return false;
}
dirty( false ); // reset to pristine state
emit projectSaved();
return true;
} // QgsProject::write