void UnquoteParser::tag_start(const QString &tag, const list<QString> &options)
{
if (tag == "br"){
res += "\n";
}else if (tag == "p"){
if (m_bPar){
res += "\n";
m_bPar = false;
}
}else if (tag == "img"){
QString src;
for (list<QString>::const_iterator it = options.begin(); it != options.end(); ++it){
QString opt = *it;
++it;
QString value = *it;
if (opt == "src")
src = value;
}
if (src.left(10) != "icon:smile")
return;
bool bOk;
unsigned nSmile = src.mid(10).toUInt(&bOk, 16);
if (!bOk)
return;
const smile *s = smiles(nSmile);
if (s){
res += s->paste;
return;
}
s = defaultSmiles(nSmile);
if (s)
res += s->paste;
}
}
ViewParser::ViewParser(bool bIgnoreColors, bool bUseSmiles)
{
m_bIgnoreColors = bIgnoreColors;
m_bUseSmiles = bUseSmiles;
m_bInLink = false;
m_bInHead = false;
m_bFirst = true;
m_bSpan = false;
m_bPara = false;
m_bParaStart = false;
m_bRTL = false;
m_bParaEnd = false;
RTL = false;
if (m_bUseSmiles){
for (unsigned i = 0; ;i++){
const smile *s = smiles(i);
if (s == NULL)
break;
#if COMPAT_QT_VERSION < 0x030000
string str;
for (const char *p = s->exp;; p++){
if ((*p == 0) || (*p == '|')){
if (!str.empty()){
Smile ss;
ss.nSmile = i;
ss.re = QRegExp(str.c_str());
if (ss.re.isValid())
m_smiles.push_back(ss);
}
if (*p == 0)
break;
str = "";
continue;
}
if (*p == '\\'){
if (*(++p) == 0)
break;
str += '\\';
str += *p;
continue;
}
str += *p;
}
#else
if (*(s->exp)){
Smile ss;
ss.nSmile = i;
ss.re = QRegExp(s->exp);
if (ss.re.isValid())
m_smiles.push_back(ss);
}
#endif
}
}
}
void ViewParser::tag_start(const QString &tag, const list<QString> &options)
{
if (tag == "img"){
QString src;
for (list<QString>::const_iterator it = options.begin(); it != options.end(); ++it){
QString opt = *it;
++it;
QString val = *it;
if (opt == "src"){
src = val;
break;
}
}
if (src.left(10) == "icon:smile"){
bool bOK;
unsigned nSmile = src.mid(10).toUInt(&bOK, 16);
if (bOK){
const smile *s = smiles(nSmile);
if (s == NULL)
return;
if (*s->exp == 0){
res += quoteString(s->paste);
return;
}
}
}
}
if (m_bIgnoreColors){
const char **p;
for (p = formatTags; *p; p++)
if (tag == *p)
break;
if (*p == NULL)
return;
}
res += "<";
res += tag;
if (!m_bIgnoreColors){
for (list<QString>::const_iterator it = options.begin(); it != options.end(); ++it){
QString opt = *it;
++it;
QString val = *it;
res += " ";
res += opt;
if (!val.isEmpty()){
res += "=\"";
res += quoteString(val);
res += "\"";
}
}
}
res += ">";
}
void JabberImageParser::tag_start(const QString &tag, const list<QString> &attrs)
{
if (tag == "img"){
QString src;
for (list<QString>::const_iterator it = attrs.begin(); it != attrs.end(); ++it){
QString name = *it;
++it;
QString value = *it;
if (name == "src"){
src = value;
break;
}
}
if (src.left(10) != "icon:smile")
return;
bool bOK;
unsigned nIcon = src.mid(10).toUInt(&bOK, 16);
if (!bOK)
return;
const smile *p = smiles(nIcon);
if (p){
res += p->paste;
return;
}
}
if (tag == "p"){
if (m_bPara){
res += "<br/>";
m_bPara = false;
}
return;
}
if (tag == "br"){
res += "<br/>";
return;
}
res += "<";
res += tag;
for (list<QString>::const_iterator it = attrs.begin(); it != attrs.end(); ++it){
QString name = *it;
++it;
QString value = *it;
res += " ";
res += name;
if (!value.isEmpty()){
res += "=\"";
res += quoteString(value);
res += "\"";
}
}
res += ">";
}
void UnquoteParser::tag_start(const QString &tag, const list<QString> &options)
{
if (tag == "pre"){
if (!m_bPre)
res += "\n";
}else if (tag == "br"){
res += "\n";
}else if (tag == "hr"){
if (!res.isEmpty() && (res[(int)(res.length() - 1)] != '\n'))
res += "\n";
res += "---------------------------------------------------\n";
}else if (tag == "td"){
if (m_bTD){
res += "\t";
m_bTD = false;
}
}else if (tag == "tr"){
if (m_bTR){
res += "\n";
m_bTR = false;
}
}else if (tag == "p"){
if (m_bPar){
res += "\n";
m_bPar = false;
}
}else if (tag == "img"){
QString src;
for (list<QString>::const_iterator it = options.begin(); it != options.end(); ++it){
QString opt = *it;
++it;
QString value = *it;
if (opt == "src")
src = value;
}
if (src.left(10) != "icon:smile")
return;
bool bOk;
unsigned nSmile = src.mid(10).toUInt(&bOk, 16);
if (!bOk)
return;
const smile *s = smiles(nSmile);
if (s){
res += s->paste;
return;
}
s = defaultSmiles(nSmile);
if (s)
res += s->paste;
}
}
void ViewParser::text(const QString &text)
{
if (!m_bUseSmiles)
res += text;
QString str = text;
list<Smile> s;
for (unsigned i = 0;; i++){
const char *p = smiles(i);
if (p == 0)
break;
for (; *p; p += strlen(p) + 1){
Smile sm;
sm.nSmile = i;
sm.smile = p;
sm.pos = str.find(p);
s.push_back(sm);
}
}
for (;;){
unsigned pos = (unsigned)(-1);
Smile *curSmile = NULL;
list<Smile>::iterator it;
for (it = s.begin(); it != s.end(); ++it){
if ((*it).pos < 0)
continue;
if ((unsigned)((*it).pos) < pos){
pos = (*it).pos;
curSmile = &(*it);
}
}
if (curSmile == NULL)
break;
if (pos)
res += quoteString(str.left(pos));
res += "<img src=\"icon:smile";
res += QString::number(curSmile->nSmile, 16).upper();
res += "\">";
int len = pos + curSmile->smile.size();
str = str.mid(len);
for (it = s.begin(); it != s.end(); ++it){
if ((*it).pos < 0)
continue;
(*it).pos -= len;
if ((*it).pos < 0)
(*it).pos = str.find((*it).smile.c_str());
}
}
res += quoteString(str);
}
ViewParser::ViewParser(bool bIgnoreColors, bool bUseSmiles)
{
m_bIgnoreColors = bIgnoreColors;
m_bUseSmiles = bUseSmiles;
if (m_bUseSmiles){
for (unsigned i = 0; ;i++){
const smile *s = smiles(i);
if (s == NULL)
break;
#if QT_VERSION < 300
string str;
for (const char *p = s->exp;; p++){
if ((*p == 0) || (*p == '|')){
if (!str.empty()){
Smile ss;
ss.nSmile = i;
ss.re = QRegExp(str.c_str());
if (ss.re.isValid())
m_smiles.push_back(ss);
}
if (*p == 0)
break;
continue;
}
if (*p == '\\'){
if (*(++p) == 0)
break;
str += '\\';
str += *p;
continue;
}
str += *p;
}
#else
if (*(s->exp)){
Smile ss;
ss.nSmile = i;
ss.re = QRegExp(s->exp);
if (ss.re.isValid())
m_smiles.push_back(ss);
}
#endif
}
}
}
void YahooParser::tag_start(const QString &tag, const list<QString> &options)
{
if (tag == "img") {
QString src;
for (list<QString>::const_iterator it = options.begin(); it != options.end(); ++it) {
QString name = (*it);
++it;
QString value = (*it);
if (name == "src") {
src = value;
break;
}
}
if (src.left(10) != "icon:smile")
return;
bool bOK;
unsigned nSmile = src.mid(10).toUInt(&bOK, 16);
if (!bOK)
return;
const smile *p = smiles(nSmile);
if (p)
text(p->paste);
return;
}
if (tag == "br") {
res += "\n";
return;
}
style s = curStyle;
s.tag = tag;
tags.push(s);
if (tag == "p") {
if (!m_bFirst)
res += "\n";
m_bFirst = false;
}
if (tag == "font") {
for (list<QString>::const_iterator it = options.begin(); it != options.end(); ++it) {
QString name = *it;
++it;
if (name == "color") {
QColor c;
c.setNamedColor(*it);
s.color = c.rgb() & 0xFFFFFF;
}
}
}
if (tag == "b") {
s.state |= 1;
return;
}
if (tag == "i") {
s.state |= 2;
return;
}
if (tag == "u") {
s.state |= 4;
return;
}
for (list<QString>::const_iterator it = options.begin(); it != options.end(); ++it) {
QString name = *it;
++it;
if (name != "style")
continue;
list<QString> styles = parseStyle(*it);
for (list<QString>::iterator its = styles.begin(); its != styles.end(); ++its) {
QString name = *its;
++its;
if (name == "color") {
QColor c;
c.setNamedColor(*its);
s.color = c.rgb() & 0xFFFFFF;
}
if (name == "font-size") {
unsigned size = atol((*its).latin1());
if (size)
s.size = size;
}
if (name == "font-family")
s.face = (*its);
if (name == "font-weight")
s.state &= ~1;
if (atol((*its).latin1()) >= 600)
s.state |= 1;
if ((name == "font-style") && ((*its) == "italic"))
s.state |= 2;
if ((name == "text-decoration") && ((*its) == "underline"))
s.state |= 4;
}
}
set_style(s);
}
void ViewParser::tag_start(const QString &tag, const list<QString> &attrs)
{
// the tag that will be actually written out
QString oTag = tag;
if (m_bInHead)
return;
QString style;
if (tag == "img"){
QString src;
for (list<QString>::const_iterator it = attrs.begin(); it != attrs.end(); ++it){
QString name = (*it).lower();
++it;
QString value = *it;
if (name == "src"){
src = value;
break;
}
}
if (src.left(10) == "icon:smile"){
bool bOK;
unsigned nSmile = src.mid(10).toUInt(&bOK, 16);
if (bOK){
const smile *s = smiles(nSmile);
if (s == NULL)
return;
if (*s->exp == 0){
res += quoteString(s->paste);
return;
}
}
}
}else if (tag == "a"){
m_bInLink = true;
}else if (tag == "html"){ // we display as a part of a larger document
return;
}else if (tag == "head"){
m_bInHead = 1;
return;
}else if (tag == "body"){ // we display as a part of a larger document
oTag = "span";
}else if (tag == "p"){
bool bRTL = false;
m_bParaEnd = false;
for (list<QString>::const_iterator it = attrs.begin(); it != attrs.end(); ++it){
QString name = (*it).lower();
++it;
QString value = *it;
if ((name == "dir") && (value.lower() == "rtl"))
bRTL = true;
}
if (m_bPara){
if (bRTL == m_bRTL){
res += "<br/>";
}else{
if (m_bParaStart)
res += "</p>";
res += "<p dir=\"";
res += bRTL ? "rtl" : "ltr";
res += "\">";
m_bParaStart = true;
}
}else{
RTL = bRTL;
m_bRTL = bRTL;
m_bPara = true;
}
return;
}
if (m_bParaEnd){
res += "<br/>";
m_bParaEnd = false;
}
QString tagText;
tagText += "<";
tagText += oTag;
for (list<QString>::const_iterator it = attrs.begin(); it != attrs.end(); ++it){
QString name = (*it).lower();
++it;
QString value = *it;
// Handling for attributes of specific tags.
if (tag == "body"){
if (name == "bgcolor"){
style += "background-color:" + value + ";";
continue;
}
}else if (tag == "font"){
if (name == "color" && m_bIgnoreColors)
continue;
}
// Handle for generic attributes.
if (name == "style"){
style += value;
continue;
}
tagText += " ";
tagText += name;
if (!value.isEmpty()){
tagText += "=\"";
tagText += value;
tagText += "\"";
}
}
// Quite crude but working CSS to remove color styling.
// It won't filter out colors as part of 'background', but life's tough.
// (If it's any comfort, Qt probably won't display it either.)
if (!style.isEmpty()){
if (m_bIgnoreColors){
list<QString> opt = parseStyle(style);
list<QString> new_opt;
for (list<QString>::iterator it = opt.begin(); it != opt.end(); ++it){
QString name = *it;
it++;
if (it == opt.end())
break;
QString value = *it;
if ((name == "color") ||
(name == "background-color") ||
(name == "font-size") ||
(name == "font-style") ||
(name == "font-weight") ||
(name == "font-family"))
continue;
new_opt.push_back(name);
new_opt.push_back(value);
}
style = makeStyle(new_opt);
}
if (!style.isEmpty())
tagText += " style=\"" + style + "\"";
}
tagText += ">";
res += tagText;
}
bool FastSearchFormat::ObtainTarget(OBConversion* pConv, OBMol& patternMol, const string& indexname)
{
//Obtains an OBMol
// either from the SMARTS string in the -s option
// or by converting the file in the -S option
//or, if neither option is provided, displays information on the index file.
stringstream smiles(stringstream::out);
ifstream patternstream;
OBConversion PatternConv(&patternstream,&smiles);
const char* p = pConv->IsOption("s",OBConversion::GENOPTIONS);
string txt;
if(p)
{
// Use the -s option
txt=p;
stringstream smarts(txt, stringstream::in);
OBConversion Convsm(&smarts);
if(!Convsm.SetInFormat("smi")) return false;
Convsm.Read(&patternMol);
//erase -s option in GeneralOptions since it will be rewritten
pConv->RemoveOption("s",OBConversion::GENOPTIONS);
if(patternMol.Empty())
{
obErrorLog.ThrowError(__FUNCTION__,
"Could not make a molecule from " + smarts.str()
+ "\nThis needs to be valid SMILES when using fastsearch."
"You can use the more versatile SMARTS in a normal substructure search." , obError);
return false;
}
}
else
{
// or Make OBMol from file in -S option or -aS option
p = pConv->IsOption("S",OBConversion::GENOPTIONS);
if(!p)
p = pConv->IsOption("S",OBConversion::INOPTIONS);//for GUI mainly
}
if(!p)
{
//neither -s or -S options provided. Output info rather than doing search
const FptIndexHeader& header = fs.GetIndexHeader();
string id(header.fpid);
if(id.empty())
id = "default";
clog << indexname << " is an index of\n " << header.datafilename
<< ".\n It contains " << header.nEntries
<< " molecules. The fingerprint type is " << id << " with "
<< OBFingerprint::Getbitsperint() * header.words << " bits.\n"
<< "Typical usage for a substructure search:\n"
<< "babel indexfile.fs -osmi -sSMILES" << endl;
return false;
}
if(p && patternMol.Empty())
{
txt=p;
string::size_type pos = txt.find_last_of('.');
if(pos==string::npos)
{
obErrorLog.ThrowError(__FUNCTION__, "Filename of pattern molecule in -S option must have an extension", obError);
return false;
}
patternstream.open(txt.c_str());
if(!patternstream)
{
stringstream errorMsg;
errorMsg << "Cannot open " << txt << endl;
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);
return false;
}
PatternConv.SetOneObjectOnly();
if(PatternConv.SetInFormat(txt.substr(pos+1).c_str()))
PatternConv.Read(&patternMol);
}
if(patternMol.Empty())
{
obErrorLog.ThrowError(__FUNCTION__, "Cannot derive a molecule from the -s or -S options", obWarning);
return false;
}
patternMol.ConvertDativeBonds();//use standard form for dative bonds
//Convert to SMILES and generate a -s option for use in the final filtering
if(!PatternConv.SetOutFormat("smi"))
return false;
PatternConv.Write(&patternMol);
//remove name to leave smiles string
string smilesstr(smiles.str());
string::size_type pos = smilesstr.find_first_of(" \t\r\n");
if(pos!=string::npos)
smilesstr = smilesstr.substr(0,pos);
pConv->AddOption("s", OBConversion::GENOPTIONS, smilesstr.c_str());
return true;
}
