34c07fa95c834c1377e4e185b1a9e19499a0d536
kate
  Tue Jan 30 15:48:56 2018 -0800
Update schema, based on input from Braney. Improve map boxes. refs #17512

diff --git src/hg/hgTracks/interactTrack.c src/hg/hgTracks/interactTrack.c
index 9650397..222a187 100644
--- src/hg/hgTracks/interactTrack.c
+++ src/hg/hgTracks/interactTrack.c
@@ -1,342 +1,373 @@
 /* interactTrack -- draw interaction between two genomic regions */
 
 /* Copyright (C) 2018 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hgTracks.h"
 #include "interact.h"
 #include "interactUi.h"
 
 static int interactTotalHeight(struct track *tg, enum trackVisibility vis)
 /* calculate height of all the interactions being displayed */
 {
 if ( tg->visibility == tvDense)
     return  tl.fontHeight;
 int min, max, deflt, current; 
 cartTdbFetchMinMaxPixels(cart, tg->tdb, 
                                 INTERACT_MINHEIGHT, INTERACT_MAXHEIGHT, atoi(INTERACT_DEFHEIGHT),
                                 &min, &max, &deflt, &current);
 //uglyf("IN totalHeight=%d. ", current);
 // FIXME DEBUG
 //return 300;
 return tg->height = current;
 }
 
 static Color interactItemColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Return color to draw an interaction */
 {
 struct interact *inter = item;
 struct rgbColor itemRgb;
 // There must be a better way...
 itemRgb.r = (inter->color & 0xff0000) >> 16;
 itemRgb.g = (inter->color & 0xff00) >> 8;
 itemRgb.b = inter->color & 0xff;
 //uglyf("IN color=%X", hvGfxFindColorIx(hvg, itemRgb.r, itemRgb.g, itemRgb.b));
 return hvGfxFindColorIx(hvg, itemRgb.r, itemRgb.g, itemRgb.b);
 }
 
 void interactLoadItems(struct track *tg)
 /* Load all interact items in region */
 {
 loadSimpleBedWithLoader(tg, (bedItemLoader)interactLoad);
 }
 
+char *getOtherChrom(struct interact *inter)
+/* Get other chromosome from an interaaction. Return NULL if same chromosome */
+{
+if (sameString(inter->sourceChrom, inter->targetChrom))
+    return NULL;
+if (inter->chromStart == inter->sourceStart)
+    return cloneString(inter->targetChrom);
+return cloneString(inter->sourceChrom);
+}
+
 static void interactDrawItems(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width, 
         MgFont *font, Color color, enum trackVisibility vis)
 /* Draw a list of interact structures. */
 {
 #define DRAW_LINE       0
 #define DRAW_CURVE      1
 #define DRAW_ELLIPSE    2
 
 char *drawMode = cartUsualStringClosestToHome(cart, tg->tdb, FALSE,
                                 INTERACT_DRAW, INTERACT_DRAW_DEFAULT);
 int draw  = DRAW_LINE;
 if (sameString(drawMode, INTERACT_DRAW_CURVE))
     draw = DRAW_CURVE;
 else if (sameString(drawMode, INTERACT_DRAW_ELLIPSE))
     draw = DRAW_ELLIPSE;
 
 double scale = scaleForWindow(width, seqStart, seqEnd);
 struct interact *inters = tg->items;
 //uglyf("Found %d items. ", slCount(inters));
 unsigned int maxWidth = 0;
 struct interact *inter;
 char buffer[1024];
 char itemBuf[2048];
 safef(buffer, sizeof buffer, "%s.%s", tg->tdb->track, INTERACT_MINSCORE);
 //double minScore = sqlDouble(cartUsualString(cart, buffer, INTERACT_DEFMINSCORE));
 
 // Determine if there are mixed inter and intra-chromosomal 
 // Suppress interchromosomal labels if they overlap
 int nSame = 0, nOther = 0;
 int prevLabelEnd = 0, prevLabelStart = 0;
 char *prevLabel = 0;
 boolean doOtherLabels = TRUE;
+char *otherChrom = NULL;
 for (inter=inters; inter; inter=inter->next)
     {
     int width = inter->chromEnd - inter->chromStart;
     if (width > maxWidth)
         maxWidth = width;
     }
 //uglyf("Max width is %d. ", maxWidth);
 for (inter=inters; inter; inter=inter->next)
     {
-    if (sameString(inter->chrom1, inter->chrom2))
+    otherChrom = getOtherChrom(inter);
+    if (otherChrom == NULL)
         nSame++;
     else
         {
         nOther++;
         if (!doOtherLabels)
             continue;
-        int labelWidth = vgGetFontStringWidth(hvg->vg, font, inter->chrom2);
+        int labelWidth = vgGetFontStringWidth(hvg->vg, font, otherChrom);
         // TODO: simplify now that center approach is abandoned
         int sx = ((inter->chromStart - seqStart) + .5) * scale + xOff; // x coord of center
         int labelStart = (double)sx - labelWidth/2;
         int labelEnd = labelStart + labelWidth - 1;
-        char *otherChrom = (inter->strand[0] == '+') ? inter->chrom2 : inter->chrom1;
         if (labelStart <= prevLabelEnd && 
                 !(labelStart == prevLabelStart && labelEnd == prevLabelEnd && 
                     sameString(otherChrom, prevLabel)))
             doOtherLabels = FALSE;
         prevLabelStart = labelStart;
         prevLabelEnd = labelEnd;
-        prevLabel = inter->chrom2;
+        prevLabel = otherChrom;
         }
     }
 int fontHeight = vgGetFontPixelHeight(hvg->vg, font);
 int otherHeight = (nOther) ? 3 * fontHeight : 0;
 int sameHeight = (nSame) ? tg->height - otherHeight: 0;
 
 // Draw items
 //uglyf("IN seqStart=%d", seqStart);
 for (inter=inters; inter; inter=inter->next)
     {
+    char *otherChrom = getOtherChrom(inter);
     safef(itemBuf, sizeof itemBuf, "%s", inter->name);
     struct dyString *ds = dyStringNew(0);
     dyStringPrintf(ds, "%s", inter->name);
     if (inter->score)
         dyStringPrintf(ds, " %d", inter->score);
     char *statusBuf = dyStringCannibalize(&ds);
 //uglyf("statusBuf: %s. ", statusBuf);
 
     color = interactItemColor(tg, inter, hvg);
     
     // TODO: simplify by using start/end instead of center and width
     // This is a holdover from longRange track implementation
-
-    // set lower and upper regions from item1 and item2, which may be ordered by type rather
-    // than genomic position (e.g. item1 are snp's, item2 are genes)
     unsigned lowStart, lowEnd, highStart, highEnd;
-    if (inter->chromStart1 < inter->chromStart2)
+    if (otherChrom)
         {
-        lowStart = inter->chromStart1;
-        lowEnd = inter->chromEnd1;
-        highStart = inter->chromStart2;
-        highEnd = inter->chromEnd2;
+        lowStart = inter->chromStart;
+        lowEnd = inter->chromEnd;
         }
-    else
+    else if (inter->sourceStart < inter->targetStart)
         {
-        lowStart = inter->chromStart2;
-        lowEnd = inter->chromEnd2;
-        highStart = inter->chromStart1;
-        highEnd = inter->chromEnd1;
+        lowStart = inter->sourceStart;
+        lowEnd = inter->sourceEnd;
+        highStart = inter->targetStart;
+        highEnd = inter->targetEnd;
         }
-    // TODO: cleanup
-    if (differentString(inter->chrom1, inter->chrom2))
+    else
         {
-        lowStart = inter->chromStart;
-        lowEnd = inter->chromEnd;
+        lowStart = inter->targetStart;
+        lowEnd = inter->targetEnd;
+        highStart = inter->sourceStart;
+        highEnd = inter->sourceEnd;
         }
+
     unsigned s = lowStart + ((double)(lowEnd - lowStart + .5) / 2);
     int sx = ((s - seqStart) + .5) * scale + xOff; // x coord of center (lower region)
 //uglyf("<br>IN seqStart=%d, start=%d, start1=%d, end1=%d, start2=%d, end2=%d, end=%d, s=%d, sx=%d. ", 
         //seqStart, inter->chromStart, inter->chromStart1, inter->chromEnd1, 
         //inter->chromStart2, inter->chromEnd2, inter->chromEnd, s, sx);
     unsigned sw = lowEnd - lowStart;
     int sFootWidth = scale * (double)sw / 2;       // width in pixels of half foot (lower)
     if (sFootWidth == 0)
         sFootWidth = 1;
 
     unsigned e = highStart + (double)(highEnd - highStart + .5) / 2;
     int ex = ((e - seqStart) + .5) * scale + xOff;
     unsigned ew = highEnd - highStart;
     int eFootWidth = scale * (double)ew / 2;
     if (eFootWidth == 0)
         eFootWidth = 1;
 //uglyf("<br>IN s=%d, sx=%d, sw=%d, sFootWidth=%d.   e=%d, ex=%d, ew=%d, eFootWidth=%d, chromStart=%d",
                 //s, sx, sw, sFootWidth, e, ex, ew, eFootWidth, inter->chromStart);
 //uglyf("<br>&nbsp;&nbsp;IN start1=%d, end1=%d, start2=%d, end2=%d.",
                 //inter->chromStart1, inter->chromEnd1, inter->chromStart2, inter->chromEnd2);
 
-    if (differentString(inter->chrom1, inter->chrom2))
+    if (otherChrom)
         {
         // different chromosomes
         //      draw below same chrom items, if any
         unsigned yPos = 0;
         int height = 0;
         int yOffOther = yOff;
         if (tg->visibility == tvDense)
             {
             height = tg->height;
             }
         else
             {
             height = otherHeight/2;
             yOffOther = yOff + sameHeight;
             }
         yPos = yOffOther + height;
 
         // draw the foot
-        int footWidth = sFootWidth;
-        hvGfxLine(hvg, sx - footWidth, yOffOther, sx + footWidth, yOffOther, color);
+        hvGfxLine(hvg, sx - sFootWidth, yOffOther, sx + sFootWidth, yOffOther, color);
 
         // draw the vertical
-        if (inter->strand[0] == '+')
+        if (sameString(inter->chrom, inter->sourceChrom))
             hvGfxLine(hvg, sx, yOffOther, sx, yPos, color);
         else
             hvGfxDottedLine(hvg, sx, yOffOther, sx, yPos, color);
         if (tg->visibility == tvFull)
             {
-            mapBoxHgcOrHgGene(hvg, s, s, sx - 2, yOffOther, 4, height,
-                                   tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
-            safef(buffer, sizeof buffer, "%s", inter->strand[0] == '+' ? 
-                                        inter->chrom2 : inter->chrom1);
+            // add map box to foot
+            char *nameBuf = (inter->chromStart == inter->sourceStart ?      
+                            inter->sourceName : inter->targetName);
+uglyf("foot name: %s. ", nameBuf);
+            mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, 
+                            sx - sFootWidth, yOffOther, sFootWidth * 2, 4,
+                            tg->track, itemBuf, nameBuf, NULL, TRUE, NULL);
 
+            // add map box to vertical
+            mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, sx - 2, yOffOther, 4, height,
+                                   tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
             if (doOtherLabels)
                 {
+                safef(buffer, sizeof buffer, "%s", sameString(inter->chrom, inter->sourceChrom) ?
+                                            inter->targetChrom : inter->sourceChrom);
                 hvGfxTextCentered(hvg, sx, yPos + 2, 4, 4, MG_BLUE, font, buffer);
                 int width = vgGetFontStringWidth(hvg->vg, font, buffer);
-                mapBoxHgcOrHgGene(hvg, s, s, sx - width/2, yPos, 
+
+                // add mapBox to label
+                mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, sx - width/2, yPos, 
                                 width, fontHeight, tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
                 }
             }
         continue;
         }
 
     // draw same chromosome interaction
     boolean sOnScreen = (s >= seqStart) && (s < seqEnd);
     boolean eOnScreen = (e >= seqStart) && (e < seqEnd);
 //uglyf("<br>IN s=%d, e=%d, sOn: %d, eOn: %d. ", s, e, sOnScreen, eOnScreen);
 //if (s>e)
     //uglyf("<br>   IN s>e start=%d, start1=%d, end1=%d, start2=%d, end2=%d, end=%d, s=%d, sx=%d. ", 
         //inter->chromStart, inter->chromStart1, inter->chromEnd1, 
         //inter->chromStart2, inter->chromEnd2, inter->chromEnd, s, sx);
 
     double interWidth = e - s;
     int peakHeight = (sameHeight - 15) * ((double)interWidth / maxWidth) + 10;
     int peak = yOff + peakHeight;
     if (tg->visibility == tvDense)
         peak = yOff + tg->height;
 
     if (sOnScreen)
         {
-        // draw foot of first region and mapbox
+        // draw foot of lower region
         hvGfxLine(hvg, sx - sFootWidth, yOff, sx + sFootWidth, yOff, color);
-        mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, 
-                            sx - sFootWidth - 2, yOff, sx + sFootWidth + 2, 4,
-                            tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
         // draw vertical
         if (!eOnScreen || draw == DRAW_LINE)
             {
-            if (inter->strand[0] == '-')
+            if (inter->chromStart == inter->targetStart)
                 hvGfxDottedLine(hvg, sx, yOff, sx, peak, color);
             else
                 hvGfxLine(hvg, sx, yOff, sx, peak, color);
             }
         }
     if (eOnScreen)
         {
-        // draw foot and mapbox of second region
+        // draw foot of upper region
         hvGfxLine(hvg, ex - eFootWidth, yOff, ex + eFootWidth, yOff, color);
-        mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, 
-                            ex - eFootWidth - 2, yOff, ex + eFootWidth + 2, 4,
-                            tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
 
         // draw vertical
         if (!sOnScreen || draw == DRAW_LINE)
             {
-            if (inter->strand[0] == '-')
-                hvGfxDottedLine(hvg, ex, yOff, ex, peak, color); //OLD
+            if (inter->chromStart == inter->targetStart)
+                hvGfxDottedLine(hvg, ex, yOff, ex, peak, color);
             else
-                hvGfxLine(hvg, ex, yOff, ex, peak, color); //OLD
+                hvGfxLine(hvg, ex, yOff, ex, peak, color);
             }
         }
     if (tg->visibility == tvFull)
         {
+        char *nameBuf = NULL;
+        if (sOnScreen)
+            {
+            /* add mapbox to lower region */
+            nameBuf = (inter->chromStart == inter->sourceStart ?      
+                            inter->sourceName : inter->targetName);
+            mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, 
+                            sx - sFootWidth, yOff, sFootWidth * 2, 4,
+                            tg->track, itemBuf, nameBuf, NULL, TRUE, NULL);
+            }
+        if (eOnScreen)
+            {
+            /* add mapbox to upper region */
+            nameBuf = (inter->chromEnd == inter->targetEnd ?      
+                            inter->targetName : inter->sourceName);
+            mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, 
+                            ex - eFootWidth, yOff, eFootWidth * 2, 4,
+                            tg->track, itemBuf, nameBuf, NULL, TRUE, NULL);
+            }
         if (sOnScreen && eOnScreen && draw != DRAW_LINE)
             {
-            boolean isDotted = (inter->strand[0] == '-');
+            boolean isDotted = (inter->sourceStart > inter->targetStart);
             if (draw == DRAW_CURVE)
                 {
                 int peakX = ((ex - sx + 1) / 2) + sx;
                 int peakY = peak + 30;
                 hvGfxCurve(hvg, sx, yOff, peakX, peakY, ex, yOff, color, isDotted);
                 // map box on peak
                 // FIXME: not working
                 /*mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd,
                                     peakX - 2, peakY - 2, 4, 4,
                                     tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
 */
                 }
             else if (draw == DRAW_ELLIPSE)
                 {
                 int yLeft = yOff + peakHeight;
                 int yTop = yOff - peakHeight;
                 hvGfxEllipseDraw(hvg, sx, yLeft, ex, yTop, color, ELLIPSE_BOTTOM, isDotted);
                 // map box on peak
                 // FIXME: not working
                 /*mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd,
                                     sx - sFootWidth - 2, yOff + peakHeight, 4, 4,
                                     tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
 */
                 }
             }
         else
             {
             // draw link horizontal line between regions (dense mode just shows feet ??)
             unsigned ePeak = eOnScreen ? ex : xOff + width;
             unsigned sPeak = sOnScreen ? sx : xOff;
-            if (inter->strand[0] == '-')
+            if (inter->sourceStart > inter->targetStart)
                 hvGfxDottedLine(hvg, sPeak, peak, ePeak, peak, color);
             else
                 hvGfxLine(hvg, sPeak, peak, ePeak, peak, color);
 
             // map box on horizontal line
             mapBoxHgcOrHgGene(hvg, s, e, sPeak, peak-2, ePeak - sPeak, 4,
                                tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
 
             // map boxes on verticals
             if (sOnScreen)
                 mapBoxHgcOrHgGene(hvg, s, e, sx - 2, yOff, 4, peak - yOff,
                                        tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
             if (eOnScreen)
                 mapBoxHgcOrHgGene(hvg, s, e, ex - 2, yOff, 4, peak - yOff,
                                        tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
             }
         }
     }
 }
 
 void interactDrawLeftLabels(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)
 /* Override default */
 {
 }
 
 void interactMethods(struct track *tg)
 /* Interact track type methods */
 {
 //tg->bedSize = 6;
 //bedMethods(tg);
 tg->loadItems = interactLoadItems;
 tg->drawItems = interactDrawItems;
 tg->drawLeftLabels = interactDrawLeftLabels;
 tg->totalHeight = interactTotalHeight;
 tg->mapsSelf = TRUE;
 }