void doJobs(struct calcJob *jobList)
{
struct calcJob *job;
for (job = jobList; job != NULL; job = job->next)
synQueuePut(toDo, job);
uglyTime("To load syn queue");
for (job = jobList; job != NULL; job = job->next)
synQueueGet(done);
}
void *workerBee(void *v)
/* Wait for jobs, and then eat them. */
{
struct calcJob *job;
for (;;)
{
job = synQueueGet(toDo);
bigCalc(job->output, job->end - job->start, job->start, job->end);
synQueuePut(done, job);
}
}
void hgExpDistance(char *database, char *posTable, char *expTable, char *outTable)
/* hgExpDistance - Create table that measures expression distance between pairs. */
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr;
char query[256];
char **row;
struct hash *expHash = hashNew(16);
int realExpCount = -1;
struct microData *gene;
int rc, t;
pthread_t *threads = NULL;
pthread_attr_t attr;
int *threadID = NULL;
void *status;
char *tempDir = ".";
int arrayNum;
struct microDataDistance *geneDistPtr = NULL;
struct microDataDistance *geneDistArray = NULL;
int geneIx;
FILE *f = NULL;
/* Get list/hash of all items with expression values. */
safef(query, sizeof(query), "select name,expCount,expScores from %s", posTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
if (!hashLookup(expHash, name))
{
int expCount = sqlUnsigned(row[1]);
int commaCount;
float *expScores = NULL;
sqlFloatDynamicArray(row[2], &expScores, &commaCount);
if (expCount != commaCount)
errAbort("expCount and expScores don't match on %s in %s", name, posTable);
if (realExpCount == -1)
realExpCount = expCount;
if (expCount != realExpCount)
errAbort("In %s some rows have %d experiments others %d",
name, expCount, realExpCount);
AllocVar(gene);
gene->expCount = expCount;
gene->expScores = expScores;
hashAddSaveName(expHash, name, gene, &gene->name);
slAddHead(&geneList, gene);
}
}
sqlFreeResult(&sr);
conn = sqlConnect(database);
slReverse(&geneList);
geneCount = slCount(geneList);
printf("Have %d elements in %s\n", geneCount, posTable);
weights = getWeights(realExpCount);
if (optionExists("lookup"))
geneList = lookupGenes(conn, optionVal("lookup", NULL), geneList);
geneCount = slCount(geneList);
printf("Got %d unique elements in %s\n", geneCount, posTable);
sqlDisconnect(&conn); /* Disconnect because next step is slow. */
if (geneCount < 1)
errAbort("ERROR: unique gene count less than one ?");
f = hgCreateTabFile(tempDir, outTable);
synQ = synQueueNew();
/* instantiate threads */
AllocArray( threadID, numThreads );
AllocArray( threads, numThreads );
pthread_attr_init( &attr );
pthread_mutex_init( &mutexDotOut, NULL );
pthread_attr_setdetachstate( &attr, PTHREAD_CREATE_JOINABLE );
for (t = 0; t < numThreads; t++) {
threadID[t] = t;
rc = pthread_create( &threads[t], &attr, computeDistance,
(void *) &threadID[t]);
if (rc)
errAbort("ERROR: in pthread_create() %d\n", rc );
}
/* this thread will write to the file from the queue */
for (arrayNum = 0; arrayNum < geneCount; arrayNum++) {
geneDistArray = (struct microDataDistance *)synQueueGet( synQ );
geneDistPtr = geneDistArray;
/* Print out closest GENEDISTS distances in tab file. */
for (geneIx=0; geneIx < GENEDISTS && geneIx < geneCount;
++geneIx, geneDistPtr++)
if (geneDistPtr != NULL)
fprintf(f, "%s\t%s\t%f\n", geneDistPtr->name1,
geneDistPtr->name2, geneDistPtr->distance);
else
errAbort("ERROR: writing distance %d to file\n",
geneIx);
freeMem( geneDistArray );
}
/* synchronize all threads */
for (t = 0; t < numThreads; t++) {
rc = pthread_join( threads[t], &status);
if (rc)
errAbort("ERROR: in pthread_join() %d\n", rc );
}
printf("Made %s.tab\n", outTable);
slFreeList( &geneList );
pthread_mutex_destroy( &mutexDotOut );
pthread_attr_destroy( &attr );
/* Create and load table. */
conn = sqlConnect(database);
distanceTableCreate(conn, outTable);
hgLoadTabFile(conn, tempDir, outTable, &f);
printf("Loaded %s\n", outTable);
/* Add indices. */
safef(query, sizeof(query), "alter table %s add index(query(12))", outTable);
sqlUpdate(conn, query);
printf("Made query index\n");
if (optionExists("targetIndex"))
{
safef(query, sizeof(query), "alter table %s add index(target(12))", outTable);
sqlUpdate(conn, query);
printf("Made target index\n");
}
hgRemoveTabFile(tempDir, outTable);
}
struct paraMessage *hubMessageGet()
/* Get message from central queue, waiting if necessary for one to appear.
* Do a paraMessageFree when you're done with this message. */
{
return synQueueGet(sq);
}
