5b97c90762187cf1993742fe8c422308e08d082c
tdreszer
  Wed Jul 11 17:08:55 2012 -0700
Next batch of many checkins as dictated by Jim.  Formatting if and limiting lines to 100 chars.  Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history.  None of these changes should affect executables in any way.
diff --git src/hg/hgTracks/wigMafTrack.c src/hg/hgTracks/wigMafTrack.c
index c993ab0..46c14c6 100644
--- src/hg/hgTracks/wigMafTrack.c
+++ src/hg/hgTracks/wigMafTrack.c
@@ -178,31 +178,32 @@
 char *speciesOrder = trackDbSetting(track->tdb, SPECIES_ORDER_VAR);
 char *speciesGroup = trackDbSetting(track->tdb, SPECIES_GROUP_VAR);
 char *speciesOff = trackDbSetting(track->tdb, SPECIES_DEFAULT_OFF_VAR);
 
 bool lowerFirstChar = TRUE;
 char *firstCase;
 
 firstCase = trackDbSetting(track->tdb, ITEM_FIRST_CHAR_CASE);
 if (firstCase != NULL)
     {
     if (sameWord(firstCase, "noChange")) lowerFirstChar = FALSE;
     }
 
 #ifndef BRANEY_SAYS_USETARG_IS_OBSOLETE
 char buffer[128];
-safef(buffer, sizeof(buffer), "%s.vis",track->track); // According to Tim, this makes no sense as "vis"
+// According to Tim, this makes no sense as ".vis"
+safef(buffer, sizeof(buffer), "%s.vis",track->track);
 if (!cartVarExists(cart, buffer) && (speciesTarget != NULL))
     useTarg = TRUE;
 else
     {
     char *val;
 
     val = cartUsualString(cart, buffer, "useCheck");
     useTarg = sameString("useTarg",val);
     }
 
 if (useTarg && (tree = phyloParseString(speciesTree)) == NULL)
     useTarg = FALSE;
 #endif///ndef BRANEY_SAYS_USETARG_IS_OBSOLETE
 
 if (speciesOrder == NULL && speciesGroup == NULL && speciesUseFile == NULL)
@@ -769,31 +770,31 @@
 }
 
 static int wigMafTotalHeight(struct track *track, enum trackVisibility vis)
 /* Return total height of maf track.  */
 {
 struct wigMafItem *mi;
 int total = 0,count=0;
 for (mi = track->items; mi != NULL; mi = mi->next)
     {
     total += mi->height;
     count++;
     }
 
 track->height = total;
 if (track->limitedVis == tvDense)
-    track->height=(tl.fontHeight+1)*count; // Evidence that track-height comes in as 9 but should be 10!
+    track->height=(tl.fontHeight+1)*count; // Evidence that track->height is 9 but should be 10!
 return track->height;
 }
 
 static int wigMafItemHeight(struct track *track, void *item)
 /* Return total height of maf track.  */
 {
 struct wigMafItem *mi = item;
 return mi->height;
 }
 
 static void wigMafFree(struct track *track)
 /* Free up maf items. */
 {
 struct mafPriv *mp = getMafPriv(track);
 if (mp->list != NULL && mp->list != (char *)-1)
@@ -2171,32 +2172,34 @@
 	if (label->stringSize > haveRoomFor)
 	    {
 	    dyStringClear(label);
 	    dyStringPrintf(label, "%c",(insertCounts[offset] % 3) == 0 ? '*' : '+');
 	    }
 	hvGfxTextCentered(hvg, x1+x - (width/winBaseCount)/2, y, x2-x1, mi->height,
 		getOrangeColor(), font, label->string);
 	dyStringFree(&label);
 	}
     }
 y += mi->height;
 
 /* draw alternating colors behind base-level alignments */
     {
     int alternateColorBaseCount, alternateColorBaseOffset;
-    alternateColorBaseCount = cartUsualIntClosestToHome(cart, track->tdb, FALSE, BASE_COLORS_VAR, 0);
-    alternateColorBaseOffset = cartUsualIntClosestToHome(cart, track->tdb, FALSE, BASE_COLORS_OFFSET_VAR, 0);
+    alternateColorBaseCount =
+            cartUsualIntClosestToHome(cart, track->tdb, FALSE, BASE_COLORS_VAR, 0);
+    alternateColorBaseOffset =
+            cartUsualIntClosestToHome(cart, track->tdb, FALSE, BASE_COLORS_OFFSET_VAR, 0);
     if (alternateColorBaseCount != 0)
         {
         int baseWidth = spreadStringCharWidth(width, winBaseCount);
         int colorX = x + alternateColorBaseOffset * baseWidth;
         alternateBlocksBehindChars(hvg, colorX, y-1, width,
                 mi->height*(lineCount-1), tl.mWidth, winBaseCount,
                 alternateColorBaseCount, shadesOfSea[0], MG_WHITE);
         }
     }
 
 /* draw base-level alignments */
 for (mi = miList->next, i=1; mi != NULL && mi->db != NULL; mi = mi->next, i++)
     {
     char *line;
 
@@ -2267,31 +2270,30 @@
 		if (mf.chromEnd > seqEnd)
 		    frame = (frame + mf.chromEnd-seqEnd  ) % 3;
 		}
 	    else
 		{
 		if (mf.chromStart < seqStart)
 		    frame = (frame + seqStart-mf.chromStart  ) % 3;
 		}
 
 	    end = mf.chromEnd > seqEnd ? seqEnd - seqStart  : mf.chromEnd - seqStart;
 	    w= end - start;
 
 	    translateCodons(conn2, conn3, tableName, mi->db, line, start ,
 		w, frame, mf.strand[0],mf.prevFramePos,mf.nextFramePos,
 		complementBases, x, y, width, mi->height,  hvg, mafFile);
-
 	    }
 	sqlFreeResult(&sr);
 
 	if (!found)
 	    {
 	    /* try the default species */
 	    safef(extra, sizeof(extra), "src='%s'",defaultCodonSpecies);
 
 	    found = TRUE; /* don't try again */
 	    goto tryagain;
 	    }
 
 	hFreeConn(&conn);
 	}