int countCassetteExons(struct altGraphX *agList, float minConfidence, FILE *outfile, FILE *bedOutFile)
/* count up the number of cassette exons that have a certain
confidence, returns number of edges. If outfile != NULL will output fasta sequences
to outfile. */
{
struct altGraphX *ag = NULL;
int edge =0;
int cassetteCount = 0;
int i =0;
int mod3 = 0;
int counter =0;
boolean outputted = FALSE;
float estPrior = cgiOptionalDouble("estPrior", 10);
FILE *log = mustOpen("confidences.log", "w");
FILE *html = mustOpen("confidences.html", "w");
FILE *sizes = mustOpen("sizes.log", "w");
int minSize = cgiOptionalInt("minSize", 0);
startHtml(html);
for(ag = agList; ag != NULL; ag = ag->next)
{
outputted = FALSE;
for(i=0;i<ag->edgeCount; i++)
{
if(ag->edgeTypes[i] == ggCassette)
{
float conf = altGraphCassetteConfForEdge(ag, i, estPrior);
struct bed *bed, *bedList = altGraphGetExonCassette(ag, i);
char buff[256];
int size = ag->vPositions[ag->edgeEnds[i]] - ag->vPositions[ag->edgeStarts[i]];
boolean filtersOk = FALSE;
if(ag->name == NULL)
ag->name = cloneString("");
slSort(&bedList, bedCmpMaxScore);
for(bed=bedList; bed != NULL; bed = bed->next)
{
snprintf(buff, sizeof(buff), "%s.%d", ag->name, counter);
bed->name = cloneString(buff);
fprintf(log, "%f\n", conf);
fprintf(sizes, "%d\n%d\n%d\n", bed->blockSizes[0], bed->blockSizes[1], bed->blockSizes[2]);
filtersOk = bedPassFilters(bed, ag, i);
if(conf >= minConfidence && size >= minSize && filtersOk)
{
writeCassetteExon(bed, ag, i, &outputted, bedOutFile, outfile, html, conf);
cassetteCount++;
if((size % 3) == 0)
mod3++;
}
counter++;
}
bedFreeList(&bedList);
}
}
}
endHtml(html);
carefulClose(&html);
carefulClose(&log);
warn("%d cassettes are mod 3", mod3);
return cassetteCount;
}
void ClientInfoForm::onWmUserUpdate() {
startHtml();
if (clientVersion.length()) {
addText("<strong>Client info:</strong><br>Name: "); addText(clientName);
addText("<br>Version: "); addText(clientVersion);
addText("<br>OS: "); addText(clientOS);
addText("<br>");
}
if (lastActivityTime.length()) {
unsigned __int64 delay=atol(lastActivityTime.c_str());
delay*=10000000;
PackedTime ct=strtime::getCurrentUtc();
void *i64ct=&ct;
(*( (__int64*)i64ct ))-=delay;
addText("<br><strong>Last activity:</strong><br>Time: "); addText(strtime::toLocalDateTime(ct));
}
if (lastActivityMessage.length()) addText("<br>Status: "); addText(lastActivityMessage);
if (clientTime.length()) addText("<br><br><strong>Contact's time:</strong> "); addText(clientTime);
endHtml();
}
void VcardForm::onWmUserUpdate() {
//std::string xml=*(vcard->toXML());
//const std::string &xml2=XMLStringPrep(xml);
//const std::wstring xml3=utf8::utf8_wchar(xml2);
//SendMessage(hwndHTML, WM_SETTEXT, 0, (LPARAM)"");
//img.reset();
imgFile=appRootPath;// + L"userdata\\avatars\\" + L"$$$_tmp.jpg";
if (savePhoto(imgFile.c_str())){
//img=ImageRef(new Image(imgFile.c_str()));
//Contact::ref contact = Contact::ref(new Contact(this->jid,"","","",""));
//contact->img_avatar=img;
}
startHtml();
addImg(L"\\vcard");
beginForm("vcard-photo", "photo");
if (img) if (img->getHBmp()) {
button("save",std::string("Save"));
if (editForm) button("clear",std::string("Clear"));
}
if (editForm) button("load",std::string("Load"));
addText("<BR>");
endForm();
//contact->img_avatar=img;
beginForm("vcard-fields", "publish");
addHtmlField("FN", NULL, "Full Name", TXT);
addHtmlField("NICKNAME", NULL, "Nickname", TXT);
addHtmlField("BDAY", NULL, "Birthday", TXT);
addHtmlField("ADR", "STREET", "Street", TXT);
addHtmlField("ADR", "EXTADR", "Street2", TXT);
addHtmlField("ADR", "LOCALITY", "City", TXT);
addHtmlField("ADR", "REGION", "State", TXT);
addHtmlField("ADR", "PCODE", "Post code", TXT);
addHtmlField("ADR", "CTRY", "Country", TXT);
addHtmlField("TEL", "HOME", "Home Phone Number", TXT);
addHtmlField("TEL", "NUMBER", "Phone Number", TXT);
addHtmlField("EMAIL", "USERID", "E-Mail", URL);
addHtmlField("TITLE", NULL, "Position", TXT);
addHtmlField("ROLE", NULL, "Role", TXT);
addHtmlField("ORG", "ORGNAME", "Organization", TXT);
addHtmlField("ORG", "ORGUNIT", "Dept", TXT);
addHtmlField("URL", NULL, "Url", URL);
addHtmlField("DESC", NULL, "About", MULTILINE);
if (editForm) button(std::string("Publish"));
//button("reload",std::string("Reload"));
endForm();
endHtml();
}
void CaptchaForm::onSubmit( JabberDataBlockRef replyForm ) {
JabberDataBlock answer("iq", NULL);
answer.setAttribute("type", "set");
answer.setAttribute("id", id);
answer.setAttribute("to", jid);
answer.addChildNS("challenge", "urn:xmpp:tmp:challenge")->addChild(replyForm);
ResourceContextRef rc=this->rc.lock();
if (rc) {
rc->jabberStream->sendStanza(answer);
startHtml();
addText("Done");
endForm();
}
}
