src/hg/hgTracks/variation.c 1.147
1.147 2010/05/11 01:43:28 kent
Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields.
Index: src/hg/hgTracks/variation.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/variation.c,v
retrieving revision 1.146
retrieving revision 1.147
diff -b -B -U 4 -r1.146 -r1.147
--- src/hg/hgTracks/variation.c 5 Dec 2009 01:29:01 -0000 1.146
+++ src/hg/hgTracks/variation.c 11 May 2010 01:43:28 -0000 1.147
@@ -432,9 +432,9 @@
* Color calculation is used as an intermediate step to represent severity. */
{
/* snp and snpMap have different loaders that do not support the color
* attribute of the snp125Extended struct */
-if(differentString(tg->mapName,"snp") && differentString(tg->mapName,"snpMap"))
+if(differentString(tg->table,"snp") && differentString(tg->table,"snpMap"))
slSort(&tg->items, snp125ExtendedColorCmp);
}
void loadSnp125Extended(struct track *tg)
@@ -448,9 +448,9 @@
struct slList *item = itemList;
struct sqlResult *sr = NULL;
struct snp125Extended *se = NULL;
enum trackVisibility visLim = limitVisibility(tg);
-int version = snpVersion(tg->mapName);
+int version = snpVersion(tg->table);
int i = 0;
snp125AvHetCutoff = atof(cartUsualString(cart, "snp125AvHetCutoff", "0.0"));
snp125WeightCutoff = atoi(cartUsualString(cart, "snp125WeightCutoff", "3"));
@@ -507,11 +507,11 @@
snp125LocTypeIncludeCart[i] = cartUsualBoolean(cart, snp125LocTypeIncludeStrings[i], snp125LocTypeIncludeDefault[i]);
}
/* load SNPs */
-sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, NULL, &rowOffset);
+sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
-if(differentString(tg->mapName,"snp") && differentString(tg->mapName,"snpMap"))
+if(differentString(tg->table,"snp") && differentString(tg->table,"snpMap"))
while ((row = sqlNextRow(sr)) != NULL)
{
/* use loader for snp125 table format */
item = (struct slList *)snp125ExtendedLoad(row + rowOffset);
@@ -824,9 +824,9 @@
w = 1;
hvGfxBox(hvg, x1, y, w, heightPer, itemColor);
/* Clip here so that text will tend to be more visible... */
if (tg->drawName && vis != tvSquish)
- mapBoxHc(hvg, sm->chromStart, sm->chromEnd, x1, y, w, heightPer, tg->mapName, tg->mapItemName(tg, sm), NULL);
+ mapBoxHc(hvg, sm->chromStart, sm->chromEnd, x1, y, w, heightPer, tg->track, tg->mapItemName(tg, sm), NULL);
}
void snpDrawItemAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
@@ -844,9 +844,9 @@
hvGfxBox(hvg, x1, y, w, heightPer, itemColor);
/* Clip here so that text will tend to be more visible... */
if (tg->drawName && vis != tvSquish)
mapBoxHc(hvg, s->chromStart, s->chromEnd, x1, y, w, heightPer,
- tg->mapName, tg->mapItemName(tg, s), NULL);
+ tg->track, tg->mapItemName(tg, s), NULL);
}
void snp125DrawItemAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
@@ -864,9 +864,9 @@
hvGfxBox(hvg, x1, y, w, heightPer, itemColor);
/* Clip here so that text will tend to be more visible... */
if (tg->drawName && vis != tvSquish)
mapBoxHc(hvg, s->chromStart, s->chromEnd, x1, y, w, heightPer,
- tg->mapName, tg->mapItemName(tg, s), NULL);
+ tg->track, tg->mapItemName(tg, s), NULL);
}
static void snpMapDrawItems(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
@@ -879,9 +879,9 @@
int w, y;
boolean withLabels = (withLeftLabels && vis == tvPack && !tg->drawName);
if (!tg->drawItemAt)
- errAbort("missing drawItemAt in track %s", tg->mapName);
+ errAbort("missing drawItemAt in track %s", tg->track);
if (vis == tvPack || vis == tvSquish)
{
struct spaceSaver *ss = tg->ss;
@@ -920,9 +920,9 @@
hvGfxTextRight(hvg, textX, y, nameWidth, heightPer,
itemNameColor, font, name);
}
if (!tg->mapsSelf && ( ( w = x2-textX ) > 0 ))
- mapBoxHgcOrHgGene(hvg, s, e, textX, y, w, heightPer, tg->mapName, tg->mapItemName(tg, item), name, NULL, FALSE, NULL);
+ mapBoxHgcOrHgGene(hvg, s, e, textX, y, w, heightPer, tg->track, tg->mapItemName(tg, item), name, NULL, FALSE, NULL);
}
hvGfxUnclip(hvg);
}
else
@@ -950,9 +950,9 @@
int y, w;
boolean withLabels = (withLeftLabels && vis == tvPack && !tg->drawName);
if (!tg->drawItemAt)
- errAbort("missing drawItemAt in track %s", tg->mapName);
+ errAbort("missing drawItemAt in track %s", tg->track);
if (vis == tvPack || vis == tvSquish)
{
struct spaceSaver *ss = tg->ss;
struct spaceNode *sn = NULL;
@@ -1010,9 +1010,9 @@
itemNameColor, font, name);
}
}
if (!tg->mapsSelf && ( ( w = x2-textX ) > 0 ) )
- mapBoxHgcOrHgGene(hvg, s, e, textX, y, w, heightPer, tg->mapName, tg->mapItemName(tg, item), name, NULL, FALSE, NULL);
+ mapBoxHgcOrHgGene(hvg, s, e, textX, y, w, heightPer, tg->track, tg->mapItemName(tg, item), name, NULL, FALSE, NULL);
}
hvGfxUnclip(hvg);
}
else
@@ -1164,9 +1164,9 @@
static struct rgbColor blue = { 0, 0, 255};
char var[512];
char *ldPos = NULL;
-char *track = tg->tdb->parent ? tg->tdb->parent->tableName : tg->tdb->tableName;
+char *track = tg->tdb->parent ? tg->tdb->parent->track : tg->tdb->track;
safef(var, sizeof(var), "%s_pos", track);
ldPos = cartUsualString(cart, var, ldPosDefault);
ldHighLodLowDprime = hvGfxFindColorIx(hvg, 255, 224, 224); /* pink */
ldHighDprimeLowLod = hvGfxFindColorIx(hvg, 192, 192, 240); /* blue */
@@ -1217,11 +1217,11 @@
void ldLoadItems(struct track *tg)
/* loadItems loads up items for the chromosome range indicated. */
{
if (tg->tdb && sameString(tg->tdb->type, "ld2"))
- bedLoadLdItem(tg, tg->mapName, (ItemLoader)ld2Load);
+ bedLoadLdItem(tg, tg->table, (ItemLoader)ld2Load);
else
- bedLoadLdItem(tg, tg->mapName, (ItemLoader)ldLoad);
+ bedLoadLdItem(tg, tg->table, (ItemLoader)ldLoad);
tg->canPack = FALSE;
}
void mapDiamondUi(struct hvGfx *hvg, int xl, int yl, int xt, int yt,
@@ -1266,30 +1266,30 @@
void mapTrackBackground(struct track *tg, struct hvGfx *hvg, int xOff, int yOff)
/* Print out image map rectangle that invokes hgTrackUi. */
{
xOff = hvGfxAdjXW(hvg, xOff, insideWidth);
-char *track = tg->tdb->parent ? tg->tdb->parent->tableName : tg->tdb->tableName;
+char *track = tg->tdb->parent ? tg->tdb->parent->track : tg->tdb->track;
if(theImgBox && curImgTrack)
{
char link[512];
safef(link,sizeof(link),"%s?%s=%u&g=%s&i=%s",hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart), track, track);
char title[128];
- safef(title,sizeof(title),"%s controls", tg->mapName);
+ safef(title,sizeof(title),"%s controls", tg->track);
// Add map item to currnent map (TODO: pass in map)
#ifdef IMAGEv2_SHORT_MAPITEMS
if(xOff < insideX && xOff+insideWidth > insideX)
- warn("mapTrackBackground(%s) map item spanning slices. LX:%d TY:%d RX:%d BY:%d link:[%s]",tg->mapName,xOff, yOff, xOff+insideWidth, yOff+tg->height, link);
+ warn("mapTrackBackground(%s) map item spanning slices. LX:%d TY:%d RX:%d BY:%d link:[%s]",tg->track,xOff, yOff, xOff+insideWidth, yOff+tg->height, link);
#endif//def IMAGEv2_SHORT_MAPITEMS
- imgTrackAddMapItem(curImgTrack,link,title,xOff, yOff, xOff+insideWidth, yOff+tg->height, tg->mapName);
+ imgTrackAddMapItem(curImgTrack,link,title,xOff, yOff, xOff+insideWidth, yOff+tg->height, tg->track);
}
else
{
hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ",
xOff, yOff, xOff+insideWidth, yOff+tg->height);
hPrintf("HREF=\"%s?%s=%u&c=%s&g=%s&i=%s\"", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart), chromName, track, track);
- mapStatusMessage("%s controls", tg->mapName);
+ mapStatusMessage("%s controls", tg->track);
hPrintf(">\n");
}
}
@@ -1378,19 +1378,19 @@
/* also, since it only goes to hgTrackUi, it is redundant with mapTrackBackground.
* so keep this disabled until there is something more specific like an hgc
* handler for diamonds. */
if (drawMap && xt-xl>5 && xb-xl>5)
- mapDiamondUi(hvg, xl, yl, xt, yt, xr, yr, xb, yb, name, tg->mapName,
- tg->tdb->parent ? tg->tdb->parent->tableName : tg->tdb->tableName);
+ mapDiamondUi(hvg, xl, yl, xt, yt, xr, yr, xb, yb, name, tg->track,
+ tg->tdb->parent ? tg->tdb->parent->track : tg->tdb->track);
}
Color getOutlineColor(struct track *tg, int itemCount)
/* get outline color from cart and set outlineColor*/
{
char *outColor = NULL;
char var[512];
-char *track = tg->tdb->parent ? tg->tdb->parent->tableName : tg->tdb->tableName;
+char *track = tg->tdb->parent ? tg->tdb->parent->track : tg->tdb->track;
safef(var, sizeof(var), "%s_out", track);
outColor = cartUsualString(cart, var, ldOutDefault);
if (winEnd-winStart > 100000)
return 0;
@@ -1549,9 +1549,9 @@
{
static struct ldStats lds;
struct ld2 *dPtr;
char var[512];
-char *track = tg->tdb->parent ? tg->tdb->parent->tableName : tg->tdb->tableName;
+char *track = tg->tdb->parent ? tg->tdb->parent->track : tg->tdb->track;
safef(var, sizeof(var), "%s_gap", track);
boolean useTInt = cartUsualBoolean(cart, var, ldGapDefault);
for (dPtr = tg->items; dPtr != NULL; dPtr = dPtr->next)
{
@@ -1599,9 +1599,9 @@
}
else
yVisOffset = tg->heightPer + height/2;
-char *track = tg->tdb->parent ? tg->tdb->parent->tableName : tg->tdb->tableName;
+char *track = tg->tdb->parent ? tg->tdb->parent->track : tg->tdb->track;
safef(var, sizeof(var), "%s_val", track);
ldVal = cartUsualString(cart, var, ldValDefault);
if (sameString(ldVal, "lod"))
ldVal = cloneString("LOD");
@@ -1615,9 +1615,9 @@
if (isNotEmpty(tg->shortLabel) && strlen(tg->shortLabel) <= 12)
safef(label, sizeof(label), "%s %s", tg->shortLabel, ldVal);
else
{
- char *pop = cloneString(tg->mapName);
+ char *pop = cloneString(tg->table);
char *ptr = strstr(pop, "ChbJpt");
if (ptr != NULL)
safef(label, sizeof(label), "LD JPT+CHB %s", ldVal);
else if ((ptr = strstr(pop, "Ceu")) || (ptr = strstr(pop, "Chb")) ||
@@ -1686,11 +1686,11 @@
boolean ldInv;
char var[512];
boolean dynamicDense = FALSE;
-safef(var, sizeof(var), "%s_inv", tg->tdb->tableName);
+safef(var, sizeof(var), "%s_inv", tg->tdb->track);
ldInv = cartUsualBoolean(cart, var, ldInvDefault);
-char *track = tg->tdb->parent ? tg->tdb->parent->tableName : tg->tdb->tableName;
+char *track = tg->tdb->parent ? tg->tdb->parent->track : tg->tdb->track;
safef(var, sizeof(var), "%s_val", track);
ldVal = cartUsualString( cart, var, ldValDefault);
safef(var, sizeof(var), "%s_trm", track);
ldTrm = cartUsualBoolean(cart, var, ldTrmDefault);