/*
*
* tests the suffix from filename
* if it is an image
*
*/
bool FileInfo::isImage(QString filePath) const {
QString s = getSuffix(filePath);
if (s == "png" || s == "jpg" || s == "jpeg" || s == "gif" || s == "svg") {
return true;
}
return false;
}
OFile& OFile::open(const std::string&path) {
plumed_assert(!cloned);
eof=false;
err=false;
fp=NULL;
gzfp=NULL;
this->path=path;
this->path=appendSuffix(path,getSuffix());
if(checkRestart()) {
fp=std::fopen(const_cast<char*>(this->path.c_str()),"a");
mode="a";
if(Tools::extension(this->path)=="gz") {
#ifdef __PLUMED_HAS_ZLIB
gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"a9");
#else
plumed_merror("file " + getPath() + ": trying to use a gz file without zlib being linked");
#endif
}
} else {
backupFile( backstring, this->path );
if(comm)comm->Barrier();
fp=std::fopen(const_cast<char*>(this->path.c_str()),"w");
mode="w";
if(Tools::extension(this->path)=="gz") {
#ifdef __PLUMED_HAS_ZLIB
gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"w9");
#else
plumed_merror("file " + getPath() + ": trying to use a gz file without zlib being linked");
#endif
}
}
if(plumed) plumed->insertFile(*this);
return *this;
}
/*
*
* tests the suffix from filename
* if it is a video
*
*/
bool FileInfo::isVideo(QString filePath) const {
QString s = getSuffix(filePath);
if (s == "mp4" || s == "mov") {
return true;
}
return false;
}
/*
*
* tests the suffix from filename
* if it is a book
*
*/
bool FileInfo::isBook(QString filePath) const {
QString s = getSuffix(filePath);
if (s == "epub") {
return true;
}
return false;
}
/*
*
* tests the suffix from filename
* if it is a audio file
*
*/
bool FileInfo::isAudio(QString filePath) const {
QString s = getSuffix(filePath);
if (s == "m4a" || s == "mp3" || s == "ogg" || s == "wav") {
return true;
}
return false;
}
/*
*
* tests the suffix from filename
* if it is a html file
*
*/
bool FileInfo::isHtml(QString filePath) const {
QString s = getSuffix(filePath);
if (s == "html" || s == "htm" || s == "xhtml") {
return true;
}
return false;
}
std::string Sequence::getCStylePattern() const
{
if( getPadding() )
return getPrefix() + "%0" + boost::lexical_cast<std::string > ( getPadding() ) + "d" + getSuffix();
else
return getPrefix() + "%d" + getSuffix();
}
/*
*
* tests the suffix from filename
* if it is a compressed document
*
*/
bool FileInfo::isCompressed(QString filePath) const {
QString s = getSuffix(filePath);
if (s == "tar" || s == "rar" || s == "gz" || s == "zip") {
return true;
}
return false;
}
XObjectPtr
FunctionGenerateID::execute(
XPathExecutionContext& executionContext,
XalanNode* context,
const LocatorType* locator) const
{
if (context == 0)
{
executionContext.error(
XalanMessageLoader::getMessage(XalanMessages::FunctionRequiresNonNullContextNode_1Param,"generate-id()"),
context,
locator);
return XObjectPtr();
}
else
{
XPathExecutionContext::GetAndReleaseCachedString theID(executionContext);
theID.get() = XalanUnicode::charLetter_N;
getSuffix(context, theID.get());
return executionContext.getXObjectFactory().createString(theID);
}
}
InputPlugin * hasMusicSuffix(char * utf8file) {
InputPlugin * ret = NULL;
char * s = getSuffix(utf8file);
if(s) ret = getInputPluginFromSuffix(s);
return ret;
}
void getSuffix(Node *node, int at) {
if (node->minchild < 0) {
suffix[at] = 0;
return;
}
suffix[at] = ALPHA_BASE + node->minchild;
getSuffix(node->children[node->minchild], at+1);
}
bool compareSuffix2(const suffix2& s1, const suffix2& s2)
{
char * kmer1, *kmer2;
unsigned int nextPos1, nextPos2;
bool result = true;
kmer1 = getSuffix((suffix2*) &s1, &nextPos1);
kmer2 = getSuffix((suffix2*) &s2, &nextPos2);
int kmerComp = strncmp((const char*) kmer1, (const char*) kmer2, Data::kl);
if (kmerComp < 0)
result = true;
else //if (kmerComp > 0)
result = false;
free(kmer1);
free(kmer2);
return result;
}
/*
*
* tests the suffix from filename
* if it is a document
*
*/
bool FileInfo::isDocument(QString filePath) const {
QString s = getSuffix(filePath);
if (s == "doc" || s == "odt" || s == "ppt" || s == "pptx"
|| s == "txt" || s == "rtf" || s == "ptx"
|| s == "pdf" || s == "zip" || s == "tar"
|| s == "rar" || s == "gz" || s == "html") {
return true;
}
return false;
}
FILE* PlumedMain::fopen(const char *path, const char *mode){
std::string mmode(mode);
std::string ppath(path);
std::string suffix(getSuffix());
std::string ppathsuf=ppath+suffix;
FILE*fp=std::fopen(const_cast<char*>(ppathsuf.c_str()),const_cast<char*>(mmode.c_str()));
if(!fp) fp=std::fopen(const_cast<char*>(ppath.c_str()),const_cast<char*>(mmode.c_str()));
plumed_massert(fp,"file " + ppath + " cannot be found");
return fp;
}
virtual cpp17::any data(const WModelIndex& index, ItemDataRole role = ItemDataRole::Display) const {
if (!index.isValid())
return cpp17::any();
Git::Object object = getObject(index);
switch (index.column()) {
case 0:
if (role == ItemDataRole::Display) {
if (object.type == Git::Tree)
return object.name + '/';
else
return object.name;
} else if (role == ItemDataRole::Decoration) {
if (object.type == Git::Blob)
return std::string("icons/git-blob.png");
else if (object.type == Git::Tree)
return std::string("icons/git-tree.png");
} else if (role == ContentsRole) {
if (object.type == Git::Blob)
return git_.catFile(object.id);
}
break;
case 1:
if (role == ItemDataRole::Display) {
if (object.type == Git::Tree)
return std::string("Folder");
else {
std::string suffix = getSuffix(object.name);
if (suffix == "C" || suffix == "cpp")
return std::string("C++ Source");
else if (suffix == "h" ||
(suffix == "" && !topLevel(index)))
return std::string("C++ Header");
else if (suffix == "css")
return std::string("CSS Stylesheet");
else if (suffix == "js")
return std::string("JavaScript Source");
else if (suffix == "md")
return std::string("Markdown");
else if (suffix == "png" || suffix == "gif")
return std::string("Image");
else if (suffix == "txt")
return std::string("Text");
else
return cpp17::any();
}
}
}
return cpp17::any();
}
void Widget::example(){
QString text = tr("example");
if(isRename()){
if(isNewName()){
text = getNewName();
}
if(isPrependExifDate()){
text.prepend(getDateTime("").toString(ui->exifLineEdit->text()));
}
if(isAppendExifDate()){
text.append(getDateTime("").toString(ui->exifLineEdit->text()));
}
if(!(getPrefix().isEmpty() && getSuffix().isEmpty())){
text.prepend(getPrefix());
text.append(getSuffix());
}
}
ui->exampleLabel->setText(text);
}
string Jce2Php::toStrSuffix(const TypeIdPtr &pPtr) const
{
ostringstream s;
int i = getSuffix(pPtr);
if(i >= 0)
{
s << "[" << i << "]";
}
return s.str();
}
long_int multiply(long_int num1, long_int num2)
{
int digits1 = numDigits(num1);
int digits2 = numDigits(num2);
if(digits1 == 1 || digits2 == 1)
{
return num1 * num2;
}
long_int a = rightShift(num1, (digits1/2));
long_int c = rightShift(num2, (digits2/2));
long_int b = getSuffix(num1, digits1/2);
long_int d = getSuffix(num2, digits2/2);
long_int ac = multiply(a, c);
long_int bd = multiply(b, d);
long_int aplusbtimescplusd = multiply(a + b, c + d);
long_int cof1 = tenPower((digits1/2) + (digits2/2));
long_int cof2 = tenPower(digits1/2);
long_int sum_term_1 = cof1 * ac;
long_int sum_term_2 = cof2 * (aplusbtimescplusd - ac - bd);
return (sum_term_1 + bd + sum_term_2);
}
string Item::getVisibleName(bool getPlural) const {
string ret;
if (!getPlural)
ret = *attributes->name;
else {
if (attributes->plural)
ret = *attributes->plural;
else
ret = *attributes->name + "s";
}
appendWithSpace(ret, getSuffix());
return ret;
}
void OFile::backupAllFiles( const std::string& str ) {
if(str=="/dev/null") return;
plumed_assert( backstring!="bck" && !checkRestart());
size_t found=str.find_last_of("/\\");
std::string filename = appendSuffix(str,getSuffix());
std::string directory=filename.substr(0,found+1);
std::string file=filename.substr(found+1);
if( FileExist(filename) ) backupFile("bck", filename);
for(int i=0;; i++) {
std::string num; Tools::convert(i,num);
std::string filestr = directory + backstring + "." + num + "." + file;
if( !FileExist(filestr) ) break;
backupFile( "bck", filestr);
}
}
bool FileBase::FileExist(const std::string& path){
FILE *ff=NULL;
bool do_exist=false;
this->path=appendSuffix(path,getSuffix());
mode="r";
ff=std::fopen(const_cast<char*>(this->path.c_str()),"r");
if(!ff){
this->path=path;
ff=std::fopen(const_cast<char*>(this->path.c_str()),"r");
mode="r";
}
if(ff) {do_exist=true; fclose(ff);}
if(comm) comm->Barrier();
return do_exist;
}
// Print the suffix array
void SuffixArray::print(const ReadTable* pRT) const
{
std::cout << "i\tSA(i)\n";
for(size_t i = 0; i < m_data.size(); ++i)
{
SAElem id1 = m_data[i];
std::string suffix = !id1.isEmpty() ? getSuffix(i, pRT) : "";
int pos = id1.getPos();
char b;
if(pos == 0)
b = '$';
else
b = pRT->getRead(id1.getID()).seq.get(pos - 1);
std::cout << i << "\t" << id1 << "\t" << b << "\t" << suffix << "\n";
}
}
string Item::getShortName(const Creature* owner, bool plural) const {
PROFILE;
if (owner && owner->isAffected(LastingEffect::BLIND) && attributes->blindName)
return getBlindName(plural);
if (attributes->artifactName)
return *attributes->artifactName + " " + getModifiers(true);
string name;
if (!attributes->prefixes.empty())
name = attributes->prefixes.back();
else if (attributes->shortName) {
name = *attributes->shortName;
appendWithSpace(name, getSuffix());
} else
name = getVisibleName(plural);
appendWithSpace(name, getModifiers(true));
return name;
}
bool Image4DSimple::saveImage(const char filename[])
{
if (!data1d || !filename)
{
v3d_msg("This image data is empty or the file name is invalid. Nothing done.\n");
return false;
}
V3DLONG mysz[4];
mysz[0] = sz0;
mysz[1] = sz1;
mysz[2] = sz2;
mysz[3] = sz3;
int dt;
switch (datatype)
{
case V3D_UINT8: dt=1; break;
case V3D_UINT16: dt=2; break;
case V3D_FLOAT32: dt=4; break;
default:
v3d_msg("The data type is unsupported. Nothing done.\n");
return false;
break;
}
if (strlen(filename) > 5 ) {
const char * suffix = getSuffix((char *)filename);
if (suffix && (strcasecmp(suffix, "nrrd")==0 ||
strcasecmp(suffix, "nhdr")==0) )
{
float pxinfo[4];
float spaceorigin[3];
// use nrrd_write
pxinfo[0] = rez_x;
pxinfo[1] = rez_y;
pxinfo[2] = rez_z;
spaceorigin[0] = origin_x;
spaceorigin[1] = origin_y;
spaceorigin[2] = origin_z;
return write_nrrd_with_pxinfo(filename, data1d, mysz, dt, pxinfo, spaceorigin);
}
}
return ::saveImage(filename, data1d, mysz, dt);
}
void Entry::onSizeHint(SizeHintEvent& ev)
{
int trailing = font()->textLength(getSuffix());
trailing = MAX(trailing, 2*theme()->getEntryCaretSize(this).w);
int w =
font()->textLength("w") * std::min(m_maxsize, 6) +
+ trailing
+ border().width();
w = std::min(w, ui::display_w()/2);
int h =
+ font()->height()
+ border().height();
ev.setSizeHint(w, h);
}
int main(int argc, char **argv) {
int i, n;
Node *root;
while (scanf("%s", string) != EOF) {
poolPos = 0;
n = strlen(string);
root = createNode();
for (i = 0; i < n; i++)
addToTrie(root, i, n);
findSuffix(root);
getSuffix(root, 0);
printf("%s\n", suffix);
// destroyNode(root);
}
return EXIT_SUCCESS;
}
void PlumedMain::init() {
// check that initialization just happens once
initialized=true;
atoms.init();
if(!log.isOpen()) log.link(stdout);
log<<"PLUMED is starting\n";
log<<"Version: "<<config::getVersionLong()<<" (git: "<<config::getVersionGit()<<") compiled on " __DATE__ " at " __TIME__ "\n";
log<<"Please cite this paper when using PLUMED ";
log<<cite("Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)");
log<<"\n";
log<<"For further information see the PLUMED web page at http://www.plumed.org\n";
log<<"Root: "<<config::getPlumedRoot()<<"\n";
log<<"For installed feature, see "<<config::getPlumedRoot() + "/src/config/config.txt\n";
log.printf("Molecular dynamics engine: %s\n",MDEngine.c_str());
log.printf("Precision of reals: %d\n",atoms.getRealPrecision());
log.printf("Running over %d %s\n",comm.Get_size(),(comm.Get_size()>1?"nodes":"node"));
log<<"Number of threads: "<<OpenMP::getNumThreads()<<"\n";
log<<"Cache line size: "<<OpenMP::getCachelineSize()<<"\n";
log.printf("Number of atoms: %d\n",atoms.getNatoms());
if(grex) log.printf("GROMACS-like replica exchange is on\n");
log.printf("File suffix: %s\n",getSuffix().c_str());
if(plumedDat.length()>0) {
readInputFile(plumedDat);
plumedDat="";
}
atoms.updateUnits();
log.printf("Timestep: %f\n",atoms.getTimeStep());
if(atoms.getKbT()>0.0)
log.printf("KbT: %f\n",atoms.getKbT());
else {
log.printf("KbT has not been set by the MD engine\n");
log.printf("It should be set by hand where needed\n");
}
log<<"Relevant bibliography:\n";
log<<citations;
log<<"Please read and cite where appropriate!\n";
log<<"Finished setup\n";
}
void decodeStart(PlayerControl * pc, OutputBuffer * cb, DecoderControl * dc) {
int ret;
InputStream inStream;
InputPlugin * plugin = NULL;
char * path;
if(isRemoteUrl(pc->utf8url)) {
path = utf8StrToLatin1Dup(pc->utf8url);
}
else path = strdup(rmp2amp(utf8ToFsCharset(pc->utf8url)));
if(!path) {
dc->error = DECODE_ERROR_FILE;
dc->state = DECODE_STATE_STOP;
dc->start = 0;
return;
}
copyMpdTagToOutputBuffer(cb, NULL);
strncpy(dc->utf8url, pc->utf8url, MAXPATHLEN);
dc->utf8url[MAXPATHLEN] = '\0';
if(openInputStream(&inStream, path) < 0) {
dc->error = DECODE_ERROR_FILE;
dc->state = DECODE_STATE_STOP;
dc->start = 0;
free(path);
return;
}
dc->seekable = inStream.seekable;
dc->state = DECODE_STATE_START;
dc->start = 0;
while(!inputStreamAtEOF(&inStream) && bufferInputStream(&inStream) < 0
&& !dc->stop)
{
/* sleep so we don't consume 100% of the cpu */
// fprintf(stderr,"In decode.c decodeParent decode start func\r\n");
// my_usleep(1000);
}
if(dc->stop) {
dc->state = DECODE_STATE_STOP;
dc->stop = 0;
free(path);
return;
}
/*if(inStream.metaName) {
MpdTag * tag = newMpdTag();
tag->name = strdup(inStream.metaName);
copyMpdTagToOutputBuffer(cb, tag);
freeMpdTag(tag);
}*/
/* reset Metadata in OutputBuffer */
ret = DECODE_ERROR_UNKTYPE;
if(isRemoteUrl(dc->utf8url)) {
cb->acceptMetadata = 1;
plugin = getInputPluginFromMimeType(inStream.mime);
if(plugin == NULL) {
plugin = getInputPluginFromSuffix(
getSuffix(dc->utf8url));
}
/* this is needed for bastard streams that don't have a suffix
or set the mimeType */
if(plugin == NULL) {
plugin = getInputPluginFromName("mp3");
}
if(plugin && (plugin->streamTypes & INPUT_PLUGIN_STREAM_URL) &&
plugin->streamDecodeFunc)
{
ret = plugin->streamDecodeFunc(cb, dc, &inStream);
}
}
else {
cb->acceptMetadata = 0;
plugin = getInputPluginFromSuffix(getSuffix(dc->utf8url));
if(plugin && (plugin->streamTypes && INPUT_PLUGIN_STREAM_FILE))
{
if(plugin->streamDecodeFunc) {
ret = plugin->streamDecodeFunc(cb, dc,
&inStream);
}
else if(plugin->fileDecodeFunc) {
closeInputStream(&inStream);
ret = plugin->fileDecodeFunc(cb, dc, path);
}
}
}
if(ret<0 || ret == DECODE_ERROR_UNKTYPE) {
strncpy(pc->erroredUrl, dc->utf8url, MAXPATHLEN);
pc->erroredUrl[MAXPATHLEN] = '\0';
if(ret != DECODE_ERROR_UNKTYPE) dc->error = DECODE_ERROR_FILE;
else {
dc->error = DECODE_ERROR_UNKTYPE;
closeInputStream(&inStream);
}
dc->stop = 0;
dc->state = DECODE_STATE_STOP;
}
free(path);
}
bool Family::lastRepeatComplete() const {
return last == getSuffix();
}
inline const char_pg* DefaultPseudoGenome<uint_read_len, uint_reads_cnt, uint_pg_len, ReadsListClass>::getSuffix(const uint_reads_cnt readsListIdx, const uint_read_len offset) {
return getSuffix(this->readsList->getReadPosition(readsListIdx) + offset);
}
