void* runWatcher(void* pArgs) {
StoreWatcher* lWatcher = (StoreWatcher*) pArgs;
Store* lStore = lWatcher->mStore;
JavaVM* lJavaVM = lWatcher->mJavaVM;
JNIEnv* lEnv = getJNIEnv(lJavaVM);
if (lEnv == NULL)
goto ERROR;
int32_t lRunning = 1;
while (lRunning) {
sleep(SLEEP_DURATION);
StoreEntry* lEntry = lWatcher->mStore->mEntries;
int32_t lScanning = 1;
while (lScanning) {
// Critical section begining, one thread at a time.
// Entries cannot be added or modified.
(*lEnv)->MonitorEnter(lEnv, lWatcher->mStoreFront);
lRunning = (lWatcher->mState == STATE_OK);
StoreEntry* lEntryEnd = lWatcher->mStore->mEntries
+ lWatcher->mStore->mLength;
lScanning = (lEntry < lEntryEnd);
if (lRunning && lScanning) {
processEntry(lEnv, lWatcher, lEntry);
}
// Critical section end.
(*lEnv)->MonitorExit(lEnv, lWatcher->mStoreFront);
// Goes to next element.
++lEntry;
}
}
ERROR: (*lJavaVM)->DetachCurrentThread(lJavaVM);
pthread_exit(NULL);
}
static int processSection(xmlElement *element, xml2lpc_context *ctx) {
xmlNode *cur_node = NULL;
xmlNode *cur_attr = NULL;
const char *name = NULL;
for (cur_attr = (xmlNode *)element->attributes; cur_attr; cur_attr = cur_attr->next) {
dumpAttr(cur_attr, ctx);
if(strcmp((const char*)cur_attr->name, "name") == 0) {
name = (const char*)cur_attr->children->content;
}
}
if(name != NULL) {
for (cur_node = element->children; cur_node; cur_node = cur_node->next) {
dumpNode(cur_node, ctx);
if (cur_node->type == XML_ELEMENT_NODE) {
if(strcmp((const char*)cur_node->name, "entry") == 0 ) {
processEntry((xmlElement*)cur_node, name, ctx);
}
}
}
} else {
xml2lpc_log(ctx, XML2LPC_WARNING, "ignored section with no \"name\" attribute, line:%d", xmlGetLineNo((xmlNode*)element));
}
return 0;
}
void extractAccsFromGb(char *gbFile, boolean missingOk, char *accFile,
char **accNames, int accCount)
/* Parse records of genBank file and print ones that match accession names. */
{
FILE *out = stdout;
struct hash *accTbl = hashNew(0);
struct lineFile *lf;
struct dyString* headLines = dyStringNew(4096);
int i;
if (accFile != NULL)
loadAccs(accFile, accTbl);
for (i = 0; i < accCount; i++)
addAcc(accTbl, accNames[i]);
/* process file */
lf = lineFileOpen(gbFile, TRUE);
while (seekLocus(lf))
processEntry(lf, accTbl, headLines, out);
lineFileClose(&lf);
/* flush and check for errors */
carefulClose(&out);
if (!missingOk)
checkMissedAccs(accTbl);
}
int main (int argc, char *argv[])
{
MrfEntry *currEntry;
int mode;
if (argc != 3) {
usage ("%s <file.annotation> <include|exclude>",argv[0]);
}
intervalFind_addIntervalsToSearchSpace (argv[1],0);
if (strEqual (argv[2],"include")) {
mode = MODE_INCLUDE;
}
else if (strEqual (argv[2],"exclude")) {
mode = MODE_EXCLUDE;
}
else {
usage ("%s <file.annotation> <include|exclude>",argv[0]);
}
mrf_init ("-");
puts (mrf_writeHeader ());
while (currEntry = mrf_nextEntry ()) {
processEntry (currEntry,mode);
}
mrf_deInit ();
return 0;
}
int main (int argc, char *argv[])
{
MrfEntry *currEntry;
char *targetName;
int targetStart,targetEnd;
WordIter w;
int count=0;
int currCount=0;
if (argc != 2) {
usage ("%s <targetName:targetStart-targetEnd>",argv[0]);
}
w = wordIterCreate (argv[1],":- ",0);
targetName = hlr_strdup (wordNext (w));
targetStart = atoi (wordNext (w));
targetEnd = atoi (wordNext (w));
wordIterDestroy (w);
mrf_init ("-");
while (currEntry = mrf_nextEntry ()) {
currCount = processEntry (currEntry,targetName,targetStart,targetEnd);
count = currCount+count;
}
printf("Count for %s:%d-%d = %d\n", targetName, targetStart, targetEnd, count);
mrf_deInit ();
hlr_free (targetName);
return 0;
}
int main (int argc, char *argv[])
{
MrfEntry *currEntry;
char *targetName;
int targetStart,targetEnd;
WordIter w;
if (argc != 2) {
usage ("%s <targetName:targetStart-targetEnd>",argv[0]);
}
w = wordIterCreate (argv[1],":- ",0);
targetName = hlr_strdup (wordNext (w));
targetStart = atoi (wordNext (w));
targetEnd = atoi (wordNext (w));
wordIterDestroy (w);
mrf_init ("-");
puts (mrf_writeHeader ());
while (currEntry = mrf_nextEntry ()) {
processEntry (currEntry,targetName,targetStart,targetEnd);
}
mrf_deInit ();
hlr_free (targetName);
return 0;
}
static void processSection_cb(const char *entry, struct __processSectionCtx *ctx) {
if(ctx->ret == 0) {
const char *comment = "#";
xmlNode *node;
xmlAttr *name_attr;
if (strncmp(comment, entry, strlen(comment)) == 0) {
lpc2xml_log(ctx->ctx, LPC2XML_WARNING, "Skipped commented entry %s", entry);
ctx->ret = 0;
return;
}
node = xmlNewChild(ctx->node, NULL, (const xmlChar *)"entry", NULL);
if(node == NULL) {
lpc2xml_log(ctx->ctx, LPC2XML_ERROR, "Can't create \"entry\" element");
ctx->ret = -1;
return;
}
name_attr = xmlSetProp(node, (const xmlChar *)"name", (const xmlChar *)entry);
if(name_attr == NULL) {
lpc2xml_log(ctx->ctx, LPC2XML_ERROR, "Can't create name attribute for \"entry\" element");
ctx->ret = -1;
return;
}
ctx->ret = processEntry(ctx->section, entry, node, ctx->ctx);
}
}
QSharedPointer<SyncObject> DatabaseSync<SO>::syncEntries()
{
qDebug() << "Running sync for type: " + getType();
// make sure root groups are the same.It has to be if we are syncing the same
// database
Q_ASSERT(db1->rootGroup()->uuid() == db2->rootGroup()->uuid());
entries1 = getEntriesMap(db1);
entries2 = getEntriesMap(db2);
QList<SO *> missingEntries;
Q_FOREACH(SO * cloudEntry, entries2) {
if (!processEntry(db2, cloudEntry)) continue;
// remote entry also exists in local database
if (entries1.contains(cloudEntry->uuid())) {
SO *localEntry = entries1[cloudEntry->uuid()];
syncEntry(localEntry, cloudEntry);
syncLocation(localEntry, cloudEntry);
}
// entry exists only in remote database
else {
missingEntries.append(cloudEntry);
}
}
if (missingEntries.length() > 0)
addMissingEntries(missingEntries);
// count whether any unique entry exist in local database
// to further decide whether we need to update remote db
Q_FOREACH(SO * localEntry, entries1) {
if (!processEntry(db1, localEntry)) continue;
if (!entries2.contains(localEntry->uuid())) {
bool isRemoved = Tools::hasChild(db1->metadata()->recycleBin(), localEntry);
if (isRemoved) {
// entry should be created and removed to recycle bin in remote database
getSyncObject()->increase(getObjectType(), SRemoved(), SRemote());
} else {
// entry is missing in remote database
getSyncObject()->increase(getObjectType(), SMissing(), SRemote());
}
}
}
return DatabaseSync::syncObject;
}
static void metaDataProcess(struct sqlConnection *conn,
struct gbStatusTbl* statusTbl,
char* raPath,
HGID faFileId, HGID pepFaId)
/* Parse a ra file looking for accessions to add to the database. If the
* ra entry matches the status->selectProc object, it will be saved for
* loading. */
{
/* parse and save all ra records, in assending file offset order */
gbMDParseOpen(raPath, conn, gOptions, gTmpDir);
while (processEntry(conn, statusTbl, faFileId, pepFaId))
continue; /* loop filler */
gbMDParseClose();
}
void SoundQueue::processEntries() {
_state = 0;
processEntry(kSoundType1);
processEntry(kSoundType2);
}
