6b66802e4a900fb25d4d55c86b2625662f390021
kent
  Sat Jun 12 22:49:27 2010 -0700
Improved a few more comments.
diff --git src/hg/hgTracks/multiWig.c src/hg/hgTracks/multiWig.c
index 1f6ce87..be4e725 100644
--- src/hg/hgTracks/multiWig.c
+++ src/hg/hgTracks/multiWig.c
@@ -1,153 +1,156 @@
 /* A container for multiple wiggles with a couple of options for combining them. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "dystring.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "container.h"
 #include "wigCommon.h"
 #include "hui.h"
 
 static boolean isOverlayTypeAggregate(char *aggregate)
 /* Return TRUE if aggregater type is one of the overlay ones. */
 {
 if (aggregate == NULL)
     return FALSE;
 return differentString(aggregate, WIG_AGGREGATE_NONE);
 }
 
 
 static void multiWigDraw(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width, 
         MgFont *font, Color color, enum trackVisibility vis)
-/* Draw items in container. */
+/* Draw items in multiWig container. */
 {
 struct track *subtrack;
 char *aggregate = cartOrTdbString(cart, tg->tdb, "aggregate", NULL);
 boolean overlay = isOverlayTypeAggregate(aggregate);
 int y = yOff;
 for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
     {
     if (isSubtrackVisible(subtrack))
 	{
 	int height = subtrack->totalHeight(subtrack, vis);
 	hvGfxSetClip(hvg, xOff, y, width, height);
         if (sameString(WIG_AGGREGATE_TRANSPARENT, aggregate))
             hvGfxSetWriteMode(hvg, MG_WRITE_MODE_MULTIPLY);
 	if (overlay)
 	    subtrack->lineHeight = tg->lineHeight;
 	subtrack->drawItems(subtrack, seqStart, seqEnd, hvg, xOff, y, width, font, color, vis);
 	if (!overlay)
 	    y += height + 1;
         hvGfxSetWriteMode(hvg, MG_WRITE_MODE_NORMAL);
 	hvGfxUnclip(hvg);
 	}
     }
 char *url = trackUrl(tg->track, chromName);
 mapBoxHgcOrHgGene(hvg, seqStart, seqEnd, xOff, y, width, tg->height, tg->track, tg->track, NULL,
 	      url, TRUE, NULL);
 }
 
 static int multiWigTotalHeight(struct track *tg, enum trackVisibility vis)
-/* Return total height of container. */
+/* Return total height of multiWigcontainer. */
 {
 char *aggregate = cartOrTdbString(cart, tg->tdb, "aggregate", NULL);
 boolean overlay = isOverlayTypeAggregate(aggregate);
 int totalHeight =  0;
 if (overlay)
     totalHeight =  wigTotalHeight(tg, vis);
 struct track *subtrack;
 for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
     {
     if (isSubtrackVisible(subtrack))
 	{
+	// Logic is slightly complicated by fact we want to call the totalHeight
+	// method for each subtrack even if in overlay mode.
 	int oneHeight = subtrack->totalHeight(subtrack, vis);
 	if (!overlay)
 	    {
 	    if (totalHeight != 0)
 	       totalHeight += 1;
 	    totalHeight += oneHeight;
 	    }
 	}
     }
 tg->height = totalHeight;
 return totalHeight;
 }
 
 static boolean graphLimitsAllSame(struct track *trackList, struct track **retFirstTrack)
 /* Return TRUE if graphUpperLimit and graphLowerLimit same for all tracks. */
 {
 struct track *firstTrack = NULL;
 struct track *track;
 for (track = trackList; track != NULL; track = track->next)
     {
     if (isSubtrackVisible(track))
         {
 	if (firstTrack == NULL)
 	    *retFirstTrack = firstTrack = track;
 	else if (track->graphUpperLimit != firstTrack->graphUpperLimit 
 	    || track->graphLowerLimit != firstTrack->graphLowerLimit)
 	    return FALSE;
 	}
     }
 return firstTrack != NULL;
 }
 
 static void multiWigLeftLabels(struct track *tg, int seqStart, int seqEnd,
 	struct hvGfx *hvg, int xOff, int yOff, int width, int height,
 	boolean withCenterLabels, MgFont *font, Color color,
 	enum trackVisibility vis)
 /* Draw left labels - by deferring to first subtrack. */
 {
 char *aggregate = cartOrTdbString(cart, tg->tdb, "aggregate", NULL);
 boolean overlay = isOverlayTypeAggregate(aggregate);
 if (overlay)
     {
     struct track *firstVisibleSubtrack = NULL;
     boolean showNumbers = graphLimitsAllSame(tg->subtracks, &firstVisibleSubtrack);
     struct track *subtrack = (showNumbers ? firstVisibleSubtrack : tg->subtracks);
     wigLeftAxisLabels(tg, seqStart, seqEnd, hvg, xOff, yOff, width, height, withCenterLabels,
 	    font, color, vis, tg->shortLabel, subtrack->graphUpperLimit, 
 	    subtrack->graphLowerLimit, showNumbers);
     }
 else
     {
     struct track *subtrack;
     int y = yOff;
     if (withCenterLabels)
        y += tl.fontHeight+1;
     for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
 	{
 	if (isSubtrackVisible(subtrack))
 	    {
 	    int height = subtrack->totalHeight(subtrack, vis);
 	    wigLeftAxisLabels(subtrack, seqStart, seqEnd, hvg, xOff, y, width, height, withCenterLabels,
 	    	font, subtrack->ixColor, vis, subtrack->shortLabel, subtrack->graphUpperLimit,
 		subtrack->graphLowerLimit, TRUE);
 	    y += height+1;
 	    }
 	}
     }
 }
 
 void multiWigLoadItems(struct track *track)
+/* Load multiWig items. */
 {
 containerLoadItems(track);
 struct track *subtrack;
 for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next)
     {
     subtrack->mapsSelf = FALSE;	/* Round about way to tell wig not to do own mapping. */
     }
 }
 
 void multiWigContainerMethods(struct track *track)
 /* Override general container methods for multiWig. */
 {
 track->loadItems = multiWigLoadItems;
 track->totalHeight = multiWigTotalHeight;
 track->drawItems = multiWigDraw;
 track->drawLeftLabels = multiWigLeftLabels;
 }