QString
GenericMediaDevice::fileName( const MetaBundle &bundle )
{
QString result = cleanPath( bundle.artist() );
if( !result.isEmpty() )
{
if( m_spacesToUnderscores )
result += "_-_";
else
result += " - ";
}
if( bundle.track() )
{
result.sprintf( "%02d", bundle.track() );
if( m_spacesToUnderscores )
result += '_';
else
result += ' ';
}
result += cleanPath( bundle.title() + '.' + bundle.type() );
return result;
}
Document* FileManager::openDocument(const QString& filename, QString* error) {
QFileInfo fi(filename);
QFile file(filename);
if (!(fi.exists() && fi.isFile())){
if(error)
*error = tr("The file <br>\"%0\" <br>does not "
"exist or is no file.")
.arg(fi.absolutePath());
return 0;
}
if (!file.open(QIODevice::ReadOnly|QIODevice::Text)){
if(error)
*error = tr("Unable to open the file<br>\"%0\" <br>"
"Check permissions or wether other programs "
"are locking the file.")
.arg(fi.absolutePath());
return 0;
}
QByteArray contents = file.readAll();
EncodingDetector detector(contents);
QTextCodec* codec = detector.GetFontEncoding();//TODO:Delete?
DocumentInfo docinfo(cleanPath(filename),codec->name(),fi.size());
Document* doc = new Document(docinfo, codec->toUnicode(contents));
file.close();
m_documents.append(doc);
m_documentMap.insert(cleanPath(filename), doc);
emit documentOpened(doc);
return doc;
}
int WsUser::createNode(const string& path, NodeType type)
{
switch (type) {
case File:
return m_client->createNode(cleanPath(path), 0);
case Directory:
return m_client->createNode(cleanPath(path), 1);
}
}
void FileLocator::addPath(const char* newPathBegin,const char* newPathEnd)
{
/* Check if the path is fully-qualified: */
if(newPathEnd-newPathBegin>1&&newPathBegin[0]=='/')
pathList.push_back(cleanPath(newPathBegin,newPathEnd));
else if(newPathEnd-newPathBegin>0)
{
/* Prefix relative paths with the current working directory: */
std::string absPath=getCurrentDirectory();
absPath.push_back('/');
absPath.append(newPathBegin,newPathEnd);
pathList.push_back(cleanPath(absPath.c_str()));
}
}
///Regarding Projects
Project* FileManager::newProject(const QString& name, const QString& rootPath, QString* error) {
QString filename = cleanPath(rootPath + "/" + name);
QFile file(filename);
if(m_documentMap.contains(filename) || m_projectMap.contains(filename)) {
if(error)
*error = tr("A file with the name <br>\"%0\" <br>is already open.").arg(filename);
return 0;
}
if(!file.open(QIODevice::Truncate|QIODevice::WriteOnly|QIODevice::Text)) {
if(error)
*error = tr("Unable to open the file <br>\"%0\"").arg(filename);
return 0;
}
Project* project = new Project(name, rootPath);
if(!project->isValid()) {
delete project;
if(error)
*error = tr("Invalid project parameters.");
}
project->setFilename(filename);
project->toXml(&file);
file.close();
m_projects.append(project);
m_projectMap.insert(filename, project);
emit projectOpened(project);
return project;
}
void
QResourcePrivate::ensureChildren() const
{
ensureInitialized();
if(!children.isEmpty() || !container || related.isEmpty())
return;
QString path = absoluteFilePath, k;
if(path.startsWith(QLatin1Char(':')))
path = path.mid(1);
QSet<QString> kids;
QString cleaned = cleanPath(path);
for(int i = 0; i < related.size(); ++i) {
QResourceRoot *res = related.at(i);
if(res->mappingRootSubdir(path, &k) && !k.isEmpty()) {
if(!kids.contains(k)) {
children += k;
kids.insert(k);
}
} else {
const int node = res->findNode(cleaned);
if(node != -1) {
QStringList related_children = res->children(node);
for(int kid = 0; kid < related_children.size(); ++kid) {
k = related_children.at(kid);
if(!kids.contains(k)) {
children += k;
kids.insert(k);
}
}
}
}
}
}
//-----------------------------------------------------------------------
void SMBUrl::updateCache()
//-----------------------------------------------------------------------
{
cleanPath();
// SMB URLs are UTF-8 encoded
kdDebug(KIO_SMB) << "updateCache " << KURL::path() << endl;
if (KURL::url() == "smb:/")
m_surl = "smb://";
else {
QString surl = "smb://";
if (KURL::hasUser()) {
surl += KURL::encode_string(KURL::user(), 106);
if (KURL::hasPass()) {
surl += ":" + KURL::encode_string(KURL::pass(), 106);
}
surl += "@";
}
surl += KURL::encode_string(KURL::host().upper(), 106);
surl += KURL::encode_string(KURL::path(), 106);
m_surl = surl.utf8();
}
m_type = SMBURLTYPE_UNKNOWN;
// update m_type
(void)getType();
}
Id ReadKkit::buildTable( const vector< string >& args )
{
string head;
string clean = cleanPath( args[2] );
string tail = pathTail( clean, head ); // Name of xtab
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
Id tab;
int mode = atoi( args[ tableMap_[ "step_mode" ] ].c_str() );
if ( mode == TAB_IO ) {
} else if ( mode == TAB_LOOP || mode == TAB_ONCE ) {
tab = shell_->doCreate( "StimulusTable", pa, tail, 1 );
assert( tab != Id() );
double stepSize = atof( args[ tableMap_[ "stepsize" ] ].c_str() );
Field< double >::set( tab, "stepSize", stepSize );
if ( mode == TAB_LOOP )
Field< bool >::set( tab, "doLoop", 1 );
double input = atof( args[ tableMap_[ "input" ] ].c_str() );
Field< double >::set( tab, "startTime", -input );
// The other StimulusTable parameters will have to wait till the
// loadTab is invoked.
}
string temp = clean.substr( 10 );
tabIds_[ temp ] = tab;
Id info = buildInfo( tab, tableMap_, args );
return tab;
}
Id ReadKkit::buildReac( const vector< string >& args )
{
string head;
string clean = cleanPath( args[2] );
string tail = pathTail( clean, head );
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
double kf = atof( args[ reacMap_[ "kf" ] ].c_str() );
double kb = atof( args[ reacMap_[ "kb" ] ].c_str() );
// We have a slight problem because MOOSE has a more precise value for
// NA than does kkit. Here we assume that the conc units from Kkit are
// meant to be OK, so they override the #/cell (lower case k) units.
// So we convert all the Kfs and Kbs in the entire system after
// the model has been created, once we know the order of each reac.
Id reac = shell_->doCreate( "Reac", pa, tail, 1 );
reacIds_[ clean.substr( 10 ) ] = reac;
// Here is another hack: The native values stored in the reac are
// Kf and Kb, in conc units. However the 'clean' values from kkit
// are the number values numKf and numKb. In the
// function convertReacRatesToNumUnits we take the numKf and numKb and
// do proper conc scaling.
Field< double >::set( reac, "Kf", kf );
Field< double >::set( reac, "Kb", kb );
Id info = buildInfo( reac, reacMap_, args );
numReacs_++;
return reac;
}
/**
* Build a Stim entry in simulation, i.e., a PulseGen
*/
Id ReadKkit::buildStim( const vector< string >& args )
{
string head;
string clean = cleanPath( args[2] );
string tail = pathTail( clean, head );
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
double level1 = atof( args[ stimMap_[ "firstLevel" ] ].c_str() );
double width1 = atof( args[ stimMap_[ "firstWidth" ] ].c_str() );
double delay1 = atof( args[ stimMap_[ "firstDelay" ] ].c_str() );
double level2 = atof( args[ stimMap_[ "secondLevel" ] ].c_str() );
double width2 = atof( args[ stimMap_[ "secondWidth" ] ].c_str() );
double delay2 = atof( args[ stimMap_[ "secondLevel" ] ].c_str() );
double baselevel = atof( args[ stimMap_[ "baseLevel" ] ].c_str() );
Id stim = shell_->doCreate( "PulseGen", pa, tail, 1 );
assert( stim != Id() );
string stimPath = clean.substr( 10 );
stimIds_[ stimPath ] = stim;
Field< double >::set( stim, "firstLevel", level1 );
Field< double >::set( stim, "firstWidth", width1 );
Field< double >::set( stim, "firstDelay", delay1 );
Field< double >::set( stim, "secondLevel", level2 );
Field< double >::set( stim, "secondWidth", width2 );
Field< double >::set( stim, "secondDelay", delay2 );
Field< double >::set( stim, "baseLevel", baselevel );
numStim_++;
return stim;
}
bool goBack( string& path ){
// Defaulting back to the wd not desired!
if( path == string( "/" ) )
return true;
cleanPath( path );
char removed;
while( path.size( ) > 0 and ( removed =
path.at( path.size( )-1 ) ) == '/' )
path.erase( path.end( )-1 );
if( removed == '.' ){
if( path.empty( ) )
path = string( "/" );
return false;
}
for( int i = path.size( )-1; i > 0; i-- ){
removed = path.at( path.size( )-1 );
path.erase( path.end( )-1 );
if( removed == '/' )
break;
}
if( path.empty( ) )
path = string( "/" );
return true;
}
static ALWAYS_INLINE void visitedURLInline(const KURL& base, const AtomicString& attributeURL, Vector<UChar, 512>& buffer)
{
if (attributeURL.isNull())
return;
const UChar* characters = attributeURL.characters();
unsigned length = attributeURL.length();
// This is a poor man's completeURL. Faster with less memory allocation.
// FIXME: It's missing a lot of what completeURL does and a lot of what KURL does.
// For example, it does not handle international domain names properly.
// FIXME: It is wrong that we do not do further processing on strings that have "://" in them:
// 1) The "://" could be in the query or anchor.
// 2) The URL's path could have a "/./" or a "/../" or a "//" sequence in it.
// FIXME: needsTrailingSlash does not properly return true for a URL that has no path, but does
// have a query or anchor.
bool hasColonSlashSlash = containsColonSlashSlash(characters, length);
if (hasColonSlashSlash && !needsTrailingSlash(characters, length)) {
buffer.append(attributeURL.characters(), attributeURL.length());
return;
}
if (hasColonSlashSlash) {
// FIXME: This is incorrect for URLs that have a query or anchor; the "/" needs to go at the
// end of the path, *before* the query or anchor.
buffer.append(characters, length);
buffer.append('/');
return;
}
if (!length)
buffer.append(base.string().characters(), base.string().length());
else {
switch (characters[0]) {
case '/':
buffer.append(base.string().characters(), base.pathStart());
break;
case '#':
buffer.append(base.string().characters(), base.pathEnd());
break;
default:
buffer.append(base.string().characters(), base.pathAfterLastSlash());
break;
}
}
buffer.append(characters, length);
cleanPath(buffer);
if (needsTrailingSlash(buffer.data(), buffer.size())) {
// FIXME: This is incorrect for URLs that have a query or anchor; the "/" needs to go at the
// end of the path, *before* the query or anchor.
buffer.append('/');
}
return;
}
string WsUser::getProperty(const string& path, const string& section, const string& attr, const string& def)
{
/* Return the property found if not empty string otherwise return def */
string ret = m_client->getProperty(section, cleanPath(path), attr);
if ( ret.size() > 0 ) return ret;
return def;
}
bool CommanderWindow::Up()
{
cleanPath();
if ( strcmp( input->Text(), "/" ) == 0 ) return true;
char *path = strdup( input->Text() );
int len = strlen( path ) - 2;
while ( len >= 0 )
{
if ( path[len] == '/' ) break;
path[len] = 0;
len -= 1;
}
if ( len < 0 ) input->SetText("/");
else
{
input->SetText( path );
}
free( path );
return true;
}
bool Path::find(StringVec::const_iterator it, StringVec::const_iterator end, const std::string& name, Path& path)
{
while (it != end)
{
#if defined(WIN32)
std::string cleanPath(*it);
if (cleanPath.size() > 1 && cleanPath[0] == '"' && cleanPath[cleanPath.size() - 1] == '"')
{
cleanPath = cleanPath.substr(1, cleanPath.size() - 2);
}
Path p(cleanPath);
#else
Path p(*it);
#endif
p.makeDirectory();
p.resolve(Path(name));
File f(p);
if (f.exists())
{
path = p;
return true;
}
++it;
}
return false;
}
/**
* There is a problem with this conversion, because of the discrepancy of
* the correct NA and the version (6e23) used in kkit. I take the
* concentration as authoritative, not the # of molecules. This is because
* I use conc units for the rates as well, and to use n for pools and
* conc for reactions will always introduce errors. This is still not
* a great solution, because, for example, simulations involving receptor
* traffic are originally framed in terms of number of receptors, not conc.
*/
Id ReadKkit::buildPool( const vector< string >& args )
{
string head;
string clean = cleanPath( args[2] );
string tail = pathTail( clean, head );
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
double nInit = atof( args[ poolMap_[ "nInit" ] ].c_str() );
double vsf = atof( args[ poolMap_[ "vol" ] ].c_str() );
/**
* vsf is vol scale factor, which is what GENESIS stores in 'vol' field
* n = vsf * conc( uM )
* Also, n = ( conc (uM) / 1e6 ) * NA * vol
* so, vol = 1e6 * vsf / NA
*/
double vol = 1.0e3 * vsf / KKIT_NA; // Converts volscale to actual vol in m^3
int slaveEnable = atoi( args[ poolMap_[ "slave_enable" ] ].c_str() );
double diffConst = atof( args[ poolMap_[ "DiffConst" ] ].c_str() );
// I used -ve D as a flag to replace pool-specific D
// with the global value of D. Here we just ignore it.
if ( diffConst < 0 )
diffConst = 0;
Id pool;
if ( slaveEnable == 0 ) {
pool = shell_->doCreate( "Pool", pa, tail, 1 );
} else if ( slaveEnable & 4 ) {
pool = shell_->doCreate( "BufPool", pa, tail, 1 );
} else {
pool = shell_->doCreate( "Pool", pa, tail, 1 );
/*
cout << "ReadKkit::buildPool: Unknown slave_enable flag '" <<
slaveEnable << "' on " << clean << "\n";
*/
poolFlags_[pool] = slaveEnable;
}
assert( pool != Id() );
// skip the 10 chars of "/kinetics/"
poolIds_[ clean.substr( 10 ) ] = pool;
Field< double >::set( pool, "nInit", nInit );
Field< double >::set( pool, "diffConst", diffConst );
// SetGet1< double >::set( pool, "setVolume", vol );
separateVols( pool, vol );
poolVols_[pool] = vol;
Id info = buildInfo( pool, poolMap_, args );
/*
cout << setw( 20 ) << head << setw( 15 ) << tail << " " <<
setw( 12 ) << nInit << " " <<
vol << " " << diffConst << " " <<
slaveEnable << endl;
*/
numPools_++;
return pool;
}
Project* FileManager::openProject(QString filename, QString* error) {
filename = cleanPath(filename);
QFileInfo fi(filename);
QFile file(filename);
if(!fi.exists()) {
if(error)
*error = tr("The file \"%0\"<br>does not exist.").arg(filename);
return 0;
}
if(!fi.isFile()) {
if(error)
*error = tr("\"%0\"<br>is not a file.").arg(filename);
return 0;
}
if(m_documentMap.contains(filename) || m_projectMap.contains(filename)) {
if(error)
*error = tr("A file with the name <br>\"%0\" <br>is already open.").arg(filename);
return 0;
}
if(!file.open(QIODevice::ReadOnly|QIODevice::Text)) {
if(error)
*error = tr("Unable to open the file <br>\"%0\".").arg(filename);
return 0;
}
Project* project = Project::fromXml(&file,cleanPath(fi.absolutePath()));
file.close();
if(!project) {
if(error)
*error = tr("Unable to read the project file <br>\"%0\".").arg(filename);
return 0;
}
if(!project->isValid()) {
delete project;
if(error)
*error = tr("Invalid project.");
}
project->setFilename(filename);
m_projects.append(project);
m_projectMap.insert(filename, project);
emit projectOpened(project);
return project;
}
Id ReadKkit::buildGraph( const vector< string >& args )
{
string head;
string tail = pathTail( cleanPath( args[2] ), head );
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
Id graph = shell_->doCreate( "Neutral", pa, tail, 1 );
assert( graph != Id() );
numOthers_++;
return graph;
}
Id ReadKkit::buildGroup( const vector< string >& args )
{
string head;
string tail = pathTail( cleanPath( args[2] ), head );
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
Id group = shell_->doCreate( "Neutral", pa, tail, 1 );
assert( group != Id() );
Id info = buildInfo( group, groupMap_, args );
numOthers_++;
return group;
}
/**
* Build a Kchan entry in simulation. For now a dummy Neutral.
*/
Id ReadKkit::buildChan( const vector< string >& args )
{
string head;
string clean = cleanPath( args[2] );
string tail = pathTail( clean, head );
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
cout << "Warning: Kchan not yet supported in MOOSE, creating dummy:\n"
<< " " << clean << "\n";
Id chan = shell_->doCreate( "Neutral", pa, tail, 1 );
assert( chan != Id() );
string chanPath = clean.substr( 10 );
chanIds_[ chanPath ] = chan;
return chan;
}
//Makes a copy of the passed DiskItem:
Directory::Directory(Directory* dir)
{
//Copies the passed directory's data:
_size = dir->getSize();
_path = dir->getPath();
_files = dir->getFiles();
_isCut = false;
if(getName() == "../")
cleanPath();
//Reads the directory's attributes into '_attr':
_attr = new struct stat;
if(stat(_path.c_str(), _attr) != 0)
throw errno;
}
bool CommanderWindow::Refresh()
{
cleanPath();
list->Empty();
const char *path = input->Text();
Directory *dir = new Directory( path );
if ( dir->Exists() == false )
{
delete dir;
Draw( Bounds() );
return false;
}
char *entry = NULL;
while ((entry = dir->NextEntry()) != NULL )
{
char *complete = (char*)malloc( strlen(path) + strlen(entry) + 2 );
strcpy( complete, path );
strcat( complete, entry );
int size = -1;
File *temp = new File( complete );
if ( temp->Open() >= 0 )
{
size = temp->Size();
temp->Close();
}
delete temp;
list->AddItem( new StringItem( entry ) );
free( complete );
}
Draw( Bounds() );
delete dir;
return true;
}
Id ReadKkit::buildPlot( const vector< string >& args )
{
string head;
string tail = pathTail( cleanPath( args[2] ), head ); // Name of plot
string temp;
string graph = pathTail( head, temp ); // Name of graph
Id pa = shell_->doFind( head ).id;
assert( pa != Id() );
Id plot = shell_->doCreate( "Table", pa, tail, 1 );
assert( plot != Id() );
temp = graph + "/" + tail;
plotIds_[ temp ] = plot;
numPlot_++;
return plot;
}
bool CMainWindow::copyFiles(const std::vector<CFileSystemObject> & files, const QString & destDir)
{
if (files.empty() || destDir.isEmpty())
return false;
const QString destPath = files.size() == 1 && files.front().isFile() ? cleanPath(destDir % toNativeSeparators("/") % files.front().fullName()) : destDir;
CFileOperationConfirmationPrompt prompt(tr("Copy files"), tr("Copy %1 %2 to").arg(files.size()).arg(files.size() > 1 ? "files" : "file"), destPath, this);
if (CSettings().value(KEY_OPERATIONS_ASK_FOR_COPY_MOVE_CONFIRMATION, true).toBool())
{
if (prompt.exec() != QDialog::Accepted)
return false;
}
CCopyMoveDialog * dialog = new CCopyMoveDialog(operationCopy, files, prompt.text(), this);
connect(this, &CMainWindow::closed, dialog, &CCopyMoveDialog::deleteLater);
dialog->connect(dialog, &CCopyMoveDialog::closed, this, &CMainWindow::deleteLater);
dialog->show();
return true;
}
bool pActionsModel::addAction( const QString& _path, QAction* action )
{
Q_ASSERT( action );
if ( !action || !path( action ).isEmpty() || this->action( _path ) ) {
return false;
}
const QString path = cleanPath( _path );
const QString subPath = path.section( QL1C( '/' ), 0, -2 );
QAction* parentAction = createCompletePathNode( subPath );
if ( !parentAction ) {
return false;
}
const int row = children( parentAction ).count();
insertAction( path, action, parentAction, row );
return true;
}
bool FileManager::saveDocument(Document* doc, const QString& filename, QString* error) {
// QFileInfo fi(filename);//doc->documentInfo()->absoluteFilePath());
QString path = cleanPath(filename);
QFile file(path);
if(!file.open(QIODevice::WriteOnly|QIODevice::Text)){
if(error)
*error = tr("Unable to open <br>\"%0\" <br>for writing.")
.arg(path);
return false;
}
QTextCodec* codec = QTextCodec::codecForName(doc->documentInfo()->encodingName().toAscii());//TODO:Delete?
if(-1 == file.write(codec->fromUnicode(doc->text()))){
if(error)
*error = tr("Writing to <br>\"%0\" <br>failed.")
.arg(path);
return false;
}
file.close();
doc->documentInfo()->setAbsoluteFilePath(path);
return true;
}
bool
QResourcePrivate::load(const QString &file)
{
related.clear();
QMutexLocker lock(resourceMutex());
const ResourceList *list = resourceList();
QString cleaned = cleanPath(file);
for(int i = 0; i < list->size(); ++i) {
QResourceRoot *res = list->at(i);
const int node = res->findNode(cleaned, locale);
if(node != -1) {
if(related.isEmpty()) {
container = res->isContainer(node);
if(!container) {
data = res->data(node, &size);
compressed = res->isCompressed(node);
} else {
data = 0;
size = 0;
compressed = 0;
}
} else if(res->isContainer(node) != container) {
qWarning("QResourceInfo: Resource [%s] has both data and children!", file.toLatin1().constData());
}
res->ref.ref();
related.append(res);
} else if(res->mappingRootSubdir(file)) {
container = true;
data = 0;
size = 0;
compressed = 0;
res->ref.ref();
related.append(res);
}
}
return !related.isEmpty();
}
bool FileManager::saveProject(Project* project, QString* error) {
Q_ASSERT(project);
//Prepare file
QString filename = cleanPath(project->filename());
QFile file(filename);
if(!file.open(QIODevice::WriteOnly|QIODevice::Text)) {
if(error)
*error = tr("Unable to open the file <br>\"%0\".").arg(filename);
return false;
}
//Save project
project->toXml(&file);
file.close();
//Store new filename
if(filename != project->filename()) {
project->setFilename(filename);
m_projectMap.remove(project->filename());
m_projectMap.insert(filename, project);
}
return true;
}
void ReadKkit::call( const vector< string >& args)
{
/// call /kinetics/foo/notes LOAD notes_string_here
if ( args.size() > 3 ) {
unsigned int len = args[1].length();
if ( ( args[1].substr( len - 5 ) == "notes" ) &&
args[2] == "LOAD" ) {
if ( args[3].length() == 0 )
return;
//HARSHA: Added CleanPath.
string objName = cleanPath(args[1].substr( 0, len - 5 ));
Id test(basePath_+objName);
Id obj( basePath_ + objName + "info" );
if ( obj != Id() ) {
string notes = "";
string space = "";
for ( unsigned int i = 3; i < args.size(); ++i ) {
unsigned int innerLength = args[i].length();
if ( innerLength == 0 )
continue;
unsigned int start = 0;
unsigned int end = innerLength;
if ( args[i][0] == '\"' )
start = 1;
if ( args[i][innerLength - 1] == '\"' )
end = innerLength - 1 - start;
notes += space + args[i].substr( start, end );
space = " ";
}
bool OK = Field< string >::set( obj, "notes", notes );
assert( OK );
}
}
}
}
Id ReadKkit::buildEnz( const vector< string >& args )
{
string head;
string clean = cleanPath( args[2] );
string tail = pathTail( clean, head );
Id pa = shell_->doFind( head ).id;
assert ( pa != Id() );
double k1 = atof( args[ enzMap_[ "k1" ] ].c_str() );
double k2 = atof( args[ enzMap_[ "k2" ] ].c_str() );
double k3 = atof( args[ enzMap_[ "k3" ] ].c_str() );
// double volscale = atof( args[ enzMap_[ "vol" ] ].c_str() );
double nComplexInit =
atof( args[ enzMap_[ "nComplexInit" ] ].c_str() );
// double vol = atof( args[ enzMap_[ "vol" ] ].c_str());
bool isMM = atoi( args[ enzMap_[ "usecomplex" ] ].c_str());
assert( poolVols_.find( pa ) != poolVols_.end() );
// double vol = poolVols_[ pa ];
/**
* vsf is vol scale factor, which is what GENESIS stores in 'vol' field
* n = vsf * conc( uM )
* Also, n = ( conc (uM) / 1e6 ) * NA * vol
* so, vol = 1e6 * vsf / NA
*/
if ( isMM ) {
Id enz = shell_->doCreate( "MMenz", pa, tail, 1 );
assert( enz != Id () );
string mmEnzPath = clean.substr( 10 );
mmEnzIds_[ mmEnzPath ] = enz;
assert( k1 > EPSILON );
double Km = ( k2 + k3 ) / k1;
Field< double >::set( enz, "Km", Km );
Field< double >::set( enz, "kcat", k3 );
Id info = buildInfo( enz, enzMap_, args );
numMMenz_++;
return enz;
} else {
Id enz = shell_->doCreate( "Enz", pa, tail, 1 );
// double parentVol = Field< double >::get( pa, "volume" );
assert( enz != Id () );
string enzPath = clean.substr( 10 );
enzIds_[ enzPath ] = enz;
// Need to figure out what to do about these. Perhaps it is OK
// to do this assignments in raw #/cell units.
Field< double >::set( enz, "k3", k3 );
Field< double >::set( enz, "k2", k2 );
Field< double >::set( enz, "k1", k1 );
string cplxName = tail + "_cplx";
string cplxPath = enzPath + "/" + cplxName;
Id cplx = shell_->doCreate( "Pool", enz, cplxName, 1 );
assert( cplx != Id () );
poolIds_[ cplxPath ] = cplx;
// Field< double >::set( cplx, "nInit", nComplexInit );
Field< double >::set( cplx, "nInit", nComplexInit );
// Use this later to assign mesh entries to enz cplx.
enzCplxMols_.push_back( pair< Id, Id >( pa, cplx ) );
separateVols( cplx, -1 ); // -1 vol is a flag to defer mesh assignment for the cplx pool.
ObjId ret = shell_->doAddMsg( "OneToAll",
ObjId( enz, 0 ), "cplx",
ObjId( cplx, 0 ), "reac" );
assert( ret != ObjId() );
// cplx()->showFields();
// enz()->showFields();
// pa()->showFields();
Id info = buildInfo( enz, enzMap_, args );
numEnz_++;
return enz;
}
}
