void CLI::run() {
bool worktime = true;
while (worktime) {
m_qout << "----------------" << endl
<< "1 - Enter array" << endl
<< "2 - Enter string" << endl
<< "3 - Quit" << endl
<< "Enter command: " << flush;
switch (m_qin.readLine().toInt()) {
case 1:
processArray();
break;
case 2:
processString();
break;
case 3:
worktime = false;
printMsg("See you later..." );
break;
default:
printMsg("Undefined command");
}
m_qout << endl << flush;
}
}
virtual void processQString(unsigned len, const char *value, const RtlFieldInfo * field)
{
size32_t charCount;
rtlDataAttr text;
rtlQStrToStrX(charCount, text.refstr(), len, value);
processString(charCount, text.getstr(), field);
}
QDomElement OOoReportBuilder::parseRow(QDomNode row)
{
QDomElement lastElement = row.toElement();
if (reportBand(row) == Detail) {
lastElement = processDetail(row.toElement());
} else {
QDomNode child = row.firstChild();
while (!child.isNull()) {
if (child.nodeName() == "table:table-cell") {
QString str = processString(cellText(child.toElement()));
bool ok;
double value = str.toDouble(&ok);
if (ok) {
setText(child.toElement(), value);
} else
setText(child.toElement(), str);
}
child = child.nextSibling();
}
}
return lastElement;
}
void IntlParametersBlock::processParametersBlock(ProcessString* processString, ClumpletWriter& pb)
{
for (pb.rewind(); !pb.isEof(); pb.moveNext())
{
UCHAR tag = pb.getClumpTag();
string s;
switch (checkTag(tag))
{
case TAG_SKIP:
break;
case TAG_STRING:
pb.getString(s);
processString(s);
pb.deleteClumplet();
pb.insertString(tag, s);
break;
case TAG_COMMAND_LINE:
pb.getString(s);
processCommandLine(processString, s);
pb.deleteClumplet();
pb.insertString(tag, s);
break;
}
}
}
Token(const TokenTypes Type, std::list<char>& DataIn) :
Bytes(NULL), _Type(Type) {
if (_Type == MODE_CHANGES) {
Bytes = processModeChange(DataIn);
} else if (_Type == STRING) {
Bytes = processString(DataIn);
}
}
void IntlParametersBlock::processParametersBlock(ProcessString* processString, ClumpletWriter& pb)
{
const char* tagName = NULL;
try
{
for (pb.rewind(); !pb.isEof(); )
{
UCHAR tag = pb.getClumpTag();
string s;
tagName = NULL;
switch (checkTag(tag, &tagName))
{
case TAG_SKIP:
pb.moveNext();
break;
case TAG_STRING:
pb.getString(s);
processString(s);
pb.deleteClumplet();
pb.insertString(tag, s);
break;
case TAG_COMMAND_LINE:
pb.getString(s);
processCommandLine(processString, s);
pb.deleteClumplet();
pb.insertString(tag, s);
break;
}
}
}
catch (const Firebird::status_exception& st)
{
LocalStatus ls;
CheckStatusWrapper l(&ls);
st.stuffException(&l);
if ((l.getState() & IStatus::STATE_ERRORS) && (l.getErrors()[1] == isc_bad_conn_str) && tagName)
{
Arg::Gds newErrors(isc_intl_char);
newErrors << tagName;
const ISC_STATUS* errors = l.getErrors();
newErrors << Arg::StatusVector(errors + 2); // skip isc_bad_conn_str
l.setErrors(newErrors.value());
status_exception::raise(&l);
}
// other case leave exception as is
throw;
}
}
/** Return the string used by SireError to identify the process */
QString SIREERROR_EXPORT getProcessString()
{
QString *s = processString();
if (s->isEmpty())
{
return *s = QObject::tr("master");
}
return *s;
}
void
TUIGame::play() {
handleCommand("new");
while (true) {
// Print last move
if (currentMove > 0) {
Position prevPos(getPos());
prevPos.unMakeMove(moveList[currentMove - 1], uiInfoList[currentMove - 1]);
std::string moveStr= TextIO::moveToString(prevPos, moveList[currentMove - 1], false);
if (haveDrawOffer())
moveStr += " (offer draw)";
std::cout << "Last move: " << prevPos.getFullMoveCounter()
<< (prevPos.isWhiteMove() ? "." : "...")
<< ' ' << moveStr << std::endl;
}
/*
{
std::stringstream ss;
ss << "Hash: " << std::hex << std::setw(16) << std::setfill('0') << pos.zobristHash();
std::cout << ss.str() << std::endl;
}
*/
{
auto et = Evaluate::getEvalHashTables();
Evaluate eval(*et);
int evScore = eval.evalPos(getPos()) * (getPos().isWhiteMove() ? 1 : -1);
std::stringstream ss;
ss.precision(2);
ss << std::fixed << "Eval: " << (evScore / 100.0);
std::cout << ss.str() << std::endl;
}
// Check game state
std::cout << TextIO::asciiBoard(getPos());
std::string stateStr = getGameStateString();
if (stateStr.length() > 0)
std::cout << stateStr << std::endl;
if (getGameState() != Game::ALIVE)
activateHumanPlayer();
// Get command from current player and act on it
Player& pl = getPos().isWhiteMove() ? *whitePlayer : *blackPlayer;
std::vector<Position> posList;
getHistory(posList);
std::string moveStr = pl.getCommand(getPos(), haveDrawOffer(), posList);
if (moveStr == "quit")
return;
bool ok = processString(moveStr);
if (!ok)
std::cout << "Invalid move: " << moveStr << std::endl;
}
}
int KSDBHandler::getId(const QString& name)
{
KSResult temp = processString("SELECT id_phrase FROM phrases WHERE name='"+name+"';");
QString output = temp["id_phrase"];
if(output.isNull())
{
return -1;
}
else
{
return output.toInt();
}
}
int main()
{
char* string;
string = getString();
processString(string);
printf("%s\n", string);
free(string);
return 0;
}
int main(){
char *chunk, *delim = ";";
//can be replaced with scanf for input.
char *tmp = "x+=3;y+=5;x*=y;";
char *str = strdup(tmp);
chunk = strtok(str, delim);
while(chunk){
processString(chunk);
chunk = strtok(NULL, delim);
}
printValues();
return 0;
}
bool GwfTranslator::translateImpl()
{
// open file and read data
bool result = true;
std::ifstream ifs(mParams.fileName.c_str());
if (ifs.is_open())
{
String data((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
result = processString(data);
} else
return false;
ifs.close();
return result;
}
int MessageState::nextMessage(reg_t buf) {
MessageRecord record;
if (!buf.isNull()) {
if (getRecord(_cursorStack, true, record)) {
outputString(buf, processString(record.string));
_lastReturned = record.tuple;
_lastReturnedModule = _cursorStack.getModule();
_cursorStack.top().seq++;
return record.talker;
} else {
MessageTuple &t = _cursorStack.top();
outputString(buf, Common::String::format("Msg %d: %d %d %d %d not found", _cursorStack.getModule(), t.noun, t.verb, t.cond, t.seq));
return 0;
}
} else {
CursorStack stack = _cursorStack;
if (getRecord(stack, true, record))
return record.talker;
else
return 0;
}
}
int main (int argc, char *argv[])
{
FILE* ftmp = NULL;
if ((Conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL)
return EXIT_FAILURE;
cgiInit();
cgiHeader("text/html");
if (argc == 3) {
GfrEntry *currGE;
Stringa buffer;
GfrPairCount *currGEPC;
GfrInterRead *currGIR;
int i;
puts ("<html>");
puts ("<head>");
html_printGenericStyleSheet (12);
puts ("<title>geneFusions Details</title>\n");
puts ("</head>");
puts ("<body>");
buffer = stringCreate (100);
stringPrintf (buffer, "%s/%s.gfr", confp_get(Conf, "WEB_DATA_DIR"),argv[1]);
gfr_init (string (buffer));
while (currGE = gfr_nextEntry ()){
fflush( stdout );
if (!strEqual (currGE->id,argv[2])) {
continue;
}
printf ("<h1>Detailed summary for potential gene fusion candidate</h1><br>");
puts ("<table border=0 cellpadding=10>");
puts ("<tr align=left valign=top>");
puts ("<td width=400>");
puts ("<h2>Summary information</h2><br>");
printf ("<b>Identifier</b>: %s<br><br>\n",currGE->id);
printf ("<b>Number of inter paired-end reads</b>: %d<br><br>\n",currGE->numInter);
printf ("<b>Type</b>: %s<br><br>\n",currGE->fusionType);
stringPrintf(buffer, "%s/GFF/%s.gff", confp_get(Conf, "WEB_DATA_DIR"),currGE->id);
ftmp = fopen( string(buffer), "r" ); // displaying this only if data are present
if (ftmp) {
printf("<b>Connected Reads</b>: <a href=%s&hgt.customText=%s/GFF/%s.gff target=blank>UCSC connectivity graph</a><br>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),currGE->id);
fclose( ftmp );
}
puts ("</td>");
puts ("<td>");
puts ("<h2>Transcript connectivity graph</h2>");
printf ("<img src=%s/IMAGES/%s.jpg alt=geneFusionImage>\n", confp_get(Conf, "WEB_DATA_LINK"), currGE->id);
puts ("</td>");
puts ("<td>");
puts ("<h2>Transcript connectivity table</h2><br>");
puts ("<table border=0>");
puts ("<tr align=left>");
puts ("<th width=200>Pair Type</th>");
puts ("<th width=200>Entry transcript 1</th>");
puts ("<th width=200>Entry transcript 2</th>");
puts ("<th width=200>Counts</th>");
puts ("</tr>");
fflush( stdout );
for (i = 0; i < arrayMax (currGE->pairCounts); i++) {
currGEPC = arrp (currGE->pairCounts,i,GfrPairCount);
printf ("<tr><td>%s</td><td>%s</td><td>%s</td><td>%.2f</td></tr>\n",
getPairTypeName(currGEPC->pairType),
getEntryNumber(currGEPC->number1, currGEPC->pairType, 1),
getEntryNumber(currGEPC->number2, currGEPC->pairType, 2),
currGEPC->count);
}
puts ("</table>");
puts ("</td>");
puts ("</tr>");
puts ("</table>");
puts ("<br>");
puts ("<h2>Transcript information</h2><br>");
puts ("<table border=1 cellpadding=10 width=\"80%\">");
puts ("<tr align=left>");
puts ("<th width=\"20%\"></th>");
puts ("<th><font color='blue'>Transcript 1</font></th>");
puts ("<th><font color='orange'>Transcript 2</font></th>");
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Gene symbol(s)</b></td>");
printf ("<td width=\"30%%\"><font color='blue'>%s</font></td>\n",processString (currGE->geneSymbolTranscript1));
printf ("<td width=\"30%%\"><font color='orange'>%s</font></td>\n",processString (currGE->geneSymbolTranscript2));
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Coordinates</b></td>");
printf ("<td width=\"30%%\">%s:%d-%d</td>\n",currGE->chromosomeTranscript1,currGE->startTranscript1,currGE->endTranscript1);
printf ("<td width=\"30%%\">%s:%d-%d</td>\n",currGE->chromosomeTranscript2,currGE->startTranscript2,currGE->endTranscript2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Strand</b></td>");
printf ("<td width=\"30%%\">%c</td>\n",currGE->strandTranscript1);
printf ("<td width=\"30%%\">%c</td>\n",currGE->strandTranscript2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Gene description(s)</b></td>");
printf ("<td width=\"30%%\">%s</td>\n",processString (currGE->descriptionTranscript1));
printf ("<td width=\"30%%\">%s</td>\n",processString (currGE->descriptionTranscript2));
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Number of exons</b></td>");
printf ("<td width=\"30%%\">%d</td>\n",currGE->numExonsTranscript1);
printf ("<td width=\"30%%\">%d</td>\n",currGE->numExonsTranscript2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Number of intra paired-end reads</b></td>");
printf ("<td width=\"30%%\">%d</td>\n",currGE->numIntra1);
printf ("<td width=\"30%%\">%d</td>\n",currGE->numIntra2);
puts ("</tr>");
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Links</b></td>");
printf ("<td width=\"30%%\">[<a href=%s&hgt.customText=%s/BED/%s_1.bed target=blank>UCSC genome browser</a>] [<a href=%s/FASTA/%s_1.fasta>FASTA file</a>]<br></td>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
printf ("<td width=\"30%%\">[<a href=%s&hgt.customText=%s/BED/%s_2.bed target=blank>UCSC genome browser</a>] [<a href=%s/FASTA/%s_2.fasta>FASTA file</a>]<br></td></tr>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
puts ("<tr align=left>");
puts ("<td width=\"20%\"><b>Expression</b></td>");
stringPrintf(buffer, "%s/BGRS/%s_%s.bgr.gz",
confp_get(Conf, "WEB_DATA_DIR"),
argv[1],
currGE->chromosomeTranscript1);
ftmp = fopen( string(buffer), "r" ); // displaying this only if data are present
puts("<td width=\"30%\">");
if( ftmp ) {
printf ("[<a href=%s&hgt.customText=%s/BGRS/%s_%s.bgr.gz target=blank>Expression %s</a>]",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
argv[1],
currGE->chromosomeTranscript1,
currGE->chromosomeTranscript1);
fclose(ftmp);
}
puts("</td>");
stringPrintf(buffer, "%s/BGRS/%s_%s.bgr.gz", confp_get(Conf, "WEB_DATA_DIR"),argv[1],currGE->chromosomeTranscript2);
ftmp = fopen( string(buffer), "r" ); // displaying this only if data are present
puts("<td width=\"30%\">");
if( ftmp ) {
printf ("[<a href=%s&hgt.customText=%s/BGRS/%s_%s.bgr.gz target=blank>Expression %s</a>]",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
argv[1],
currGE->chromosomeTranscript2,
currGE->chromosomeTranscript2);
fclose(ftmp);
}
puts("</td>");
puts("</tr>");
puts ("</table><br><br>");
puts ("<h2>Breakpoint analysis</h2><br>");
puts ("<table border=1 width=\"80%\" cellpadding=10><thead><tr><th>Orientation</th><th>Alignments</th><th colspan=2>Breakpoints</th></tr></thead><tbody>");
puts ("<tr><td>Orientation AB</td>");
if (currGE->strandTranscript1=='+') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "AB_trans1F_trans2F") : stringPrintf(buffer, "AB_trans1F_trans2R");
} else if( currGE->strandTranscript1 == '-') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "AB_trans1R_trans2F") : stringPrintf(buffer, "AB_trans1R_trans2R");
} else {
die("Strand informatation is not correct (transcript 1): %c", currGE->strandTranscript1);
}
printf ("<td align=center><a href=%s/ALIGNMENTS/%s_AB_breakPointAlignments.txt><img src=%s/IMAGES/%s.png></img> AB</a></td>",
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
string(buffer));
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_AB_breakPointsTranscript1.wig target=blank>Breakpoints transcript 1 UCSC Genome Browser</a></td>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_AB_breakPointsTranscript2.wig target=blank>Breakpoints transcript 2 UCSC Genome Browser</a></td></tr>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
fflush(stdout);
puts ("<tr><td>Orientation BA</td>");
if (currGE->strandTranscript1 == '+') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "BA_trans1F_trans2F") : stringPrintf(buffer, "BA_trans1F_trans2R");
} else if( currGE->strandTranscript1 == '-') {
currGE->strandTranscript2=='+' ? stringPrintf(buffer, "BA_trans1R_trans2F") : stringPrintf(buffer, "BA_trans1R_trans2R");
} else {
die("Strand informatation is not correct (transcript2): %c", currGE->strandTranscript2);
}
printf ("<td align=center><a href=%s/ALIGNMENTS/%s_BA_breakPointAlignments.txt><img src=%s/IMAGES/%s.png></img> BA</a></td>",
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id,
confp_get(Conf, "WEB_DATA_LINK"),
string(buffer));
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_BA_breakPointsTranscript2.wig target=blank>Breakpoints transcript 2 UCSC Genome Browser</a></td>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
printf ("<td align=center><a href=%s&hgt.customText=%s/WIGS/%s_BA_breakPointsTranscript1.wig target=blank>Breakpoints transcript 1 UCSC Genome Browser</a></td></tr>",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
confp_get(Conf, "WEB_DATA_LINK"),
currGE->id);
puts ("</tbody></table>");
puts ("<br><br><br>");
fflush(stdout);
puts ("<h2>Read coordinates</h2><br>");
puts ("<table border=0>");
puts ("<tr align=left>");
puts ("<th width=\"10%\">Pair Type</th>");
puts ("<th width=\"10%\">Entry Transcript 1</th>");
puts ("<th width=\"10%\">Read start transcript 1</th>");
puts ("<th width=\"10%\">Read end transcript 1</th>");
puts ("<th width=\"10%\">Entry Transcript 2</th>");
puts ("<th width=\"10%\">Read start transcript 2</th>");
puts ("<th width=\"10%\">Read end transcript 2</th>");
puts ("</tr>");
for (i = 0; i < arrayMax (currGE->interReads); i++) {
currGIR = arrp (currGE->interReads,i,GfrInterRead);
printf ("<tr><td>%s</td><td>%s</td><td>%d</td><td>%d</td><td>%s</td><td>%d</td><td>%d</td></tr>\n",
getPairTypeName(currGIR->pairType),
getEntryNumber(currGIR->number1, currGIR->pairType, 1),
currGIR->readStart1,currGIR->readEnd1,
getEntryNumber(currGIR->number2,currGIR->pairType, 2),
currGIR->readStart2,
currGIR->readEnd2);
}
puts ("</table><br><br><br>");
puts ("</body>");
puts ("</html>");
fflush (stdout);
}
}
confp_close(Conf);
return EXIT_SUCCESS;
}
/** Set the string that SireError will use to identify this process */
void SIREERROR_EXPORT setProcessString(const QString &s)
{
*(processString()) = s;
}
static void generateOutput (char* prefix, char* typeSelected, int minNum)
{
GfrEntry *currGE;
Stringa buffer;
char *pos;
puts ("<html>");
puts ("<head>");
puts ("<title>Results - Gene Fusions</title>");
html_printGenericStyleSheet (12);
puts ("</head>");
puts ("<body>");
if (prefix[0] == '\0') {
die ("Invalid prefix");
}
printf ("<h1>Results - %s</h1><br><br><br>",prefix);
buffer = stringCreate(50);
//Chromosome expression, if present
LineStream ls;
char* chrSignal=NULL;
stringPrintf(buffer, "ls -1 %s/BGRS/%s_chr*.bgr.gz 2> /dev/null",
confp_get(Conf, "WEB_DATA_DIR"),
prefix);
ls = ls_createFromPipe(string(buffer));
int countCol = 0;
puts ("Expression signal: ");
fflush(stdout);
while( chrSignal = ls_nextLine(ls)) {
char* chrTmp = stringBetween( prefix, ".bgr.gz", chrSignal );
chrTmp++;
printf ("[<a href=%s&hgt.customText=%s/BGRS/%s_%s.bgr.gz target='blank'>%s</a>] ",
htmlLinker_generateLinkToGenomeBrowserAtUCSC("hg18","vertebrate","human", chrTmp,
confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"),
50000000 + confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
confp_get(Conf, "WEB_DATA_LINK"),
prefix,
chrTmp,
chrTmp);
if (countCol > 10) {
puts( "<BR>" );
countCol=0;
}
countCol++;
}
if( countCol==0) puts( "No data available yet" );
ls_destroy(ls);
puts ("<br><br>");
puts ("For a definition of SPER, DASPER and RESPER see <a href=http://rnaseq.gersteinlab.org/fusionseq/>FusionSeq</a>");
puts ("<br><br>");
puts ("<br><table border=0 width=100% align=center cellpadding=10>");
puts ("<tr align=left>");
puts ("<th>SPER</th>");
puts ("<th>DASPER</th>");
puts ("<th>RESPER</th>");
puts ("<th>Number of inter paired-end reads</th>");
puts ("<th>Type</th>");
puts ("<th>Genomic coordinates</th>");
puts ("<th>Gene symbol</th>");
puts ("<th>Description</th>");
puts ("<th>Genomic coordinates</th>");
puts ("<th>Gene symbol</th>");
puts ("<th>Description</th>");
puts ("<th></th>");
puts ("</tr>");
fflush(stdout);
stringPrintf (buffer,"%s/%s.gfr", confp_get(Conf, "WEB_DATA_DIR"), prefix);
gfr_init (string (buffer));
int countElements = 0;
while (currGE = gfr_nextEntry ()) {
if (currGE->numInter < minNum) {
continue;
}
if (strEqual (typeSelected,"all") || strEqual (currGE->fusionType,typeSelected) ||
( strEqual(currGE->fusionType,"cis") && strEqual( typeSelected,"same") ) ||
( strEqual(currGE->fusionType,"read-through") && strEqual( typeSelected,"same") ) ) {
if (pos = strchr (currGE->descriptionTranscript1,'|')) {
*pos = '\0';
}
if (pos = strchr (currGE->descriptionTranscript2,'|')) {
*pos = '\0';
}
puts ("<tr>");
printf ("<td align=left>%1.3f</td>\n",currGE->SPER);
printf ("<td align=left>%1.3f</td>\n",currGE->DASPER);
printf ("<td align=left>%1.3f</td>\n",currGE->RESPER);
printf ("<td align=left>%d</td>\n",currGE->numInter);
printf ("<td align=left>%s</td>\n",currGE->fusionType);
printf ("<td align=left><a href=%s target=blank>%s:%d-%d</a></td>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript1,
currGE->startTranscript1 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript1 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
currGE->chromosomeTranscript1,currGE->startTranscript1,currGE->endTranscript1);
printf ("<td align=left>%s</td>\n",processString (currGE->geneSymbolTranscript1));
printf ("<td align=left>%s</td>\n",currGE->descriptionTranscript1);
printf ("<td align=left><a href=%s target=blank>%s:%d-%d</a></td>\n",
htmlLinker_generateLinkToGenomeBrowserAtUCSC ("hg18","vertebrate","human",
currGE->chromosomeTranscript2,
currGE->startTranscript2 - atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION")),
currGE->endTranscript2 + atoi(confp_get(Conf, "UCSC_GENOME_BROWSER_FLANKING_REGION"))),
currGE->chromosomeTranscript2,currGE->startTranscript2,currGE->endTranscript2);
printf ("<td align=left>%s</td>\n",processString (currGE->geneSymbolTranscript2));
printf ("<td align=left>%s</td>\n",currGE->descriptionTranscript2);
printf ("<td align=left><a href=%s/showDetails_cgi?%s+%s>Details</a></td>\n", confp_get(Conf, "WEB_URL_CGI"), prefix,currGE->id);
puts ("</tr>");
countElements++;
}
}
gfr_deInit ();
stringDestroy (buffer);
puts ("</table><br><br>");
if( countElements == 0) puts("No fusion candidates can be found satisfying all specified criteria.");
puts ("</body>");
puts ("</html>");
fflush (stdout);
}
void Telos2101Driver::textData(int type,int line,const QString &str)
{
processString((BusDriver::Element)type,line,str);
}
bool tokenise(std::string::const_iterator& s, std::string::const_iterator& e, Token& tok)
{
std::string::const_iterator t = s;
// Hand constructed state machine recogniser
enum {
START,
REJECT,
IDENTIFIER,
ZERO,
DIGIT,
HEXDIGIT_START,
HEXDIGIT,
OCTDIGIT,
BINDIGIT_START,
BINDIGIT,
DECIMAL_START,
DECIMAL,
EXPONENT_SIGN,
EXPONENT_START,
EXPONENT,
ACCEPT_IDENTIFIER,
ACCEPT_INC,
ACCEPT_NOINC
} state = START;
TokenType tokType = T_EOS;
while (true)
switch (state) {
case START:
if (t==e) {tok = Token(T_EOS, s, "<END>"); return true;}
else if (std::isspace(*t)) {++t; ++s; continue;}
else switch (*t) {
case '(': tokType = T_LPAREN; state = ACCEPT_INC; continue;
case ')': tokType = T_RPAREN; state = ACCEPT_INC; continue;
case ',': tokType = T_COMMA; state = ACCEPT_INC; continue;
case '+': tokType = T_PLUS; state = ACCEPT_INC; continue;
case '-': tokType = T_MINUS; state = ACCEPT_INC; continue;
case '*': tokType = T_MULT; state = ACCEPT_INC; continue;
case '/': tokType = T_DIV; state = ACCEPT_INC; continue;
case '=': tokType = T_EQUAL; state = ACCEPT_INC; continue;
case '<':
++t;
if (t==e || (*t!='>' && *t!='='))
{tokType = T_LESS; state = ACCEPT_NOINC; continue; }
else
{tokType = (*t=='>') ? T_NEQ : T_LSEQ; state = ACCEPT_INC; continue; }
case '>':
++t;
if (t==e || *t!='=')
{tokType = T_GRT; state = ACCEPT_NOINC; continue;}
else
{tokType = T_GREQ; state = ACCEPT_INC; continue;}
default:
break;
}
if (isIdentifierStart(*t)) {++t; state = IDENTIFIER;}
else if (*t=='\'') {return processString(s, e, '\'', T_STRING, tok);}
else if (*t=='\"') {return processString(s, e, '\"', T_IDENTIFIER, tok);}
else if (*t=='0') {++t; state = ZERO;}
else if (std::isdigit(*t)) {++t; state = DIGIT;}
else if (*t=='.') {++t; state = DECIMAL_START;}
else state = REJECT;
continue;
case IDENTIFIER:
if (t==e) {state = ACCEPT_IDENTIFIER;}
else if (isIdentifierPart(*t)) {++t; state = IDENTIFIER;}
else state = ACCEPT_IDENTIFIER;
continue;
case DECIMAL_START:
if (t==e) {state = REJECT;}
else if (std::isdigit(*t)) {++t; state = DECIMAL;}
else state = REJECT;
continue;
case EXPONENT_SIGN:
if (t==e) {state = REJECT;}
else if (*t=='-' || *t=='+') {++t; state = EXPONENT_START;}
else if (std::isdigit(*t)) {++t; state = EXPONENT;}
else state = REJECT;
continue;
case EXPONENT_START:
if (t==e) {state = REJECT;}
else if (std::isdigit(*t)) {++t; state = EXPONENT;}
else state = REJECT;
continue;
case ZERO:
if (t==e) {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
else if (*t=='.') {++t; state = DECIMAL;}
else if (*t=='x' || *t=='X') {++t; state = HEXDIGIT_START;}
else if (*t=='b' || *t=='B') {++t; state = BINDIGIT_START;}
else state = OCTDIGIT;
continue;
case HEXDIGIT_START:
if (t==e) {state = REJECT;}
else if (std::isxdigit(*t)) {++t; state = HEXDIGIT;}
else state = REJECT;
continue;
case HEXDIGIT:
if (t==e) {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
else if (*t=='l' || *t=='L') {tokType = T_NUMERIC_EXACT; state = ACCEPT_INC;}
else if (std::isxdigit(*t) || *t=='_') {++t; state = HEXDIGIT;}
else if (*t=='p' || *t=='P') {++t; state = EXPONENT_SIGN;}
else {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
continue;
case BINDIGIT_START:
if (t==e) {state = REJECT;}
else if (*t=='0' || *t=='1') {++t; state = BINDIGIT;}
else state = REJECT;
continue;
case BINDIGIT:
if (t==e) {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
else if (*t=='l' || *t=='L') {tokType = T_NUMERIC_EXACT; state = ACCEPT_INC;}
else if (*t=='0' || *t=='1' || *t=='_') {++t; state = BINDIGIT;}
else {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
continue;
case OCTDIGIT:
if (t==e) {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
else if (*t=='l' || *t=='L') {tokType = T_NUMERIC_EXACT; state = ACCEPT_INC;}
else if ((std::isdigit(*t) && *t<'8') || *t=='_') {++t; state = OCTDIGIT;}
else {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
continue;
case DIGIT:
if (t==e) {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
else if (*t=='l' || *t=='L') {tokType = T_NUMERIC_EXACT; state = ACCEPT_INC;}
else if (*t=='f' || *t=='F' || *t=='d' || *t=='D') {tokType = T_NUMERIC_APPROX; state = ACCEPT_INC;}
else if (std::isdigit(*t) || *t=='_') {++t; state = DIGIT;}
else if (*t=='.') {++t; state = DECIMAL;}
else if (*t=='e' || *t=='E') {++t; state = EXPONENT_SIGN;}
else {tokType = T_NUMERIC_EXACT; state = ACCEPT_NOINC;}
continue;
case DECIMAL:
if (t==e) {tokType = T_NUMERIC_APPROX; state = ACCEPT_NOINC;}
else if (std::isdigit(*t) || *t=='_') {++t; state = DECIMAL;}
else if (*t=='e' || *t=='E') {++t; state = EXPONENT_SIGN;}
else if (*t=='f' || *t=='F' || *t=='d' || *t=='D') {tokType = T_NUMERIC_APPROX; state = ACCEPT_INC;}
else {tokType = T_NUMERIC_APPROX; state = ACCEPT_NOINC;}
continue;
case EXPONENT:
if (t==e) {tokType = T_NUMERIC_APPROX; state = ACCEPT_NOINC;}
else if (std::isdigit(*t)) {++t; state = EXPONENT;}
else if (*t=='f' || *t=='F' || *t=='d' || *t=='D') {tokType = T_NUMERIC_APPROX; state = ACCEPT_INC;}
else {tokType = T_NUMERIC_APPROX; state = ACCEPT_NOINC;}
continue;
case ACCEPT_INC:
++t;
case ACCEPT_NOINC:
tok = Token(tokType, s, t);
s = t;
return true;
case ACCEPT_IDENTIFIER:
tok = Token(T_IDENTIFIER, s, t);
s = t;
tokeniseReservedWord(tok);
return true;
case REJECT:
return false;
};
}
