void Sound::bgPlay(const char *base, const char *ext, SoundType type, int count) {
if (!_bgatmos)
return;
debugC(1, kDebugSound, "BackgroundAtmosphere: Playing \"%s\" (%d)", base, count);
_bgatmos->stopBA();
_bgatmos->queueClear();
int length = strlen(base) + 7;
char *fileName = new char[length];
SoundDesc *sndDesc;
for (int i = 1; i <= count; i++) {
snprintf(fileName, length, "%s%02d.%s", base, i, ext);
sndDesc = new SoundDesc;
if (sampleLoad(sndDesc, type, fileName))
_bgatmos->queueSample(*sndDesc);
else
delete sndDesc;
}
_bgatmos->playBA();
}
float aveSScoreForRegion(char *db, char *chrom, int chromStart, int chromEnd)
{
float currentSum = 0;
int count = 0;
float ave = 0;
int sPos = 0;
struct sample *sList=NULL, *s = NULL;
char *tableName = optionVal("sampleTable", "hg15Mm3L");
struct sqlConnection *conn = hAllocConn(db);
struct sqlResult *sr=NULL;
char **row;
char buff[256];
int rowOffset=0;
safef(buff,sizeof(buff),"%s_%s",chrom, tableName);
if(hTableExists(db, buff))
{
sr = hRangeQuery(conn, tableName, chrom, chromStart, chromEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
s = sampleLoad(row + rowOffset);
slAddHead(&sList, s);
}
for(s = sList; s != NULL; s = s->next)
{
int i=0;
for(i=0; i<s->sampleCount; i++)
{
sPos = s->chromStart + s->samplePosition[i];
if(sPos >= chromStart && sPos <= chromEnd)
{
currentSum += ((float) s->sampleHeight[i]) / 1000 * 8.0;
count++;
}
}
}
sqlFreeResult(&sr);
slFreeList(&sList);
}
hFreeConn(&conn);
if(count > 0)
ave = currentSum / count;
else
ave = -1;
return ave;
}
void Sound::bgPlay(const char *file, SoundType type) {
if (!_bgatmos)
return;
debugC(1, kDebugSound, "BackgroundAtmosphere: Playing \"%s\"", file);
_bgatmos->stopBA();
_bgatmos->queueClear();
SoundDesc *sndDesc = new SoundDesc;
if (!sampleLoad(sndDesc, type, file)) {
delete sndDesc;
return;
}
_bgatmos->queueSample(*sndDesc);
_bgatmos->playBA();
}
void Sound::bgPlay(const char *base, const char *ext, SoundType type, int count) {
if (!_bgatmos)
return;
debugC(1, kDebugSound, "BackgroundAtmosphere: Playing \"%s\" (%d)", base, count);
_bgatmos->stopBA();
_bgatmos->queueClear();
SoundDesc *sndDesc;
for (int i = 1; i <= count; i++) {
Common::String fileName = Common::String::format("%s%02d.%s", base, i, ext);
sndDesc = new SoundDesc;
if (sampleLoad(sndDesc, type, fileName.c_str()))
_bgatmos->queueSample(*sndDesc);
else
delete sndDesc;
}
_bgatmos->playBA();
}
void loadAffyTranscriptome(struct track *tg)
/* Convert sample info in window to linked feature. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
struct sample *sample;
struct linkedFeatures *lfList = NULL, *lf;
char *hasDense = NULL;
char *where = NULL;
char query[256];
char tableName[256];
int zoom1 = 23924, zoom2 = 2991; /* bp per data point */
float pixPerBase = 0;
/* Set it up so we don't have linear interpretation.. */
char *noLinearInterpString = wiggleEnumToString(wiggleNoInterpolation);
cartSetString(cart, "affyTranscriptome.linear.interp", noLinearInterpString);
if(tl.picWidth == 0)
errAbort("hgTracks.c::loadAffyTranscriptome() - can't have pixel width of 0");
pixPerBase = (winEnd - winStart)/ tl.picWidth;
/* Determine zoom level. */
if(pixPerBase >= zoom1)
safef(tableName, sizeof(tableName), "%s_%s", "zoom1", tg->table);
else if(pixPerBase >= zoom2)
safef(tableName, sizeof(tableName), "%s_%s", "zoom2", tg->table);
else
safef(tableName, sizeof(tableName), "%s", tg->table);
/*see if we have a summary table*/
if(hTableExists(database, tableName))
safef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tableName, tg->shortLabel);
else
{
warn("<p>Couldn't find table %s<br><br>", tableName);
safef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel);
safef(tableName, sizeof(tableName), "%s", tg->table);
}
hasDense = sqlQuickQuery(conn, query, query, sizeof(query));
/* If we're in dense mode and have a summary table load it. */
if(tg->visibility == tvDense)
{
if(hasDense != NULL)
{
safef(query, sizeof(query), " name = '%s' ", tg->shortLabel);
where = cloneString(query);
}
}
sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
sample = sampleLoad(row+rowOffset);
lf = lfFromSample(sample);
slAddHead(&lfList, lf);
sampleFree(&sample);
}
if(where != NULL)
freez(&where);
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&lfList);
/* sort to bring items with common names to the same line
but only for tracks with a summary table (with name=shortLabel) in
dense mode*/
if( hasDense != NULL )
{
sortGroupList = tg; /* used to put track name at top of sorted list. */
slSort(&lfList, lfNamePositionCmp);
sortGroupList = NULL;
}
tg->items = lfList;
}
void loadSampleZoo(struct track *tg)
/* Convert sample info in window to linked feature. */
{
int maxWiggleTrackHeight = 2500;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
struct sample *sample;
struct linkedFeatures *lfList = NULL, *lf;
char *hasDense = NULL;
char *where = NULL;
char query[256];
char option[64];
zooSpeciesHashInit();
/*see if we have a summary table*/
safef(query, sizeof(query), "select name from %s where name = '%s' limit 1", tg->table, tg->shortLabel);
//errAbort( "%s", query );
hasDense = sqlQuickQuery(conn, query, query, sizeof(query));
/* If we're in dense mode and have a summary table load it. */
if(tg->visibility == tvDense)
{
if(hasDense != NULL)
{
safef(query, sizeof(query), " name = '%s' ", tg->shortLabel);
where = cloneString(query);
}
}
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
sample = sampleLoad(row + rowOffset);
lf = lfFromSample(sample);
safef( option, sizeof(option), "zooSpecies.%s", sample->name );
if( cartUsualBoolean(cart, option, TRUE ))
slAddHead(&lfList, lf);
sampleFree(&sample);
}
if(where != NULL)
freez(&where);
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&lfList);
/* sort to bring items with common names to the same line
* but only for tracks with a summary table
* (with name=shortLabel) in dense mode */
if( hasDense != NULL )
{
sortGroupList = tg; /* used to put track name at top of sorted list. */
slSort(&lfList, lfNamePositionCmp);
sortGroupList = NULL;
}
/* Sort in species phylogenetic order */
slSort(&lfList, lfZooCmp);
tg->items = lfList;
/*turn off full mode if there are too many rows or each row is too
* large. A total of maxWiggleTrackHeight is allowed for number of
* rows times the rowHeight*/
if( tg->visibility == tvFull && sampleTotalHeight( tg, tvFull ) > maxWiggleTrackHeight )
{
tg->limitedVisSet = TRUE;
tg->limitedVis = tvDense;
}
}
void loadHumMusL(struct track *tg)
/* Load humMusL track with 2 zoom levels and one normal level.
* Also used for loading the musHumL track (called Human Cons)
* on the mouse browser. It decides which of 4 tables to
* load based on how large of a window the user is looking at*/
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
struct sample *sample;
struct linkedFeatures *lfList = NULL, *lf;
char *hasDense = NULL;
char *where = NULL;
char tableName[256];
int z;
float pixPerBase = 0;
if(tl.picWidth == 0)
errAbort("hgTracks.c::loadHumMusL() - can't have pixel width of 0");
pixPerBase = (winEnd - winStart)/ tl.picWidth;
/* Determine zoom level. */
if (!strstr(tg->table,"HMRConservation"))
z = humMusZoomLevel();
else z=0;
if(z == 1 )
safef(tableName, sizeof(tableName), "%s_%s", "zoom1",
tg->table);
else if( z == 2)
safef(tableName, sizeof(tableName), "%s_%s", "zoom50",
tg->table);
else if(z == 3)
safef(tableName, sizeof(tableName), "%s_%s",
"zoom2500", tg->table);
else
safef(tableName, sizeof(tableName), "%s", tg->table);
//printf("(%s)", tableName );
sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd,
where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
sample = sampleLoad(row+rowOffset);
lf = lfFromSample(sample);
slAddHead(&lfList, lf);
sampleFree(&sample);
}
if(where != NULL)
freez(&where);
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&lfList);
/* sort to bring items with common names to the same line
but only for tracks with a summary table (with name=shortLabel)
in
dense mode*/
if( hasDense != NULL )
{
sortGroupList = tg; /* used to put track name at
* top of sorted list. */
slSort(&lfList, lfNamePositionCmp);
sortGroupList = NULL;
}
tg->items = lfList;
}
/* Main */
int main()
{
matrix MX;
mnew(&MX, 200, 8);
sampleLoad("data_200x8.txt", &MX);
printf("data=\n");
mprint(&MX);
double mean[2][8]=
{{4.427227e-001, 7.671556e-001, -9.523772e-001, 3.867558e-001, -7.916976e-001, 1.165247e-001, -1.261666e-001, 8.550054e-002},
{-2.383899e-001, -4.130850e-001, 5.128200e-001, -2.082537e-001, 4.263000e-001, -6.274427e-002, 6.793605e-002, -4.603889e-002}};
matrix MUK;
mnew(&MUK, 2, 8);
MUK.pr = *mean;
matrix *Var0;
Var0 = new matrix[2];
for(int i=0; i<2; i++) {
mnew(Var0+i, 8, 8);
}
sampleLoad("var0.txt", Var0);
printf("var0=\n");
mprint(Var0);
sampleLoad("var1.txt", Var0+1);
printf("var1=\n");
mprint(Var0+1);
double W[] = {3.500007e-001, 6.499993e-001};
vector w0;
vnew(&w0, 2);
w0.pr = W;
matrix Gxn;
mnew(&Gxn, 200, 2);
vector Fx;
vnew(&Fx, 200);
veModel(&MX, &MUK, Var0, &w0, &Gxn, &Fx);
printf("Gxn=\n");
mprint(&Gxn);
printf("Fx=\n");
vprint(&Fx);
matrix tmp;
mnew(&tmp, 1, 8);
matrix tmp2;
mnew(&tmp2, 1, 1);
matrix cen_Dj;
mnew(&cen_Dj, 1, 8);
matrix cen_Dj_t;
mnew(&cen_Dj_t, 8, 1);
for(i=0; i<8; i++) {
*(cen_Dj.pr+i) = *(MX.pr+0+i) - *(MUK.pr+8+i);
}
transpose(&cen_Dj, &cen_Dj_t);
printf("\ncen_Dj=\n");
mprint(&cen_Dj);
mprint(&cen_Dj_t);
matrix inv_Var1;
mnew(&inv_Var1, 8, 8);
sampleLoad("inv_var1.txt", &inv_Var1);
mprint(&inv_Var1);
mmMul(&cen_Dj, &inv_Var1, &tmp);
printf("\ntmp=\n");
mprint(&tmp);
mmMul(&tmp, &cen_Dj_t, &tmp2);
printf("\ntmp2=\n");
mprint(&tmp2);
double val = *(tmp2.pr);
printf("\nval=%e\n", val);
mdelete(&MX);
mdelete(&MUK);
mdelete(Var0);
mdelete(Var0+1);
vdelete(&w0);
mdelete(&Gxn);
vdelete(&Fx);
return 0;
}
