void TemplateManager::readTemplates(FileName const & path)
{
PathChanger p(path);
enum {
TM_PREAMBLEDEF = 1,
TM_PREAMBLEDEF_END,
TM_TEMPLATE,
TM_TEMPLATE_END
};
LexerKeyword templatetags[] = {
{ "preambledef", TM_PREAMBLEDEF },
{ "preambledefend", TM_PREAMBLEDEF_END },
{ "template", TM_TEMPLATE },
{ "templateend", TM_TEMPLATE_END }
};
Lexer lex(templatetags);
FileName const filename = libFileSearch("", "external_templates");
if (filename.empty() || !lex.setFile(filename)) {
lex.printError("external::TemplateManager::readTemplates: "
"No template file");
return;
}
char const * const preamble_end_tag =
templatetags[TM_PREAMBLEDEF_END-1].tag;
while (lex.isOK()) {
switch (lex.lex()) {
case TM_PREAMBLEDEF: {
lex.next();
string const name = lex.getString();
preambledefs[name] = lex.getLongString(preamble_end_tag);
}
break;
case TM_TEMPLATE: {
lex.next();
string const name = lex.getString();
Template & tmp = templates[name];
tmp.lyxName = name;
tmp.readTemplate(lex);
}
break;
case TM_TEMPLATE_END:
lex.printError("Warning: End outside Template.");
break;
case TM_PREAMBLEDEF_END:
lex.printError("Warning: End outside PreambleDef.");
break;
}
}
}
void Loader::Impl::resetFile(FileName const & file)
{
FileName const old_file = cached_item_ ?
cached_item_->filename() : FileName();
if (file == old_file)
return;
// If monitoring() the current file, should continue to monitor the
// new file.
bool continue_monitoring = false;
if (!old_file.empty()) {
continue_monitoring = cached_item_->monitoring();
// cached_item_ is going to be reset, so the connected
// signal needs to be disconnected.
sc_.disconnect();
cached_item_.reset();
if (status_ != Converting) {
Cache::get().remove(old_file);
} else {
//TODO remove cache item when it is not busy any more, see #7163
}
}
status_ = cached_item_ ? cached_item_->status() : WaitingToLoad;
image_.reset();
if (cached_item_ || file.empty())
return;
Cache & gc = Cache::get();
if (!gc.inCache(file))
gc.add(file);
// We /must/ make a local copy of this.
cached_item_ = gc.item(file);
status_ = cached_item_->status();
if (continue_monitoring && !cached_item_->monitoring())
cached_item_->startMonitoring();
sc_ = cached_item_->connect(bind(&Impl::statusChanged, this));
}
bool File::Exists(FileName const& fn) {
if (!fn.empty()) {
FILE* infile = fopen(fn.full(), "rb");
if (infile==0) {
fileErrMsg_.assign( strerror(errno) );
return false;
}
fclose(infile);
return true;
}
return false;
}
// ParmFile::ReadTopology()
int ParmFile::ReadTopology(Topology& Top, FileName const& fnameIn,
ArgList const& argListIn, int debugIn)
{
if (fnameIn.empty()) {
mprinterr("Error: No input topology name given.\n");
return 1;
}
if (!File::Exists( fnameIn )) {
mprinterr("Error: Topology '%s' does not exist.\n", fnameIn.full());
return 1;
}
parmName_ = fnameIn;
ArgList argIn = argListIn;
ParmFormatType pfType;
ParmIO* parmio = 0;
Top.SetDebug( debugIn );
// Only force bond search when 'bondsearch' is specified.
bool bondsearch = false;
if (argIn.Contains("bondsearch")) {
Top.SetOffset( argIn.getKeyDouble("bondsearch", -1.0) );
bondsearch = true;
}
// 'as' keyword specifies a format
std::string as_arg = argIn.GetStringKey("as");
if (!as_arg.empty()) {
pfType = (ParmFormatType)FileTypes::GetFormatFromString( PF_KeyArray, as_arg, UNKNOWN_PARM );
if (pfType == UNKNOWN_PARM) {
mprinterr("Error: Topology format '%s' not recognized.\n", as_arg.c_str());
return 1;
}
parmio = (ParmIO*)FileTypes::AllocIO( PF_AllocArray, pfType, false );
} else
parmio = DetectFormat( parmName_, pfType );
if (parmio == 0) {
mprinterr("Error: Could not determine format of topology '%s'\n", parmName_.full());
return 1;
}
mprintf("\tReading '%s' as %s\n", parmName_.full(),
FileTypes::FormatDescription(PF_AllocArray, pfType) );
parmio->SetDebug( debugIn );
if (parmio->processReadArgs(argIn)) return 1;
int err = parmio->ReadParm( parmName_.Full(), Top);
// Perform setup common to all parm files.
if (err == 0)
err = Top.CommonSetup(bondsearch || parmio->NeedsBondSearch());
else
mprinterr("Error reading topology file '%s'\n", parmName_.full());
delete parmio;
if (err > 0) return 1;
return 0;
}
bool ConverterCache::copy(FileName const & orig_from, string const & to_format,
FileName const & dest) const
{
if (!lyxrc.use_converter_cache || orig_from.empty() || dest.empty())
return false;
LYXERR(Debug::FILES, orig_from << ' ' << to_format << ' ' << dest);
// FIXME: Should not hardcode this (see bug 3819 for details)
if (to_format == "pstex") {
FileName const dest_eps(changeExtension(dest.absFileName(), "eps"));
if (!copy(orig_from, "eps", dest_eps))
return false;
} else if (to_format == "pdftex") {
FileName const dest_pdf(changeExtension(dest.absFileName(), "pdf"));
if (!copy(orig_from, "pdf", dest_pdf))
return false;
}
CacheItem * const item = pimpl_->find(orig_from, to_format);
LASSERT(item, /**/);
Mover const & mover = getMover(to_format);
return mover.copy(item->cache_name, dest,
onlyFileName(dest.absFileName()));
}
string const LyXVC::getLogFile() const
{
if (!vcs)
return string();
TempFile tempfile("lyxvclog");
tempfile.setAutoRemove(false);
FileName const tmpf = tempfile.name();
if (tmpf.empty()) {
LYXERR(Debug::LYXVC, "Could not generate logfile " << tmpf);
return string();
}
LYXERR(Debug::LYXVC, "Generating logfile " << tmpf);
vcs->getLog(tmpf);
return tmpf.absFileName();
}
void ConverterCache::remove(FileName const & orig_from,
string const & to_format) const
{
if (!lyxrc.use_converter_cache || orig_from.empty())
return;
LYXERR(Debug::FILES, orig_from << ' ' << to_format);
CacheType::iterator const it1 = pimpl_->cache.find(orig_from);
if (it1 == pimpl_->cache.end())
return;
FormatCacheType & format_cache = it1->second.cache;
FormatCacheType::iterator const it2 = format_cache.find(to_format);
if (it2 == format_cache.end())
return;
format_cache.erase(it2);
if (format_cache.empty())
pimpl_->cache.erase(it1);
}
/** Add lowest replica file name and names from comma-separated list. */
int TrajIOarray::AddReplicasFromArgs(FileName const& name0,
std::string const& commaNames)
{
if (name0.empty()) return 1;
if (!File::Exists( name0 )) {
File::ErrorMsg( name0.full() );
return 1;
}
replica_filenames_.push_back( name0 );
ArgList remdtraj_list( commaNames, "," );
for (ArgList::const_iterator fname = remdtraj_list.begin();
fname != remdtraj_list.end(); ++fname)
{
FileName trajFilename( *fname );
if (!File::Exists( trajFilename )) {
File::ErrorMsg( trajFilename.full() );
return 1;
}
replica_filenames_.push_back( trajFilename );
}
return 0;
}
/** Each rank checks that specified file is present. */
int TrajIOarray::AddReplicasFromArgs(FileName const& name0,
std::string const& commaNames,
Parallel::Comm const& ensComm,
Parallel::Comm const& trajComm)
{
// First set up filename array on all ranks.
if (name0.empty()) return 1;
replica_filenames_.push_back( name0 );
ArgList remdtraj_list( commaNames, "," );
for (ArgList::const_iterator fname = remdtraj_list.begin();
fname != remdtraj_list.end(); ++fname)
replica_filenames_.push_back( FileName( *fname ) );
if (ensComm.Size() != (int)replica_filenames_.size())
return 1;
else if (trajComm.Master()) { // Only traj comm master checks file
if (!File::Exists( replica_filenames_[ ensComm.Rank() ])) {
File::ErrorMsg( replica_filenames_[ensComm.Rank()].full() );
rprinterr("Error: File '%s' not accessible.\n", replica_filenames_[ensComm.Rank()].full());
return 1;
}
}
return 0;
}
int main(int argc, char * argv[])
{
using namespace lyx;
//setlocale(LC_CTYPE, "");
lyxerr.setStream(cerr);
os::init(argc, argv);
easyParse(argc, argv);
if (argc <= 1)
error_message("Not enough arguments.");
try {
init_package(internal_path(os::utf8_argv(0)),
cl_system_support, cl_user_support,
top_build_dir_is_two_levels_up);
} catch (ExceptionMessage const & message) {
cerr << to_utf8(message.title_) << ":\n"
<< to_utf8(message.details_) << endl;
if (message.type_ == ErrorException)
return EXIT_FAILURE;
}
// Now every known option is parsed. Look for input and output
// file name (the latter is optional).
string infilename = internal_path(os::utf8_argv(1));
infilename = makeAbsPath(infilename).absFileName();
string outfilename;
if (roundtrip) {
if (argc > 2) {
// Do not allow a user supplied output filename
// (otherwise it could easily happen that LyX would
// overwrite the original .tex file)
cerr << "Error: output filename must not be given in roundtrip mode."
<< endl;
return EXIT_FAILURE;
}
outfilename = changeExtension(infilename, ".lyx.lyx");
} else if (argc > 2) {
outfilename = internal_path(os::utf8_argv(2));
if (outfilename != "-")
outfilename = makeAbsPath(outfilename).absFileName();
} else
outfilename = changeExtension(infilename, ".lyx");
// Read the syntax tables
FileName const system_syntaxfile = libFileSearch("", "syntax.default");
if (system_syntaxfile.empty()) {
cerr << "Error: Could not find syntax file \"syntax.default\"." << endl;
return EXIT_FAILURE;
}
read_syntaxfile(system_syntaxfile);
if (!syntaxfile.empty())
read_syntaxfile(makeAbsPath(syntaxfile));
// Read the encodings table.
FileName const symbols_path = libFileSearch(string(), "unicodesymbols");
if (symbols_path.empty()) {
cerr << "Error: Could not find file \"unicodesymbols\"."
<< endl;
return EXIT_FAILURE;
}
FileName const enc_path = libFileSearch(string(), "encodings");
if (enc_path.empty()) {
cerr << "Error: Could not find file \"encodings\"."
<< endl;
return EXIT_FAILURE;
}
encodings.read(enc_path, symbols_path);
if (!default_encoding.empty() && !encodings.fromLaTeXName(default_encoding))
error_message("Unknown LaTeX encoding `" + default_encoding + "'");
// Load the layouts
LayoutFileList::get().read();
//...and the modules
theModuleList.read();
// The real work now.
masterFilePath = onlyPath(infilename);
parentFilePath = masterFilePath;
if (outfilename == "-") {
if (tex2lyx(FileName(infilename), cout, default_encoding))
return EXIT_SUCCESS;
} else if (roundtrip) {
if (tex2tex(infilename, FileName(outfilename), default_encoding))
return EXIT_SUCCESS;
} else {
if (tex2lyx(infilename, FileName(outfilename), default_encoding))
return EXIT_SUCCESS;
}
return EXIT_FAILURE;
}
void ConverterCache::add(FileName const & orig_from, string const & to_format,
FileName const & converted_file) const
{
if (!lyxrc.use_converter_cache || orig_from.empty() ||
converted_file.empty())
return;
LYXERR(Debug::FILES, ' ' << orig_from
<< ' ' << to_format << ' ' << converted_file);
// FIXME: Should not hardcode this (see bug 3819 for details)
if (to_format == "pstex") {
FileName const converted_eps(changeExtension(converted_file.absFileName(), "eps"));
add(orig_from, "eps", converted_eps);
} else if (to_format == "pdftex") {
FileName const converted_pdf(changeExtension(converted_file.absFileName(), "pdf"));
add(orig_from, "pdf", converted_pdf);
}
// Is the file in the cache already?
CacheItem * item = pimpl_->find(orig_from, to_format);
time_t const timestamp = orig_from.lastModified();
Mover const & mover = getMover(to_format);
if (item) {
LYXERR(Debug::FILES, "ConverterCache::add(" << orig_from << "):\n"
"The file is already in the cache.");
// First test for timestamp
if (timestamp == item->timestamp) {
LYXERR(Debug::FILES, "Same timestamp.");
return;
}
// Maybe the contents is still the same?
item->timestamp = timestamp;
unsigned long const checksum = orig_from.checksum();
if (checksum == item->checksum) {
LYXERR(Debug::FILES, "Same checksum.");
return;
}
item->checksum = checksum;
if (!mover.copy(converted_file, item->cache_name,
onlyFileName(item->cache_name.absFileName()))) {
LYXERR(Debug::FILES, "Could not copy file " << orig_from << " to "
<< item->cache_name);
} else if (!item->cache_name.changePermission(0600)) {
LYXERR(Debug::FILES, "Could not change file mode"
<< item->cache_name);
}
} else {
CacheItem new_item(orig_from, to_format, timestamp,
orig_from.checksum());
if (mover.copy(converted_file, new_item.cache_name,
onlyFileName(new_item.cache_name.absFileName()))) {
if (!new_item.cache_name.changePermission(0600)) {
LYXERR(Debug::FILES, "Could not change file mode"
<< new_item.cache_name);
}
FormatCache & format_cache = pimpl_->cache[orig_from];
if (format_cache.from_format.empty())
format_cache.from_format =
formats.getFormatFromFile(orig_from);
format_cache.cache[to_format] = new_item;
} else
LYXERR(Debug::FILES, "ConverterCache::add(" << orig_from << "):\n"
"Could not copy file.");
}
}
// Action_NativeContacts::Init()
Action::RetType Action_NativeContacts::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
masterDSL_ = init.DslPtr();
debug_ = debugIn;
// Get Keywords
image_.InitImaging( !(actionArgs.hasKey("noimage")) );
double dist = actionArgs.getKeyDouble("distance", 7.0);
byResidue_ = actionArgs.hasKey("byresidue");
resoffset_ = actionArgs.getKeyInt("resoffset", 0) + 1;
if (resoffset_ < 1) {
mprinterr("Error: Residue offset must be >= 0\n");
return Action::ERR;
}
includeSolvent_ = actionArgs.hasKey("includesolvent");
series_ = actionArgs.hasKey("series");
saveNonNative_ = actionArgs.hasKey("savenonnative");
if (actionArgs.hasKey("skipnative"))
determineNativeContacts_ = false;
if (!determineNativeContacts_ && !saveNonNative_) {
mprintf("Warning: 'skipnative' specified; implies 'savenonnative'.\n");
saveNonNative_ = true;
}
# ifdef MPI
if (saveNonNative_) {
mprinterr("Error: Saving non-native contact data not yet supported for MPI\n");
return Action::ERR;
}
# endif
distance_ = dist * dist; // Square the cutoff
first_ = actionArgs.hasKey("first");
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
Rseries_ = NO_RESSERIES;
if (series_) {
seriesout_ = init.DFL().AddDataFile(actionArgs.GetStringKey("seriesout"), actionArgs);
init.DSL().SetDataSetsPending( true );
if (saveNonNative_)
seriesNNout_ = init.DFL().AddDataFile(actionArgs.GetStringKey("seriesnnout"), actionArgs);
std::string rs_arg = actionArgs.GetStringKey("resseries");
if (!rs_arg.empty()) {
if (rs_arg == "present")
Rseries_ = RES_PRESENT;
else if (rs_arg == "sum")
Rseries_ = RES_SUM;
else {
mprinterr("Error: '%s' is not a valid 'resseries' keyword.\n", rs_arg.c_str());
return Action::ERR;
}
seriesRout_ = init.DFL().AddDataFile(actionArgs.GetStringKey("resseriesout"), actionArgs);
}
} else {
if (KeywordError(actionArgs,"seriesout")) return Action::ERR;
if (KeywordError(actionArgs,"seriesnnout")) return Action::ERR;
if (KeywordError(actionArgs,"resseries")) return Action::ERR;
if (KeywordError(actionArgs,"resseriesout")) return Action::ERR;
}
cfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("writecontacts"), "Native Contacts",
DataFileList::TEXT, true);
pfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("contactpdb"), "Contact PDB",
DataFileList::PDB);
if (saveNonNative_)
nfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("nncontactpdb"),
"Non-native Contact PDB", DataFileList::PDB);
rfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("resout"), "Contact Res Pairs",
DataFileList::TEXT, true);
if (cfile_ == 0 || rfile_ == 0) return Action::ERR;
pdbcut_ = (float)actionArgs.getKeyDouble("pdbcut", -1.0);
usepdbcut_ = (pdbcut_ > -1.0);
// Get reference for native contacts. Do this even if we wont be
// determining native contacts in order to set up contact lists.
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (!first_) {
if (REF.error()) return Action::ERR;
if (REF.empty()) {
mprintf("Warning: No reference structure specified. Defaulting to first.\n");
first_ = true;
}
} else {
if (!REF.empty()) {
mprinterr("Error: Must only specify 'first' or a reference structure, not both.\n");
return Action::ERR;
}
}
// Create data sets
std::string name = actionArgs.GetStringKey("name");
if (name.empty())
name = init.DSL().GenerateDefaultName("Contacts");
numnative_ = init.DSL().AddSet(DataSet::INTEGER, MetaData(name, "native"));
nonnative_ = init.DSL().AddSet(DataSet::INTEGER, MetaData(name, "nonnative"));
if (outfile != 0) {
outfile->AddDataSet(numnative_);
outfile->AddDataSet(nonnative_);
}
if (numnative_ == 0 || nonnative_ == 0) return Action::ERR;
if (actionArgs.hasKey("mindist")) {
mindist_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(name, "mindist"));
if (mindist_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet(mindist_);
}
if (actionArgs.hasKey("maxdist")) {
maxdist_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(name, "maxdist"));
if (maxdist_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet(maxdist_);
}
DataFile *natmapfile = 0, *nonmapfile = 0;
if (actionArgs.hasKey("map")) {
nativeMap_ = (DataSet_MatrixDbl*)init.DSL().AddSet(DataSet::MATRIX_DBL, MetaData(name, "nativemap"));
if (nativeMap_ == 0) return Action::ERR;
nonnatMap_ = (DataSet_MatrixDbl*)init.DSL().AddSet(DataSet::MATRIX_DBL, MetaData(name, "nonnatmap"));
if (nonnatMap_ == 0) return Action::ERR;
FileName mapFilename;
mapFilename.SetFileName( actionArgs.GetStringKey("mapout") );
if (!mapFilename.empty()) {
natmapfile = init.DFL().AddDataFile(mapFilename.PrependFileName("native."));
if (natmapfile != 0) natmapfile->AddDataSet(nativeMap_);
nonmapfile = init.DFL().AddDataFile(mapFilename.PrependFileName("nonnative."));
if (nonmapfile != 0) nonmapfile->AddDataSet(nonnatMap_);
}
}
// Get Masks
if (Mask1_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
std::string mask2 = actionArgs.GetMaskNext();
if (!mask2.empty()) {
if (Mask2_.SetMaskString( mask2 )) return Action::ERR;
}
mprintf(" NATIVECONTACTS: Mask1='%s'", Mask1_.MaskString());
if (Mask2_.MaskStringSet())
mprintf(" Mask2='%s'", Mask2_.MaskString());
if (determineNativeContacts_) {
mprintf(", native contacts set up based on");
if (first_)
mprintf(" first frame.\n");
else
mprintf("'%s'.\n", REF.refName());
} else {
mprintf(", skipping native contacts set up.\n");
}
if (byResidue_) {
mprintf("\tContacts will be ignored for residues spaced < %i apart.\n", resoffset_);
if (nativeMap_ != 0)
mprintf("\tMap will be printed by residue.\n");
}
if (saveNonNative_)
mprintf("\tSaving non-native contacts as well (may use a lot of memory).\n");
mprintf("\tDistance cutoff is %g Angstroms,", sqrt(distance_));
if (!image_.UseImage())
mprintf(" imaging is off.\n");
else
mprintf(" imaging is on.\n");
if (includeSolvent_)
mprintf("\tMask selection will including solvent.\n");
else
mprintf("\tMask selection will not include solvent.\n");
mprintf("\tData set name: %s\n", name.c_str());
if (maxdist_ != 0)
mprintf("\tSaving maximum observed distances in set '%s'\n", maxdist_->legend());
if (mindist_ != 0)
mprintf("\tSaving minimum observed distances in set '%s'\n", mindist_->legend());
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
mprintf("\tContact stats will be written to '%s'\n", cfile_->Filename().full());
mprintf("\tContact res pairs will be written to '%s'\n", rfile_->Filename().full());
if (pfile_ != 0) {
mprintf("\tContact PDB will be written to '%s'\n", pfile_->Filename().full());
if (usepdbcut_) mprintf("\tOnly atoms with values > %g will be written to PDB.\n", pdbcut_);
}
if (nfile_ != 0) {
mprintf("\tNon-native contact PDB will be written to '%s'\n", nfile_->Filename().full());
if (usepdbcut_) mprintf("\tOnly atoms with values > %g will be written to PDB.\n", pdbcut_);
}
if (nativeMap_ != 0) {
mprintf("\tNative contacts map will be saved as set '%s'\n"
"\tNon-native contacts map will be saved as set '%s'\n",
nativeMap_->legend(), nonnatMap_->legend());
if (natmapfile!=0) mprintf("\tNative map output to '%s'\n",natmapfile->DataFilename().full());
if (nonmapfile!=0) mprintf("\tNative map output to '%s'\n",nonmapfile->DataFilename().full());
}
if (series_) {
mprintf("\tSaving native contact time series %s[NC].\n", name.c_str());
if (seriesout_ != 0) mprintf("\tWriting native contact time series to %s\n",
seriesout_->DataFilename().full());
if (saveNonNative_) {
mprintf("\tSaving non-native contact time series %s[NN]\n", name.c_str());
if (seriesNNout_ != 0) mprintf("\tWriting non-native contact time series to %s\n",
seriesNNout_->DataFilename().full());
}
if (Rseries_ != NO_RESSERIES) {
if (Rseries_ == RES_PRESENT)
mprintf("\tResidue contact time series will reflect presence of individual contacts.\n");
else if (Rseries_ == RES_SUM)
mprintf("\tResidue contact time series will reflect sum of individual contacts.\n");
if (seriesRout_ != 0) mprintf("\tWriting residue contact time series to %s\n",
seriesRout_->DataFilename().full());
}
}
// Set up reference if necessary.
if (!first_) {
// Set up imaging info for ref parm
image_.SetupImaging( REF.CoordsInfo().TrajBox().Type() );
if (image_.ImageType() == NONORTHO)
REF.Coord().BoxCrd().ToRecip(ucell_, recip_);
if (DetermineNativeContacts( REF.Parm(), REF.Coord() )) return Action::ERR;
}
return Action::OK;
}
FileName GuiClipboard::getAsGraphics(Cursor const & cur, GraphicsType type) const
{
// get the filename from the user
FileName filename = getPastedGraphicsFileName(cur, type);
if (filename.empty())
return FileName();
// handle image cases first
if (type == PngGraphicsType || type == JpegGraphicsType) {
// get image from QImage from clipboard
QImage image = qApp->clipboard()->image();
if (image.isNull()) {
LYXERR(Debug::ACTION, "No image in clipboard");
return FileName();
}
// convert into graphics format
QByteArray ar;
QBuffer buffer(&ar);
buffer.open(QIODevice::WriteOnly);
if (type == PngGraphicsType)
image.save(toqstr(filename.absFileName()), "PNG");
else if (type == JpegGraphicsType)
image.save(toqstr(filename.absFileName()), "JPEG");
else
LATTEST(false);
return filename;
}
// get mime for type
QString mime;
switch (type) {
case PdfGraphicsType: mime = pdfMimeType(); break;
case LinkBackGraphicsType: mime = pdfMimeType(); break;
case EmfGraphicsType: mime = emfMimeType(); break;
case WmfGraphicsType: mime = wmfMimeType(); break;
default: LASSERT(false, return FileName());
}
// get data
if (!cache_.hasFormat(mime))
return FileName();
// data from ourself or some other LyX instance
QByteArray const ar = cache_.data(mime);
LYXERR(Debug::ACTION, "Getting from clipboard: mime = " << mime.constData()
<< "length = " << ar.count());
QFile f(toqstr(filename.absFileName()));
if (!f.open(QIODevice::WriteOnly | QIODevice::Truncate)) {
LYXERR(Debug::ACTION, "Error opening file "
<< filename.absFileName() << " for writing");
return FileName();
}
// write the (LinkBack) PDF data
f.write(ar);
if (type == LinkBackGraphicsType) {
#ifdef Q_WS_MACX
void const * linkBackData;
unsigned linkBackLen;
getLinkBackData(&linkBackData, &linkBackLen);
f.write((char *)linkBackData, linkBackLen);
quint32 pdfLen = ar.size();
QDataStream ds(&f);
ds << pdfLen; // big endian by default
#else
// only non-Mac this should never happen
LATTEST(false);
#endif // Q_WS_MACX
}
f.close();
return filename;
}
// Much of this is borrowed from LayoutFileList::read()
bool ModuleList::read()
{
FileName const real_file = libFileSearch("", "lyxmodules.lst");
LYXERR(Debug::TCLASS, "Reading modules from `" << real_file << '\'');
if (real_file.empty()) {
LYXERR0("unable to find modules file `lyxmodules.lst'.\n"
<< "No modules will be available.");
return false;
}
Lexer lex;
if (!lex.setFile(real_file)) {
LYXERR0("lyxlex was not able to set file: "
<< real_file << ".\nNo modules will be available.");
return false;
}
if (!lex.isOK()) {
LYXERR0("unable to open modules file `"
<< to_utf8(makeDisplayPath(real_file.absFileName(), 1000))
<< "'\nNo modules will be available.");
return false;
}
bool finished = false;
// Parse modules files
LYXERR(Debug::TCLASS, "Starting parsing of lyxmodules.lst");
while (lex.isOK() && !finished) {
LYXERR(Debug::TCLASS, "\tline by line");
switch (lex.lex()) {
case Lexer::LEX_FEOF:
finished = true;
break;
default:
string const modname = lex.getString();
LYXERR(Debug::TCLASS, "Module name: " << modname);
if (!lex.next())
break;
string const fname = lex.getString();
LYXERR(Debug::TCLASS, "Filename: " << fname);
if (!lex.next(true))
break;
string const desc = lex.getString();
LYXERR(Debug::TCLASS, "Description: " << desc);
//FIXME Add packages
if (!lex.next())
break;
string str = lex.getString();
LYXERR(Debug::TCLASS, "Packages: " << str);
vector<string> pkgs;
while (!str.empty()) {
string p;
str = split(str, p, ',');
pkgs.push_back(p);
}
if (!lex.next())
break;
str = lex.getString();
LYXERR(Debug::TCLASS, "Required: " << str);
vector<string> req;
while (!str.empty()) {
string p;
str = split(str, p, '|');
req.push_back(p);
}
if (!lex.next())
break;
str = lex.getString();
LYXERR(Debug::TCLASS, "Excluded: " << str);
vector<string> exc;
while (!str.empty()) {
string p;
str = split(str, p, '|');
exc.push_back(p);
}
if (!lex.next())
break;
string const catgy = lex.getString();
LYXERR(Debug::TCLASS, "Category: " << catgy);
if (!lex.next())
break;
bool const local = lex.getString() == "true";
LYXERR(Debug::TCLASS, "Local: " << local);
// This code is run when we have
// modName, fname, desc, pkgs, req, exc, catgy, and local
addLayoutModule(modname, fname, desc, pkgs, req, exc, catgy, local);
} // end switch
} //end while
LYXERR(Debug::TCLASS, "End of parsing of lyxmodules.lst");
if (!theModuleList.empty())
sort(theModuleList.begin(), theModuleList.end(), ModuleSorter());
return true;
}
// Action_Spam::init()
Action::RetType Action_Spam::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Always use imaged distances
InitImaging(true);
// This is needed everywhere in this function scope
FileName filename;
// See if we're doing pure water. If so, we don't need a peak file
purewater_ = actionArgs.hasKey("purewater");
if (purewater_) {
// We still need the cutoff
double cut = actionArgs.getKeyDouble("cut", 12.0);
cut2_ = cut * cut;
doublecut_ = 2 * cut;
onecut2_ = 1 / cut2_;
// See if we write to a data file
datafile_ = actionArgs.GetStringKey("out");
// Generate the data set name, and hold onto the master data set list
std::string ds_name = actionArgs.GetStringKey("name");
if (ds_name.empty())
ds_name = myDSL_.GenerateDefaultName("SPAM");
// We only have one data set averaging over every water. Add it here
myDSL_.AddSet(DataSet::DOUBLE, ds_name, NULL);
solvname_ = actionArgs.GetStringKey("solv");
if (solvname_.empty())
solvname_ = std::string("WAT");
}else {
// Get the file name with the peaks defined in it
filename.SetFileName( actionArgs.GetStringNext() );
if (filename.empty() || !File::Exists(filename)) {
mprinterr("Spam: Error: Peak file [%s] does not exist!\n", filename.full());
return Action::ERR;
}
// Get the remaining optional arguments
solvname_ = actionArgs.GetStringKey("solv");
if (solvname_.empty())
solvname_ = std::string("WAT");
reorder_ = actionArgs.hasKey("reorder");
bulk_ = actionArgs.getKeyDouble("bulk", 0.0);
double cut = actionArgs.getKeyDouble("cut", 12.0);
cut2_ = cut * cut;
doublecut_ = 2 * cut;
onecut2_ = 1 / cut2_;
std::string infoname = actionArgs.GetStringKey("info");
if (infoname.empty())
infoname = std::string("spam.info");
infofile_ = DFL->AddCpptrajFile(infoname, "SPAM info");
if (infofile_ == 0) return Action::ERR;
// The default maskstr is the Oxygen atom of the solvent
summaryfile_ = actionArgs.GetStringKey("summary");
// Divide site size by 2 to make it half the edge length (or radius)
site_size_ = actionArgs.getKeyDouble("site_size", 2.5) / 2.0;
sphere_ = actionArgs.hasKey("sphere");
// If it's a sphere, square the radius to compare with
if (sphere_)
site_size_ *= site_size_;
datafile_ = actionArgs.GetStringKey("out");
std::string ds_name = actionArgs.GetStringKey("name");
if (ds_name.empty())
ds_name = myDSL_.GenerateDefaultName("SPAM");
// Parse through the peaks file and extract the peaks
CpptrajFile peakfile;
if (peakfile.OpenRead(filename)) {
mprinterr("SPAM: Error: Could not open %s for reading!\n", filename.full());
return Action::ERR;
}
std::string line = peakfile.GetLine();
int npeaks = 0;
while (!line.empty()) {
if (sscanf(line.c_str(), "%d", &npeaks) != 1) {
line = peakfile.GetLine();
continue;
}
line = peakfile.GetLine();
break;
}
while (!line.empty()) {
double x, y, z, dens;
if (sscanf(line.c_str(), "C %lg %lg %lg %lg", &x, &y, &z, &dens) != 4) {
line = peakfile.GetLine();
continue;
}
line = peakfile.GetLine();
peaks_.push_back(Vec3(x, y, z));
}
peakfile.CloseFile();
// Check that our initial number of peaks matches our parsed peaks. Warn
// otherwise
if (npeaks != (int)peaks_.size())
mprinterr("SPAM: Warning: %s claims to have %d peaks, but really has %d!\n",
filename.full(), npeaks, peaks_.size());
// Now add all of the data sets
MetaData md(ds_name);
for (int i = 0; i < (int)peaks_.size(); i++) {
md.SetAspect( integerToString(i+1) ); // TODO: Should this be Idx?
if (myDSL_.AddSet(DataSet::DOUBLE, md) == 0) return Action::ERR;
// Add a new list of integers to keep track of omitted frames
std::vector<int> vec;
peakFrameData_.push_back(vec);
}
}
// Print info now
if (purewater_) {
mprintf("SPAM: Calculating bulk value for pure solvent\n");
if (!datafile_.empty())
mprintf("SPAM: Printing solvent energies to %s\n", datafile_.c_str());
mprintf("SPAM: Using a %.2f Angstrom non-bonded cutoff with shifted EEL.\n",
sqrt(cut2_));
if (reorder_)
mprintf("SPAM: Warning: Re-ordering makes no sense for pure solvent.\n");
if (!summaryfile_.empty())
mprintf("SPAM: Printing solvent SPAM summary to %s\n", summaryfile_.c_str());
}else {
mprintf("SPAM: Solvent [%s] density peaks taken from %s.\n",
solvname_.c_str(), filename.base());
mprintf("SPAM: %d density peaks will be analyzed from %s.\n",
peaks_.size(), filename.base());
mprintf("SPAM: Occupation information printed to %s.\n", infofile_->Filename().full());
mprintf("SPAM: Sites are ");
if (sphere_)
mprintf("spheres with diameter %.3lf\n", site_size_);
else
mprintf("boxes with edge length %.3lf\n", site_size_);
if (reorder_) {
mprintf("SPAM: Re-ordering trajectory so each site always has ");
mprintf("the same water molecule.\n");
}
if (summaryfile_.empty() && datafile_.empty()) {
if (!reorder_) {
mprinterr("SPAM: Error: Not re-ordering trajectory or calculating energies. ");
mprinterr("Nothing to do!\n");
return Action::ERR;
}
mprintf("SPAM: Not calculating any SPAM energies\n");
}else {
mprintf("SPAM: Using a non-bonded cutoff of %.2lf Ang. with a EEL shifting function.\n",
sqrt(cut2_));
mprintf("SPAM: Bulk solvent SPAM energy taken as %.3lf kcal/mol\n", bulk_);
}
}
mprintf("#Citation: Cui, G.; Swails, J.M.; Manas, E.S.; \"SPAM: A Simple Approach\n"
"# for Profiling Bound Water Molecules\"\n"
"# J. Chem. Theory Comput., 2013, 9 (12), pp 5539–5549.\n");
return Action::OK;
}
// Reads a textclass structure from file.
TextClass::ReturnValues TextClass::read(Lexer & lexrc, ReadType rt)
{
if (!lexrc.isOK())
return ERROR;
// Format of files before the 'Format' tag was introduced
int format = 1;
bool error = false;
// parsing
while (lexrc.isOK() && !error) {
int le = lexrc.lex();
switch (le) {
case Lexer::LEX_FEOF:
continue;
case Lexer::LEX_UNDEF:
lexrc.printError("Unknown TextClass tag `$$Token'");
error = true;
continue;
default:
break;
}
// used below to track whether we are in an IfStyle or IfCounter tag.
bool ifstyle = false;
bool ifcounter = false;
switch (static_cast<TextClassTags>(le)) {
case TC_FORMAT:
if (lexrc.next())
format = lexrc.getInteger();
break;
case TC_OUTPUTFORMAT:
if (lexrc.next())
outputFormat_ = lexrc.getString();
break;
case TC_OUTPUTTYPE:
readOutputType(lexrc);
switch(outputType_) {
case LATEX:
outputFormat_ = "latex";
break;
case DOCBOOK:
outputFormat_ = "docbook";
break;
case LITERATE:
outputFormat_ = "literate";
break;
}
break;
case TC_INPUT: // Include file
if (lexrc.next()) {
string const inc = lexrc.getString();
FileName tmp = libFileSearch("layouts", inc,
"layout");
if (tmp.empty()) {
lexrc.printError("Could not find input file: " + inc);
error = true;
} else if (!read(tmp, MERGE)) {
lexrc.printError("Error reading input file: " + tmp.absFileName());
error = true;
}
}
break;
case TC_DEFAULTSTYLE:
if (lexrc.next()) {
docstring const name = from_utf8(subst(lexrc.getString(),
'_', ' '));
defaultlayout_ = name;
}
break;
case TC_IFSTYLE:
ifstyle = true;
// fall through
case TC_STYLE: {
if (!lexrc.next()) {
lexrc.printError("No name given for style: `$$Token'.");
error = true;
break;
}
docstring const name = from_utf8(subst(lexrc.getString(),
'_', ' '));
if (name.empty()) {
string s = "Could not read name for style: `$$Token' "
+ lexrc.getString() + " is probably not valid UTF-8!";
lexrc.printError(s);
Layout lay;
// Since we couldn't read the name, we just scan the rest
// of the style and discard it.
error = !readStyle(lexrc, lay);
} else if (hasLayout(name)) {
Layout & lay = operator[](name);
error = !readStyle(lexrc, lay);
} else if (!ifstyle) {
Layout layout;
layout.setName(name);
error = !readStyle(lexrc, layout);
if (!error)
layoutlist_.push_back(layout);
if (defaultlayout_.empty()) {
// We do not have a default layout yet, so we choose
// the first layout we encounter.
defaultlayout_ = name;
}
}
else {
// this was an ifstyle where we didn't have the style
// scan the rest and discard it
Layout lay;
readStyle(lexrc, lay);
}
// reset flag
ifstyle = false;
break;
}
case TC_NOSTYLE:
if (lexrc.next()) {
docstring const style = from_utf8(subst(lexrc.getString(),
'_', ' '));
if (!deleteLayout(style))
lyxerr << "Cannot delete style `"
<< to_utf8(style) << '\'' << endl;
}
break;
case TC_COLUMNS:
if (lexrc.next())
columns_ = lexrc.getInteger();
break;
case TC_SIDES:
if (lexrc.next()) {
switch (lexrc.getInteger()) {
case 1: sides_ = OneSide; break;
case 2: sides_ = TwoSides; break;
default:
lyxerr << "Impossible number of page"
" sides, setting to one."
<< endl;
sides_ = OneSide;
break;
}
}
break;
case TC_PAGESTYLE:
lexrc.next();
pagestyle_ = rtrim(lexrc.getString());
break;
case TC_DEFAULTFONT:
defaultfont_ = lyxRead(lexrc);
if (!defaultfont_.resolved()) {
lexrc.printError("Warning: defaultfont should "
"be fully instantiated!");
defaultfont_.realize(sane_font);
}
break;
case TC_SECNUMDEPTH:
lexrc.next();
secnumdepth_ = lexrc.getInteger();
break;
case TC_TOCDEPTH:
lexrc.next();
tocdepth_ = lexrc.getInteger();
break;
// First step to support options
case TC_CLASSOPTIONS:
readClassOptions(lexrc);
break;
case TC_PREAMBLE:
preamble_ = from_utf8(lexrc.getLongString("EndPreamble"));
break;
case TC_HTMLPREAMBLE:
htmlpreamble_ = from_utf8(lexrc.getLongString("EndPreamble"));
break;
case TC_HTMLTOCSECTION:
html_toc_section_ = from_utf8(trim(lexrc.getString()));
break;
case TC_ADDTOPREAMBLE:
preamble_ += from_utf8(lexrc.getLongString("EndPreamble"));
break;
case TC_ADDTOHTMLPREAMBLE:
htmlpreamble_ += from_utf8(lexrc.getLongString("EndPreamble"));
break;
case TC_PROVIDES: {
lexrc.next();
string const feature = lexrc.getString();
lexrc.next();
if (lexrc.getInteger())
provides_.insert(feature);
else
provides_.erase(feature);
break;
}
case TC_REQUIRES: {
lexrc.eatLine();
vector<string> const req
= getVectorFromString(lexrc.getString());
requires_.insert(req.begin(), req.end());
break;
}
case TC_DEFAULTMODULE: {
lexrc.next();
string const module = lexrc.getString();
if (find(default_modules_.begin(), default_modules_.end(), module) == default_modules_.end())
default_modules_.push_back(module);
break;
}
case TC_PROVIDESMODULE: {
lexrc.next();
string const module = lexrc.getString();
if (find(provided_modules_.begin(), provided_modules_.end(), module) == provided_modules_.end())
provided_modules_.push_back(module);
break;
}
case TC_EXCLUDESMODULE: {
lexrc.next();
string const module = lexrc.getString();
// modules already have their own way to exclude other modules
if (rt == MODULE) {
LYXERR0("ExcludesModule tag cannot be used in a module!");
break;
}
if (find(excluded_modules_.begin(), excluded_modules_.end(), module) == excluded_modules_.end())
excluded_modules_.push_back(module);
break;
}
case TC_LEFTMARGIN: // left margin type
if (lexrc.next())
leftmargin_ = lexrc.getDocString();
break;
case TC_RIGHTMARGIN: // right margin type
if (lexrc.next())
rightmargin_ = lexrc.getDocString();
break;
case TC_INSETLAYOUT: {
if (!lexrc.next()) {
lexrc.printError("No name given for InsetLayout: `$$Token'.");
error = true;
break;
}
docstring const name = subst(lexrc.getDocString(), '_', ' ');
if (name.empty()) {
string s = "Could not read name for InsetLayout: `$$Token' "
+ lexrc.getString() + " is probably not valid UTF-8!";
lexrc.printError(s);
InsetLayout il;
// Since we couldn't read the name, we just scan the rest
// of the style and discard it.
il.read(lexrc, *this);
// Let's try to continue rather than abort.
// error = true;
} else if (hasInsetLayout(name)) {
InsetLayout & il = insetlayoutlist_[name];
error = !il.read(lexrc, *this);
} else {
InsetLayout il;
il.setName(name);
error = !il.read(lexrc, *this);
if (!error)
insetlayoutlist_[name] = il;
}
break;
}
case TC_FLOAT:
error = !readFloat(lexrc);
break;
case TC_CITEFORMAT:
readCiteFormat(lexrc);
break;
case TC_IFCOUNTER:
ifcounter = true;
case TC_COUNTER:
if (lexrc.next()) {
docstring const name = lexrc.getDocString();
if (name.empty()) {
string s = "Could not read name for counter: `$$Token' "
+ lexrc.getString() + " is probably not valid UTF-8!";
lexrc.printError(s.c_str());
Counter c;
// Since we couldn't read the name, we just scan the rest
// and discard it.
c.read(lexrc);
} else
error = !counters_.read(lexrc, name, !ifcounter);
}
else {
lexrc.printError("No name given for style: `$$Token'.");
error = true;
}
// reset flag
ifcounter = false;
break;
case TC_TITLELATEXTYPE:
readTitleType(lexrc);
break;
case TC_TITLELATEXNAME:
if (lexrc.next())
titlename_ = lexrc.getString();
break;
case TC_NOFLOAT:
if (lexrc.next()) {
string const nofloat = lexrc.getString();
floatlist_.erase(nofloat);
}
break;
} // end of switch
// Note that this is triggered the first time through the loop unless
// we hit a format tag.
if (format != LAYOUT_FORMAT)
return FORMAT_MISMATCH;
}
// at present, we abort if we encounter an error,
// so there is no point continuing.
if (error)
return ERROR;
if (rt != BASECLASS)
return (error ? ERROR : OK);
if (defaultlayout_.empty()) {
LYXERR0("Error: Textclass '" << name_
<< "' is missing a defaultstyle.");
return ERROR;
}
// Try to erase "stdinsets" from the provides_ set.
// The
// Provides stdinsets 1
// declaration simply tells us that the standard insets have been
// defined. (It's found in stdinsets.inc but could also be used in
// user-defined files.) There isn't really any such package. So we
// might as well go ahead and erase it.
// If we do not succeed, then it was not there, which means that
// the textclass did not provide the definitions of the standard
// insets. So we need to try to load them.
int erased = provides_.erase("stdinsets");
if (!erased) {
FileName tmp = libFileSearch("layouts", "stdinsets.inc");
if (tmp.empty()) {
frontend::Alert::warning(_("Missing File"),
_("Could not find stdinsets.inc! This may lead to data loss!"));
error = true;
} else if (!read(tmp, MERGE)) {
frontend::Alert::warning(_("Corrupt File"),
_("Could not read stdinsets.inc! This may lead to data loss!"));
error = true;
}
}
min_toclevel_ = Layout::NOT_IN_TOC;
max_toclevel_ = Layout::NOT_IN_TOC;
const_iterator lit = begin();
const_iterator len = end();
for (; lit != len; ++lit) {
int const toclevel = lit->toclevel;
if (toclevel != Layout::NOT_IN_TOC) {
if (min_toclevel_ == Layout::NOT_IN_TOC)
min_toclevel_ = toclevel;
else
min_toclevel_ = min(min_toclevel_, toclevel);
max_toclevel_ = max(max_toclevel_, toclevel);
}
}
LYXERR(Debug::TCLASS, "Minimum TocLevel is " << min_toclevel_
<< ", maximum is " << max_toclevel_);
return (error ? ERROR : OK);
}
