bfdef4b81463c8e17b972da81c3fa7d94118af22
kate
Wed Oct 10 14:04:37 2018 -0700
Cleanup.
diff --git src/hg/hgTracks/interactTrack.c src/hg/hgTracks/interactTrack.c
index ecf21f5..6994269 100644
--- src/hg/hgTracks/interactTrack.c
+++ src/hg/hgTracks/interactTrack.c
@@ -145,69 +145,68 @@
return (struct interactLfEndNames *)lf->original;
}
void interactFreeItems(struct track *tg)
/* Free up interact items track */
{
interactFreeList((struct interact **)(&tg->items));
}
static struct linkedFeatures *interactToLf(struct interact *inter, boolean doColor)
/* Convert interact BED to linkedFeatures */
{
struct bed *bed = interactToBed(inter);
struct linkedFeatures *lf = lfFromBed(bed);
-// save source and target names to extra field of linked feature, so we can display them in pack mode
+// save source and target names to extra field of linked feature, so we can display them
+// in pack mode
// TODO: code to free
setInteractLfEndNames(lf, cloneString(inter->sourceName), cloneString(inter->targetName));
// not sure why this is needed -- lfFromBed seems to reorder blocks, sometimes ?
linkedFeaturesSortAndBound(lf);
if (doColor)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor = bed->itemRgb;
}
bedFree(&bed);
-// TODO: use lfFromBedExtra with scoreMin, scoreMax ?
return lf;
}
static boolean isLinkedFeaturesMode(struct track *tg)
/* Determine if linked feature display will be used */
{
return (tg->visibility != tvFull);
}
int interactSize(struct interact *inter)
/* Compute length of interaction (distance between middle of each region) in bp */
{
int sourceCenter = 0, targetCenter = 0;
interactRegionCenters(inter, &sourceCenter, &targetCenter);
return abs(targetCenter - sourceCenter);
}
int getX(int pos, int seqStart, double scale, int xOff)
/* Get x coordinate of a genomic location. Return -1 if off-screen */
{
if (pos < seqStart)
return -1;
return ((double)(pos - seqStart + .5) * scale) + xOff;
}
-
static void setYOff(struct track *tg, int yOff)
/* Stash y offset for this track */
{
tg->customInt = yOff;
}
static int getYOff(struct track *tg)
/* Get y offset for this track (stashed by DrawItems) */
{
return tg->customInt;
}
static int flipY(struct track *tg, int y)
/* Invert y coordinate if flipped display is requested */
{
@@ -286,39 +285,30 @@
struct interactLfEndNames *ends = getInteractLfEndNames(lf);
char *rightLabel = ends->target;
if (lf->orientation != 0)
rightLabel = (lf->orientation < 0 ? ends->source : ends->target);
return mgFontStringWidth(tl.font, rightLabel);
}
static char *interactLfLeftEndName(struct track *tg, void *item)
/* Return name of left end in single interaction linked feature, for left label */
{
struct linkedFeatures *lf = (struct linkedFeatures *)item;
struct interactLfEndNames *ends = getInteractLfEndNames(lf);
return (lf->orientation < 0 ? ends->target : ends->source);
}
-#ifdef FOO
-static char *interactLfItemName(struct track *tg, void *item)
-/* Return item name of interaction linked feature, for map */
-{
-struct linkedFeatures *lf = (struct linkedFeatures *)item;
-return lf->name;
-}
-#endif
-
static void interactLfMapItem(struct track *tg, struct hvGfx *hvg, void *item,
char *itemName, char *mapItemName, int start, int end,
int x, int y, int width, int height)
/* Draw mapbox on interact item when displayed as linked feature */
{
struct linkedFeatures *lf = (struct linkedFeatures *)item;
// restore full item name (using end name for label)
itemName = mapItemName = lf->name;
linkedFeaturesMapItem(tg, hvg, item, itemName, mapItemName, start, end, x, y, width, height);
}
void interactLoadItems(struct track *tg)
/* Load interact items in interact format */
{
loadAndFilterItems(tg);
@@ -332,31 +322,30 @@
tInfo->clusterMode = interactUiClusterMode(cart, tg->track, tg->tdb);
if (!tInfo->clusterMode && !isLinkedFeaturesMode(tg))
{
// draw curve display
tg->mapsSelf = TRUE;
tg->totalHeight = interactTotalHeight;
tg->drawLeftLabels = interactNoLeftLabels;
tg->freeItems = interactFreeItems;
return;
}
// convert to BEDs for linked feature display
tg->itemName = interactLfLeftEndName;
tg->mapItem = interactLfMapItem;
-//tg->mapItemName = interactLfItemName;
struct interact *inters = tg->items, *inter;
struct linkedFeatures *lfs = NULL, *lf;
struct hash *intersCluster = hashNew(0);
boolean doColor = !tg->colorShades;
for (inter = inters; inter; inter = inter->next)
{
if (tInfo->clusterMode)
{
boolean byTarget = sameString(tInfo->clusterMode, INTERACT_CLUSTER_TARGET);
// hash by source or target name
char *name = (byTarget ? inter->targetName : inter->sourceName);
lf = (struct linkedFeatures *) hashFindVal(intersCluster, name);
if (lf)
{
// add a simple feature for the other end (source or target) to the linked feature
@@ -554,31 +543,31 @@
char buffer[1024];
char itemBuf[2048];
// Gather info for layout
interactGetLayoutInfo(tg, seqStart, hvg, xOff, font, scale);
struct interactTrackInfo *tInfo = (struct interactTrackInfo *)tg->customPt;
setYOff(tg, yOff); // TODO: better to stash this in tInfo, and save that in track struct */
int highlightColor = MG_WHITE;
boolean drawUp = trackDbSettingClosestToHomeOn(tg->tdb, INTERACT_UP) && vis == tvFull;
// Get spectrum range
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000"));
// Draw items
-struct hash *footHash = hashNew(0); // track feet so we can override color to black for overlapping
+struct hash *footHash = hashNew(0); // track feet so we can override color to black
struct hash *footHashOther = hashNew(0); // has for items on other chrom
for (inter = (struct interact *)tg->items; inter; inter = inter->next)
{
char *otherChrom = interactOtherChrom(inter);
safef(itemBuf, sizeof itemBuf, "%s", inter->name);
char *statusBuf = interactMouseover(inter, otherChrom);
// Pick colors
#define MG_LIGHT_MAGENTA 0xffffbbff
#define MG_LIGHT_GRAY 0xff909090
color = interactItemColor(tg, inter, hvg, scoreMin, scoreMax);
if (vis == tvDense && otherChrom && color == MG_BLACK)
// use highlight color for other chrom items in dense mode
color = MG_LIGHT_MAGENTA;
@@ -598,31 +587,32 @@
else
{
height = tInfo->otherHeight/2;
yOffOther = yOff + tInfo->sameHeight;
}
unsigned r = interactRegionCenter(inter->chromStart, inter->chromEnd);
int x = getX(r, seqStart, scale, xOff);
int footWidth = regionFootWidth(inter->chromStart, inter->chromEnd, scale);
unsigned yPos = yOffOther + height;
// draw the foot (2 pixels high)
drawFoot(tg, hvg, inter->chrom, inter->chromStart, inter->chromEnd,
x - footWidth, yOffOther, footWidth + footWidth + 1, color, drawUp, footHashOther);
// draw the vertical
- boolean isReversed = tInfo->isDirectional && differentString(inter->chrom, inter->sourceChrom);
+ boolean isReversed = tInfo->isDirectional &&
+ differentString(inter->chrom, inter->sourceChrom);
drawLine(tg, hvg, x, yOffOther, x, yPos, color, isReversed && doDashes, drawUp);
if (vis == tvDense)
continue;
// add map box to foot
char *nameBuf = (inter->chromStart == inter->sourceStart ?
inter->sourceName : inter->targetName);
drawFootMapbox(tg, hvg, inter->chromStart, inter->chromEnd, nameBuf, statusBuf,
x - footWidth, yOffOther, footWidth, peakColor, highlightColor, drawUp);
// add map box to vertical
mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, x - 2, yOffOther, 4,
height, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
@@ -780,31 +770,31 @@
}
hvGfxEllipseDraw(hvg, lowerX, yLeft, upperX, yTop, color, ellipseOrient,
isReversed && doDashes);
// draw grab box and map box on peak
int maxY = peakHeight + yOff;
int peakX = ((upperX - lowerX + 1) / 2) + lowerX;
drawPeakMapbox(tg, hvg, inter->chromStart, inter->chromEnd, inter->name, statusBuf,
peakX, maxY, peakColor, highlightColor, drawUp);
}
}
}
void interactLinkedFeaturesDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
-/* Draw a item with target in contrasting color */
+/* Draw an item with target in contrasting color */
{
struct linkedFeatures *lf = item;
if (vis == tvDense)
{
lf->filterColor = slightlyDarkerColor(hvg, MG_GRAY);
// can't distinguish overlapping colors, so force to gray
}
struct interactTrackInfo *tInfo = tg->customPt;
linkedFeaturesDrawAt(tg, item, hvg, xOff, y, scale, font, color, vis);
// draw overlapping items in white and add right label
if (tInfo->clusterMode)
{
struct simpleFeature *sf;