static Color cytoBandColorGiemsa(struct cytoBand *band,
struct hvGfx *hvg, Color aColor, Color bColor,
Color *shades, int maxShade)
/* Figure out color of band based on gieStain field. */
{
char *stain = band->gieStain;
if (startsWith("gneg", stain))
{
return shades[1];
}
else if (startsWith("gpos", stain))
{
int percentage = 100;
stain += 4;
if (isdigit(stain[0]))
percentage = atoi(stain);
return shades[hGrayInRange(percentage, -30, 100, maxShade)];
}
else if (startsWith("gvar", stain))
{
return shades[maxShade];
}
else
{
return bColor;
}
}
static Color colorByAltOnly(int refs, int alts, int unks)
/* Coloring alternate alleles only: shade by proportion of alt alleles to refs, unknowns */
{
if (unks > (refs + alts))
return undefYellow;
int grayIx = hGrayInRange(alts, 0, alts+refs+unks, maxShade+1) - 1; // undo force to 1
return shadesOfGray[grayIx];
}
void chainLoadItems(struct track *tg)
/* Load up all of the chains from correct table into tg->items
* item list. At this stage to conserve memory for other tracks
* we don't load the links into the components list until draw time. */
{
char *table = tg->table;
struct chain chain;
int rowOffset;
char **row;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
struct linkedFeatures *list = NULL, *lf;
int qs;
char *optionChrStr;
char extraWhere[128] ;
struct cartOptions *chainCart;
chainCart = (struct cartOptions *) tg->extraUiData;
optionChrStr = cartUsualStringClosestToHome(cart, tg->tdb, FALSE,
"chromFilter", "All");
if (startsWith("chr",optionChrStr))
{
snprintf(extraWhere, sizeof(extraWhere),
"qName = \"%s\" and score > %d",optionChrStr,
chainCart->scoreFilter);
sr = hRangeQuery(conn, table, chromName, winStart, winEnd,
extraWhere, &rowOffset);
}
else
{
if (chainCart->scoreFilter > 0)
{
snprintf(extraWhere, sizeof(extraWhere),
"score > \"%d\"",chainCart->scoreFilter);
sr = hRangeQuery(conn, table, chromName, winStart, winEnd,
extraWhere, &rowOffset);
}
else
{
snprintf(extraWhere, sizeof(extraWhere), " ");
sr = hRangeQuery(conn, table, chromName, winStart, winEnd,
NULL, &rowOffset);
}
}
while ((row = sqlNextRow(sr)) != NULL)
{
char buf[16];
chainHeadStaticLoad(row + rowOffset, &chain);
AllocVar(lf);
lf->start = lf->tallStart = chain.tStart;
lf->end = lf->tallEnd = chain.tEnd;
lf->grayIx = maxShade;
if (chainCart->chainColor == chainColorScoreColors)
{
float normScore = sqlFloat((row+rowOffset)[11]);
lf->grayIx = hGrayInRange(normScore, 0, 100, maxShade+1);
lf->score = normScore;
}
else
lf->score = chain.score;
lf->filterColor = -1;
if (chain.qStrand == '-')
{
lf->orientation = -1;
qs = chain.qSize - chain.qEnd;
}
else
{
lf->orientation = 1;
qs = chain.qStart;
}
int len = strlen(chain.qName) + 32;
lf->name = needMem(len);
safef(lf->name, len, "%s %c %dk", chain.qName, chain.qStrand, qs/1000);
safef(buf, sizeof(buf), "%d", chain.id);
lf->extra = cloneString(buf);
slAddHead(&list, lf);
}
/* Make sure this is sorted if in full mode. Sort by score when
* coloring by score and in dense */
if (tg->visibility != tvDense)
slSort(&list, linkedFeaturesCmpStart);
else if ((tg->visibility == tvDense) &&
(chainCart->chainColor == chainColorScoreColors))
slSort(&list, chainCmpScore);
else
slReverse(&list);
tg->items = list;
/* Clean up. */
sqlFreeResult(&sr);
hFreeConn(&conn);
} /* chainLoadItems() */
