void PlayerSource::run()
{
// initial data
if (m_player == QString("mpd")) {
// mpd
QHash<QString, QVariant> data = getPlayerMpdInfo(m_mpdAddress);
for (auto key : data.keys())
values[key] = data[key];
} else if (m_player == QString("mpris")) {
// players which supports mpris
QString mpris = m_mpris == QString("auto") ? getAutoMpris() : m_mpris;
QHash<QString, QVariant> data = getPlayerMprisInfo(mpris);
for (auto key : data.keys())
values[key] = data[key];
}
// dymanic properties
// solid
values[QString("player/salbum")]
= stripString(values[QString("player/album")].toString(), m_symbols);
values[QString("player/sartist")]
= stripString(values[QString("player/artist")].toString(), m_symbols);
values[QString("player/stitle")]
= stripString(values[QString("player/title")].toString(), m_symbols);
// dynamic
values[QString("player/dalbum")]
= buildString(values[QString("player/dalbum")].toString(),
values[QString("player/album")].toString(), m_symbols);
values[QString("player/dartist")]
= buildString(values[QString("player/dartist")].toString(),
values[QString("player/artist")].toString(), m_symbols);
values[QString("player/dtitle")]
= buildString(values[QString("player/dtitle")].toString(),
values[QString("player/title")].toString(), m_symbols);
}
void readAllSts(FILE *asf)
/* Read in current sequences for sts markers */
{
struct dnaSeq *ds;
struct sts *s;
char *words[8], *acc=NULL, *line;
int wordCount;
while (faReadMixedNext(asf, 0, "default", TRUE, &line, &ds))
{
/* Determine the UCSC id */
wordCount = chopByWhite(line, words, ArraySize(words));
stripString(words[0], ">");
if (wordCount == 3)
acc = cloneString(words[2]);
else
acc = NULL;
/* Find the record and attach */
if (hashLookup(stsHash, ds->name))
{
s = hashMustFindVal(stsHash, ds->name);
s->fa = ds;
s->faAcc = acc;
s->si->sequence = 1;
}
else
{
dnaSeqFree(&ds);
freez(&line);
if (acc != NULL)
freez(&acc);
}
}
}
struct hash *getUniqueStringHash(char *columnName, char *tableName)
/* Read tableName. Store column as string, unique values only. */
/* Remove 'rs'. */
{
struct hash *ret;
char query[512];
struct sqlConnection *conn = hAllocConn();
struct sqlResult *sr;
char **row;
struct hashEl *helName = NULL;
int count = 0;
ret = newHash(18);
safef(query, sizeof(query), "select %s from %s", columnName, tableName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
stripString(row[0], "rs");
helName = hashLookup(ret, row[0]);
if (helName == NULL)
{
hashAdd(ret, cloneString(row[0]), NULL);
count++;
}
}
sqlFreeResult(&sr);
hFreeConn(&conn);
verbose(1, "%d unique %s in %s\n", count, columnName, tableName);
return ret;
}
struct hash *readFasta(char *chromName)
/* read moltype from chrN_fasta into hash. */
/* Read again for random */
/* Also called to create the chrN_multi hash. */
{
char query[512];
struct sqlConnection *conn = hAllocConn();
struct sqlResult *sr;
char **row;
char fastaTableName[64];
struct hash *newChromHash = NULL;
char *adjustedChromName = cloneString(chromName);
char *randomSubstring = NULL;
newChromHash = newHash(0);
randomSubstring = strstr(chromName, "random");
if (randomSubstring != NULL)
stripString(adjustedChromName, "_random");
safef(fastaTableName, ArraySize(fastaTableName), "%s_snpFasta", adjustedChromName);
if(!hTableExistsDb(snpDb, fastaTableName))
errAbort("can't get table %s\n", fastaTableName);
safef(query, sizeof(query), "select rsId, molType from %s", fastaTableName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
/* could check for duplicates here */
hashAdd(newChromHash, cloneString(row[0]), cloneString(row[1]));
sqlFreeResult(&sr);
hFreeConn(&conn);
return newChromHash;
}
char *abbreviateSummary(char *summary)
/* Get rid of some repetitious stuff. */
{
char *pattern =
"Publication Note: This RefSeq record includes a subset "
"of the publications that are available for this gene. "
"Please see the Entrez Gene record to access additional publications.";
stripString(summary, pattern);
return summary;
}
/** @brief Read a file and return non-comment output string
Call the first time with 0 lineNumber to get the number of lines to read
Then call with each lineNumber to get one camera parameter. There should
be one property=value entry on each line, i.e. "exposure=auto"
* @param inputFile filename to read
* @param outputString one string
* @param lineNumber if 0, return number of lines; else return that line number
* @return int number of lines or -1 if error
**/
int processFile(char *inputFile, char *outputString, int lineNumber)
{
FILE *infile;
int stringSize = 80; // max size of one line in file
char inputStr[stringSize];
int lineCount=0;
if (lineNumber < 0)
return (-1);
if ((infile = fopen (inputFile, "r")) == NULL) {
printf ("Fatal error opening file %s\n",inputFile);
return (0);
}
while (!feof(infile)) {
if (fgets (inputStr, stringSize, infile) != NULL) {
// Skip empty lines
if (emptyString(inputStr))
continue;
// Skip comment lines
if (inputStr[0] == '#' || inputStr[0] == '!')
continue;
lineCount++;
if (lineNumber == 0)
continue;
else
{
if (lineCount == lineNumber)
break;
}
}
}
// close file
fclose (infile);
// if number lines requested return the count
if (lineNumber == 0)
return (lineCount);
// check for input out of range
if (lineNumber > lineCount)
return (-1);
// return the line selected
if (lineCount) {
stripString(inputStr);
strcpy(outputString, inputStr);
return(lineCount);
}
else {
return(-1);
}
}
float edfa::EDFAReadPh2(){
QString message;
if(ready){
writeSerial("Ph 2\r\n");
message=readSerial();
if (message.contains("PDM2: ",Qt::CaseInsensitive)){
message = stripString(message, "PDM2:");
}
}
return message.toFloat();
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
char *db = NULL;
char *ignored;
struct trackDb *tracks;
struct trackRef *tr;
struct group *group, *groups = NULL;
cart = theCart;
cartWebStart(cart, NULL, "ENCODE Track Data Versions (%s)", db);
getDbAndGenome(cart, &db, &ignored, NULL);
tracks = hTrackDb(db);
groups = groupTracks(db, tracks);
for (group = groups; group != NULL; group = group->next)
{
if (group->tracks == NULL || !startsWith("encode", group->name))
continue;
hTableStart();
puts("<TR>");
puts("<TH align=LEFT colspan=3 BGCOLOR=#536ED3>");
printf("<B> %s</B> ", wrapWhiteFont(group->label));
printf(" ");
puts("</TH>\n");
puts("</TR>");
for (tr = group->tracks; tr != NULL; tr = tr->next)
{
char *version = trackDbSetting(tr->track, "dataVersion");
if (version)
stripString(version, "ENCODE ");
puts("<TR><TD>");
printf(" %s", tr->track->shortLabel);
puts("</TD><TD>");
printf(" %s", version ? version : " ");
puts("</TD><TD>");
printf(" %s", tr->track->longLabel);
puts("</TD></TR>");
}
/*
printf("\t%s\t%s\t%s\n", version,
tr->track->shortLabel, tr->track->longLabel);
*/
hTableEnd();
puts("<BR>");
}
cartWebEnd();
}
bool edfa::getEmission(){
bool emission = false; //This needs to be made better so that the method will return something if no emission is found.
QString message;
if(ready){
writeSerial("OM\r\n");
message = readSerial();
qDebug() << "get EDFA emission message " << message;
if (message.contains("OM ",Qt::CaseInsensitive)){
message = stripString(message, "OM");
qDebug() << "message contains OM";
qDebug() << "New message " << message;
}
}
if(message == "O"){
emission = false;
}
if(message == "2"){
emission = true;
}
return emission;
}
/*
* readConnectionMatrix
*
* This function reads the network settings and place them in the
* connection matrix (float array with size "len" x "len".
*
* @param pointer to begin of connection matrix
* @param pointer to filename
* @param number of elements in each connection matrix line
* @return 0 if function was successfull, 1 if an error happened
*/
int
readConnectionMatrix(float *connectionMatrix, char *filename, int len)
{
FILE *file = fopen(filename, "r");
if (!file) {
return 1;
}
char buffer[1024];
while (fgets(buffer, 1024, file)) {
int from, to;
float propability;
char *line = stripString(buffer);
DPRINT("%s\n", line);
if (line[0] == '#' || line[0] == 0) {
continue;
}
if (sscanf(line, "%d %d %f", &from, &to, &propability) != 3) {
continue;
}
if (from < 0 || from >= len || to < 0 || to >= len || from == to) {
continue;
}
connectionMatrix[GRID(from, to, len)] = propability;
if (connectionMatrix[GRID(to, from, len)] == 0) {
connectionMatrix[GRID(to, from, len)] = propability;
}
}
fclose(file);
return 0;
}
int
main(int argc, char** argv)
{
if (argc == 1) {
fprintf(stderr, "Usage: %s (save|load|add|delete|rename|select|list|statusbar|toggle_statusbar|checkupdate|set_checkupdate) [params]\n", argv[0]);
return 1;
}
bool isSuccess = false;
if (strcmp(argv[1], "select") == 0) {
if (argc < 3) {
fprintf(stderr, "Usage: %s select index\n", argv[0]);
goto finish;
}
int index = atoi(argv[2]);
isSuccess = setSelectedIndex(index);
} else if (strcmp(argv[1], "add") == 0) {
isSuccess = appendConfig();
} else if (strcmp(argv[1], "delete") == 0) {
if (argc < 3) {
fprintf(stderr, "Usage: %s delete index\n", argv[0]);
goto finish;
}
int index = atoi(argv[2]);
isSuccess = removeConfig(index);
} else if (strcmp(argv[1], "rename") == 0) {
// sysctl_ctl rename "index" "newname"
if (argc < 4) {
fprintf(stderr, "Usage: %s rename index newname\n", argv[0]);
goto finish;
}
int index = atoi(argv[2]);
char buf[512];
snprintf(buf, sizeof(buf), "%s", argv[3]);
stripString(buf, sizeof(buf));
if (buf[0] == '\0') {
snprintf(buf, sizeof(buf), "(null)");
}
isSuccess = renameConfig(index, buf);
} else if (strcmp(argv[1], "list") == 0) {
outputConfigList();
return 0;
} else if (strcmp(argv[1], "statusbar") == 0) {
printf("%ld\n", getValue(CFSTR("isStatusbarEnable")));
return 0;
} else if (strcmp(argv[1], "toggle_statusbar") == 0) {
CFStringRef name = CFSTR("isStatusbarEnable");
CFIndex value = getValue(name);
isSuccess = setValue(name, ! value);
} else if (strcmp(argv[1], "checkupdate") == 0) {
printf("%ld\n", getValue(CFSTR("isCheckUpdate")));
return 0;
} else if (strcmp(argv[1], "set_checkupdate") == 0) {
if (argc < 3) {
fprintf(stderr, "Usage: %s set_checkupdate value\n", argv[0]);
goto finish;
}
CFStringRef name = CFSTR("isCheckUpdate");
CFIndex value = atoi(argv[2]);
isSuccess = setValue(name, value);
} else if ((strcmp(argv[1], "save") == 0) || (strcmp(argv[1], "load") == 0)) {
CFIndex value = getSelectedIndex();
CFStringRef identify = getIdentify(value);
const char* targetFiles[] = {
"/Library/org.pqrs/KeyRemap4MacBook/prefpane/checkbox.xml",
"/Library/org.pqrs/KeyRemap4MacBook/prefpane/number.xml",
NULL,
};
if (strcmp(argv[1], "save") == 0) {
isSuccess = saveToFile(targetFiles, identify);
}
if (strcmp(argv[1], "load") == 0) {
system("/Library/org.pqrs/KeyRemap4MacBook/bin/KeyRemap4MacBook_sysctl_reset");
isSuccess = loadFromFile(targetFiles, identify);
}
}
CFPreferencesAppSynchronize(applicationID);
finish:
if (isSuccess) {
fprintf(stderr, "[DONE]\n");
} else {
fprintf(stderr, "[ERROR]\n");
}
return 0;
}
void LobbyGUI::newNotification(const std::string& notif) {
mLobbyOverlay->addAction( stripString(notif) );
}
void LobbyGUI::newMessage(const std::string& user, const std::string& line) {
mLobbyOverlay->addText( stripString(user), stripString(line) );
}
void gensatImageDownload(char *gensatXml, char *outDir, char *outLog)
/* gensatImageDownload - Download images from gensat guided by xml file.. */
{
struct xap *xap;
struct gsGensatImage *image;
char *ftpUri = "ftp://ftp.ncbi.nih.gov/pub/gensat";
char *jpgCgiUri = "http://www.ncbi.nlm.nih.gov/projects/gensat/gensat_img.cgi?action=image&mode=full&fmt=jpeg&id=";
char finalJpg[PATH_LEN];
char finalDir[PATH_LEN];
char wgetSource[PATH_LEN];
struct hash *dirHash = newHash(16);
struct dyString *mkdir = dyStringNew(0);
int imageIx = 0;
fLog = mustOpen(outLog, "a");
fprintf(fLog, "starting gensatImageDownload from %s to %s\n", gensatXml, outDir);
xap = xapListOpen(gensatXml, "GensatImageSet", gsStartHandler, gsEndHandler);
while ((image = xapListNext(xap, "GensatImage")) != NULL)
{
int id = image->gsGensatImageId->text;
char *imageFile = image->gsGensatImageImageInfo->gsGensatImageImageInfoFullImg
->gsGensatImageInfo->gsGensatImageInfoFilename->text;
/* Mangle file name a little */
subChar(imageFile, '(', '_');
stripChar(imageFile, ')');
/* Figure out name of jpeg file in outDir. */
verbose(1, "image %d, id %d\n", ++imageIx, id);
safef(finalJpg, sizeof(finalJpg), "%s/%s", outDir, imageFile);
stripString(finalJpg, ".full"); /* Image magick can't handle two suffixes */
chopSuffix(finalJpg);
strcat(finalJpg, ".jpg");
/* Create directory that it goes in if necessary */
splitPath(finalJpg, finalDir, NULL, NULL);
if (!hashLookup(dirHash, finalDir))
{
hashAdd(dirHash, finalDir, NULL);
dyStringClear(mkdir);
dyStringPrintf(mkdir, "mkdir -p %s", finalDir);
if (system(mkdir->string) != 0)
errAbort("Couldn't %s", mkdir->string);
}
/* Download it - either directly via ftp, or indirectly via cgi. */
if (fileExists(finalJpg))
{
verbose(1, "already have %s\n", imageFile);
fprintf(fLog, "%s already downloaded\n", finalJpg);
}
else
{
if (endsWith(imageFile, ".jpg"))
{
safef(wgetSource, sizeof(wgetSource), "%s/%s", ftpUri, imageFile);
if (safeGetOne(wgetSource, finalJpg))
fprintf(fLog, "Got via ftp %s\n", finalJpg);
}
else
{
safef(wgetSource, sizeof(wgetSource), "%s%d", jpgCgiUri, id);
if (safeGetOne(wgetSource, finalJpg))
fprintf(fLog, "Got via cgi %s\n", finalJpg);
}
}
}
carefulClose(&fLog);
}
void Songs::setData(std::string *dataInput)
{
dataString = dataInput->substr(0,dataInput->length());
std::string substring;
substring = getParent(dataInput);
stripString(&substring, "[],");
// std::cout << "OUTPUT>"<< dataString << std::endl;
std::istringstream s(substring);
s >> data.id;
substring = getParent(dataInput);
stripString(&substring, "[]");
data.Title = substring;
substring = getParent(dataInput);
stripString(&substring, "[]");
data.Artists = substring;
// data.Artists.append("\0");
substring = getParent(dataInput);
// std::cout << substring << std::endl;
stripString(&substring, "[]");
// std::cout << substring << std::endl;
int i;
std::string subSubString;
std::string token;
data.rCount = 0;
for(i = 0; ((int)substring.find("(")) != -1; i++)
{
// std::cout << "INPUT>" << substring << std::endl;
subSubString = getChild(&substring);
// std::cout << "OUTPUT>"<< subSubString << std::endl;
// std::cout << "STRLEN>" << substring.size() << std::endl;
// std::cout << "MASTER>" << substring << std::endl;
stripString(&subSubString, "()");
// std::cout << "SEARCH>" << (((int)substring.find("(")) == -1) << std::endl;
// std::cout << "CLEANED>" << subSubString << std::endl;
//std::cout << std::count(substring.begin(), substring.end(), ')') << std::endl;
//std::cout << substring << std::endl;
// std::cout << subSubString << std::endl;
token = getCSV(&subSubString);
// std::cout << "TOKEN1>" << token << std::endl;
// std::cout << "OUTPUT>"<< subSubString << std::endl;
data.ratings[i].User = token;
token = getCSV(&subSubString);
// std::cout << "TOKEN2>" << token << std::endl;
// std::cout << "OUTPUT>"<< subSubString << std::endl;
std::istringstream r(token);
// std::cout << "INT>" << integer << std::endl;
r >> data.ratings[i].rating;
data.rCount++;
}
}
static void hgPositionsJson(struct jsonWrite *jw, char *db, struct hgPositions *hgp, struct cart *cart)
/* Write out JSON description of multiple position matches. */
{
struct hgPosTable *table;
jsonWriteListStart(jw, "positionMatches");
struct trackDb *tdbList = NULL;
for (table = hgp->tableList; table != NULL; table = table->next)
{
if (table->posList != NULL)
{
char *tableName = table->name;
// clear the tdb cache if this track is a hub track
if (isHubTrack(tableName))
tdbList = NULL;
struct trackDb *tdb = tdbForTrack(db, tableName, &tdbList);
if (!tdb && startsWith("all_", tableName))
tdb = tdbForTrack(db, tableName+strlen("all_"), &tdbList);
if (!tdb)
errAbort("no track for table \"%s\" found via a findSpec", tableName);
char *trackName = tdb->track;
jsonWriteObjectStart(jw, NULL);
jsonWriteString(jw, "name", table->name);
jsonWriteString(jw, "trackName", trackName);
jsonWriteString(jw, "description", table->description);
jsonWriteString(jw, "vis", hCarefulTrackOpenVis(db, trackName));
jsonWriteListStart(jw, "matches");
struct hgPos *pos;
for (pos = table->posList; pos != NULL; pos = pos->next)
{
char *encMatches = cgiEncode(pos->browserName);
jsonWriteObjectStart(jw, NULL); // begin one match
if (pos->chrom != NULL)
jsonWriteStringf(jw, "position", "%s:%d-%d",
pos->chrom, pos->chromStart+1, pos->chromEnd);
else
// GenBank results set position to GB accession instead of chr:s-e position.
jsonWriteString(jw, "position", pos->name);
// this is magic to tell the browser to make the
// composite and this subTrack visible
if (tdb->parent)
{
if (tdbIsSuperTrackChild(tdb))
jsonWriteStringf(jw, "extraSel", "%s=show&", tdb->parent->track);
else
{
// tdb is a subtrack of a composite or a view
jsonWriteStringf(jw, "extraSel", "%s_sel=1&%s_sel=1&",
trackName, tdb->parent->track);
}
}
jsonWriteString(jw, "hgFindMatches", encMatches);
jsonWriteString(jw, "posName", htmlEncodeText(pos->name, FALSE));
if (pos->description)
{
stripString(pos->description, "\n");
jsonWriteString(jw, "description", stripAnchor(pos->description));
}
jsonWriteObjectEnd(jw); // end one match
}
jsonWriteListEnd(jw); // end matches
jsonWriteObjectEnd(jw); // end one table
}
}
jsonWriteListEnd(jw); // end positionMatches
}
/** main: initialize our shell, and loop until user specifies
* exit with the appropriate commands.
* @param c - user input (beginning with "cd ")
*/
int main(int argc, char * argv[]) {
char input[SIZE];
int fk = 0;
fillPathStack();
int OopsOrNah = -1;
bool bg = false;
if(argc == 2){
OopsOrNah = open(argv[1], O_RDWR);
if( OopsOrNah >= 0){
dup2(OopsOrNah, STDIN_FILENO);
} else {
return throwError();
}
}
// loop until user exits
while (1) {
if (OopsOrNah < 0){
char* prompt = "CShell> ";
write(STDOUT_FILENO, (void*) prompt, sizeof(prompt)-1);
}
fgets(input, SIZE, stdin);
stripString(input);
if(OopsOrNah >=0){puts(input);}
int lastcharidx = lastChar(input);
if (lastcharidx >= 0) {
if (input[lastcharidx] == '&') {
stripChar(input, '&');
stripEndSpace(input);
fk = fork();
bg = true;
}
}
//fork failed; exit
if (fk < 0) {
fprintf(stderr, "fork failed\n");
exit(1);
}
// child process: runs bash
else if (fk == 0) {
if (bg) {
strcat(input, " &");
bg = false;
}
int result = parse(input);
if (result == ERROR_CODE) {
continue;
} if (result == FORCE_EXIT) {
return SUCCESS;
}
}
//parent does nothing
else {
wait(NULL);
exit(0);
}
}
return SUCCESS;
}
