a1b655b331852fe7c80823042ccfe6d3913159cc
fanhsu
Tue Mar 8 08:22:45 2011 -0800
Updated functions for new OMIM tracks.
diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index 0414010..d3932ae 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -10938,150 +10938,336 @@
tg->nextItemButtonable = TRUE;
tg->nextPrevItem = linkedFeaturesLabelNextPrevItem;
}
void oregannoMethods (struct track *tg)
/* load so can allow filtering on type */
{
tg->loadItems = loadOreganno;
tg->itemColor = oregannoColor;
tg->itemNameColor = oregannoColor;
tg->nextItemButtonable = TRUE;
tg->nextPrevItem = linkedFeaturesLabelNextPrevItem;
}
/* reserve space no more than 20 unique OMIM entries */
-char omimGeneClass3Buffer[21 * OMIM_MAX_DESC_LEN];
+char omimGene2Buffer[21 * OMIM_MAX_DESC_LEN];
-char *omimGeneClass3DisorderList(struct track *tg, struct bed *item)
+char *omimGene2DisorderList(struct track *tg, struct bed *item)
/* Return list of disorders associated with a OMIM entry */
{
struct sqlConnection *conn;
char query[256];
struct sqlResult *sr;
char **row;
-char *chp;
-int i=0;
+int i;
+
+// initialize omimGene2Buffer
+omimGene2Buffer[0]='\0';
// get gene symbol(s) first
conn = hAllocConn(database);
safef(query,sizeof(query),
"select geneSymbol from omimGeneMap where omimId =%s", item->name);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
- safef(omimGeneClass3Buffer, sizeof(omimGeneClass3Buffer), "%s; disorder(s): ", row[0]);
+ safecat(omimGene2Buffer, sizeof(omimGene2Buffer), row[0]);
}
-chp = omimGeneClass3Buffer + (long)strlen(row[0]) + 15L;
sqlFreeResult(&sr);
safef(query,sizeof(query),
- "select distinct disorder from omimDisorderMap, omimGeneClass3 where name='%s' and name=cast(omimId as char) order by disorder", item->name);
+ "select distinct disorder from omimDisorderMap, omimGene2 where name='%s' and name=cast(omimId as char) order by disorder", item->name);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
+if (row == NULL)
+ {
+ hFreeConn(&conn);
+ sqlFreeResult(&sr);
+ return(omimGene2Buffer);
+ }
+else
+ {
+ safecat(omimGene2Buffer, sizeof(omimGene2Buffer), "; disorder(s): ");
+ }
+
/* show up to 20 max entries */
+i=0;
while ((row != NULL) && i<20)
{
- int lengthLeft = sizeof(omimGeneClass3Buffer) - strlen(omimGeneClass3Buffer);
/* omimDisorderMap disorder field some times have trailing blanks. */
eraseTrailingSpaces(row[0]);
if (i != 0)
{
- safef(chp, 3, "; ");
- chp++;chp++;
+ safecat(omimGene2Buffer, sizeof(omimGene2Buffer), "; ");
}
- safecpy(chp, lengthLeft, row[0]);
- lengthLeft = lengthLeft - strlen(row[0]) - 2;
-
- safecpy(chp, OMIM_MAX_DESC_LEN, row[0]);
-
+ safecat(omimGene2Buffer, sizeof(omimGene2Buffer), row[0]);
- chp = chp+strlen(row[0]);
row = sqlNextRow(sr);
i++;
}
+if (i == 0) errAbort("in omimGene2DisorderList(), no entry found in omimDisorderMap");
+
if ((i == 20) && (row != NULL))
{
- safef(chp, 5, " ...");
- chp++;chp++;chp++;chp++;
+ safecat(omimGene2Buffer, sizeof(omimGene2Buffer), " ...");
}
-*chp = '\0';
+hFreeConn(&conn);
+sqlFreeResult(&sr);
+return(omimGene2Buffer);
+}
+
+char *getDisorderClass(char *omimId)
+{
+struct sqlConnection *conn;
+char query[256];
+struct sqlResult *sr;
+char **row;
+char *answer;
+conn = hAllocConn(database);
+safef(query,sizeof(query),
+ "select phenotypeClass from omimDisorderPhenotype where omimId =%s", omimId);
+ sr = sqlMustGetResult(conn, query);
+ row = sqlNextRow(sr);
+if (row != NULL)
+ {
+ answer = strdup(row[0]);
+ }
+else
+ {
+ answer = strdup("0");
+ }
hFreeConn(&conn);
sqlFreeResult(&sr);
-return(omimGeneClass3Buffer);
+return(answer);
}
-static void omimGeneClass3DrawAt(struct track *tg, void *item,
+boolean doThisOmimEntry(struct track *tg, char *omimId)
+{
+char *disorderClass = NULL;
+boolean doIt;
+
+char labelName[255];
+boolean doClass1 = FALSE;
+boolean doClass2 = FALSE;
+boolean doClass3 = FALSE;
+boolean doClass4 = FALSE;
+boolean doOthers = FALSE;
+
+struct hashEl *omimLocationLabels;
+struct hashEl *label;
+
+safef(labelName, sizeof(labelName), "%s.label", tg->table);
+omimLocationLabels = cartFindPrefix(cart, labelName);
+/* if user has not made selection(s) from the filter, enable every item */
+if (omimLocationLabels == NULL) return(TRUE);
+
+/* check which classes have been selected */
+for (label = omimLocationLabels; label != NULL; label = label->next)
+ {
+ if (endsWith(label->name, "class1") && differentString(label->val, "0"))
+ {
+ doClass1 = TRUE;
+ }
+ if (endsWith(label->name, "class2") && differentString(label->val, "0"))
+ {
+ doClass2 = TRUE;
+ }
+ if (endsWith(label->name, "class3") && differentString(label->val, "0"))
+ {
+ doClass3 = TRUE;
+ }
+ if (endsWith(label->name, "class4") && differentString(label->val, "0"))
+ {
+ doClass4 = TRUE;
+ }
+ if (endsWith(label->name, "others") && differentString(label->val, "0"))
+ {
+ doOthers = TRUE;
+ }
+ }
+
+disorderClass = getDisorderClass(omimId);
+
+doIt = FALSE;
+doIt = doIt || (doClass1 && sameWord(disorderClass, "1")) ;
+doIt = doIt || (doClass2 && sameWord(disorderClass, "2")) ;
+doIt = doIt || (doClass3 && sameWord(disorderClass, "3")) ;
+doIt = doIt || (doClass4 && sameWord(disorderClass, "4")) ;
+doIt = doIt || (doOthers && sameWord(disorderClass, "0")) ;
+
+return(doIt);
+}
+
+char *omimLocationName(struct track *tg, void *item)
+/* set name for omimLcation track */
+{
+struct bed *el = item;
+
+/* return empty string if this OMIM entry should not be presented */
+if (!doThisOmimEntry(tg, el->name))
+ return("");
+else
+ return(el->name);
+}
+
+char *omimGene2Name(struct track *tg, void *item)
+/* set name for omimGene2 track */
+{
+struct bed *el = item;
+
+/* return empty string if this OMIM entry should not be presented */
+if (!doThisOmimEntry(tg, el->name))
+ return("");
+else
+ return(el->name);
+}
+
+static void omimGene2DrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single superfamily item at position. */
{
struct bed *bed = item;
char *sPhenotypes;
int heightPer = tg->heightPer;
int x1 = round((double)((int)bed->chromStart-winStart)*scale) + xOff;
int x2 = round((double)((int)bed->chromEnd-winStart)*scale) + xOff;
int w;
-sPhenotypes = omimGeneClass3DisorderList(tg, item);
+if (!doThisOmimEntry(tg, bed->name)) return;
+
+sPhenotypes = omimGene2DisorderList(tg, item);
w = x2-x1;
if (w < 1)
w = 1;
if (color)
{
hvGfxBox(hvg, x1, y, w, heightPer, color);
if (vis == tvFull)
{
hvGfxTextRight(hvg, x1-mgFontStringWidth(font, sPhenotypes)-2, y,
mgFontStringWidth(font, sPhenotypes),
heightPer, MG_BLACK, font, sPhenotypes);
}
-
if (vis != tvDense)
+ {
mapBoxHc(hvg, bed->chromStart, bed->chromEnd, x1, y, x2 - x1, heightPer,
tg->track, tg->mapItemName(tg, bed), sPhenotypes);
+ /* enable display of disorder info when user mouse over item name */
+ mapBoxHc(hvg, bed->chromStart, bed->chromEnd, x1-mgFontStringWidth(font, bed->name)-2, y,
+ mgFontStringWidth(font, bed->name), heightPer,
+ tg->track, tg->mapItemName(tg, bed), sPhenotypes);
+ }
}
if (tg->subType == lfWithBarbs)
{
int dir = 0;
if (bed->strand[0] == '+')
dir = 1;
else if(bed->strand[0] == '-')
dir = -1;
if (dir != 0 && w > 2)
{
int midY = y + (heightPer>>1);
Color textColor = hvGfxContrastingColor(hvg, color);
clippedBarbs(hvg, x1, midY, w, tl.barbHeight, tl.barbSpacing,
dir, textColor, TRUE);
}
}
}
-void omimGeneClass3Methods (struct track *tg)
+Color omimGene2Color(struct track *tg, void *item, struct hvGfx *hvg)
+/* set the color for omimLocation track items */
{
-tg->drawItemAt = omimGeneClass3DrawAt;
+struct bed *el = item;
+char *omimId;
+char *phenClass;
+char query[256];
+struct sqlResult *sr;
+char **row;
+
+struct sqlConnection *conn = hAllocConn(database);
+
+safef(query, sizeof(query),
+ "select omimId, phenotypeClass from omimDisorderPhenotype where omimId=%s", el->name);
+sr = sqlMustGetResult(conn, query);
+row = sqlNextRow(sr);
+
+hFreeConn(&conn);
+
+if (row == NULL)
+ {
+ // set to gray if this entry does not have any disorder info
+ sqlFreeResult(&sr);
+ return hvGfxFindColorIx(hvg, 200, 200, 200);
+ }
+else
+ {
+ omimId = row[0];
+ phenClass = row[1];
+
+ if (sameWord(phenClass, "3"))
+ {
+ // set to dark red, the same color as omimGene2 track
+ sqlFreeResult(&sr);
+ return hvGfxFindColorIx(hvg, 220, 0, 0);
+ }
+ else
+ {
+ if (sameWord(phenClass, "2"))
+ {
+ // set to green for class 2
+ sqlFreeResult(&sr);
+ return hvGfxFindColorIx(hvg, 0, 255, 0);
+ }
+ else
+ {
+ if (sameWord(phenClass, "1"))
+ {
+ // set to orange for class 1
+ sqlFreeResult(&sr);
+ return hvGfxFindColorIx(hvg, 200, 0, 200);
+ }
+ else
+ {
+ // set to purplish color for phenClass 4
+ sqlFreeResult(&sr);
+ return hvGfxFindColorIx(hvg, 200, 100, 100);
+ }
+ }
+
+ }
+ }
+}
+
+void omimGene2Methods (struct track *tg)
+{
+tg->itemColor = omimGene2Color;
+tg->itemName = omimGene2Name;
+tg->itemNameColor = omimGene2Color;
+tg->drawItemAt = omimGene2DrawAt;
}
char omimAvSnpBuffer[OMIM_MAX_DESC_LEN];
char *omimAvSnpAaReplacement(struct track *tg, struct bed *item)
/* Return replacement string associated with a OMIM AV entry */
{
struct sqlConnection *conn;
char query[256];
struct sqlResult *sr;
char **row;
char *chp;
omimAvSnpBuffer[0] = '\0';
@@ -11093,57 +11279,63 @@
chp = omimAvSnpBuffer;
if (row != NULL)
{
safef(omimAvSnpBuffer, sizeof(omimAvSnpBuffer), "%s, %s: %s", row[0], row[1], row[2]);
}
hFreeConn(&conn);
sqlFreeResult(&sr);
return(omimAvSnpBuffer);
}
static void omimAvSnpDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
-/* Draw a single superfamily item at position. */
+/* Draw a omimAvSnp item at position. */
{
struct bed *bed = item;
-char *sPhenotypes;
+char *itemDesc;
int heightPer = tg->heightPer;
int x1 = round((double)((int)bed->chromStart-winStart)*scale) + xOff;
int x2 = round((double)((int)bed->chromEnd-winStart)*scale) + xOff;
int w;
-sPhenotypes = omimAvSnpAaReplacement(tg, item);
+itemDesc = omimAvSnpAaReplacement(tg, item);
w = x2-x1;
if (w < 1)
w = 1;
if (color)
{
hvGfxBox(hvg, x1, y, w, heightPer, color);
if (vis == tvFull)
{
- hvGfxTextRight(hvg, x1-mgFontStringWidth(font, sPhenotypes)-2, y,
- mgFontStringWidth(font, sPhenotypes),
- heightPer, MG_BLACK, font, sPhenotypes);
+ hvGfxTextRight(hvg, x1-mgFontStringWidth(font, itemDesc)-2, y,
+ mgFontStringWidth(font, itemDesc),
+ heightPer, MG_BLACK, font, itemDesc);
}
if (vis != tvDense)
+ {
mapBoxHc(hvg, bed->chromStart, bed->chromEnd, x1, y, x2 - x1, heightPer,
- tg->track, tg->mapItemName(tg, bed), sPhenotypes);
+ tg->track, tg->mapItemName(tg, bed), itemDesc);
+ /* enable display of disorder info when user mouse over item name */
+ mapBoxHc(hvg, bed->chromStart, bed->chromEnd, x1-mgFontStringWidth(font, bed->name)-2, y,
+ mgFontStringWidth(font, bed->name), heightPer,
+ tg->track, tg->mapItemName(tg, bed), itemDesc);
+ }
}
if (tg->subType == lfWithBarbs)
{
int dir = 0;
if (bed->strand[0] == '+')
dir = 1;
else if(bed->strand[0] == '-')
dir = -1;
if (dir != 0 && w > 2)
{
int midY = y + (heightPer>>1);
Color textColor = hvGfxContrastingColor(hvg, color);
clippedBarbs(hvg, x1, midY, w, tl.barbHeight, tl.barbSpacing,
dir, textColor, TRUE);
@@ -11206,31 +11398,31 @@
hFreeConn(&conn);
if (row == NULL)
{
// set to gray if this entry does not have any disorder info
sqlFreeResult(&sr);
return hvGfxFindColorIx(hvg, 200, 200, 200);
}
else
{
omimId = row[0];
phenClass = row[1];
if (sameWord(phenClass, "3"))
{
- // set to dark red, the same color as omimGeneClass3 track
+ // set to dark red, the same color as omimGene2 track
sqlFreeResult(&sr);
return hvGfxFindColorIx(hvg, 220, 0, 0);
}
else
{
if (sameWord(phenClass, "2"))
{
// set to green for class 2
sqlFreeResult(&sr);
return hvGfxFindColorIx(hvg, 0, 255, 0);
}
else
{
if (sameWord(phenClass, "1"))
{
@@ -11250,54 +11442,59 @@
}
}
static void omimLocationDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single superfamily item at position. */
{
struct bed *bed = item;
char *omimTitle;
int heightPer = tg->heightPer;
int x1 = round((double)((int)bed->chromStart-winStart)*scale) + xOff;
int x2 = round((double)((int)bed->chromEnd-winStart)*scale) + xOff;
int w;
+/* skip if the entry is not amount the class(es) selected */
+if (!doThisOmimEntry(tg, bed->name))
+ return;
+
omimTitle = omimLocationDescription(tg, item);
w = x2-x1;
if (w < 1)
w = 1;
if (color)
{
hvGfxBox(hvg, x1, y, w, heightPer, omimLocationColor(tg, item, hvg));
if (vis == tvFull)
{
hvGfxTextRight(hvg, x1-mgFontStringWidth(font, omimTitle)-2, y,
mgFontStringWidth(font, omimTitle),
heightPer, MG_BLACK, font, omimTitle);
}
if (vis != tvDense)
mapBoxHc(hvg, bed->chromStart, bed->chromEnd, x1, y, x2 - x1, heightPer,
tg->track, tg->mapItemName(tg, bed), omimTitle);
}
}
void omimLocationMethods (struct track *tg)
{
tg->drawItemAt = omimLocationDrawAt;
+tg->itemName = omimLocationName;
tg->itemColor = omimLocationColor;
}
char *omimGeneName(struct track *tg, void *item)
/* set name for omimGene track */
{
struct bed *el = item;
char query[256];
struct sqlConnection *conn = hAllocConn(database);
char *geneLabel = NULL;
char *omimGeneLabel = cartUsualString(cart, "omimGene.label", "OMIM ID");
if (sameWord(omimGeneLabel, "OMIM ID"))
{
@@ -11339,30 +11536,52 @@
/* set the color to red if the entry is listed in morbidmap */
safef(query, sizeof(query), "select geneSymbols from omimMorbidMap where omimId=%s", el->name);
geneSymbols = sqlQuickString(conn, query);
hFreeConn(&conn);
if (geneSymbols != NULL)
{
return hvGfxFindColorIx(hvg, 255, 0, 0);
}
else
{
return hvGfxFindColorIx(hvg, 0, 0, 200);
}
}
+Color omimGeneColor2(struct track *tg, void *item, struct hvGfx *hvg)
+/* set the color for omimGene track items */
+{
+struct bed *el = item;
+char *geneSymbols;
+char query[256];
+struct sqlConnection *conn = hAllocConn(database);
+
+/* set the color to red if the entry is listed in morbidmap */
+safef(query, sizeof(query), "select geneSymbols from omimMorbidMap where omimId=%s", el->name);
+geneSymbols = sqlQuickString(conn, query);
+hFreeConn(&conn);
+if (geneSymbols != NULL)
+ {
+ return hvGfxFindColorIx(hvg, 255, 0, 0);
+ }
+else
+ {
+ return hvGfxFindColorIx(hvg, 0, 0, 200);
+ }
+}
+
/* reserve space no more than 20 unique OMIM entries */
char omimGeneBuffer[20 * OMIM_MAX_DESC_LEN];
char *omimGeneDiseaseList(struct track *tg, struct bed *item)
/* Return list of diseases associated with a OMIM entry */
{
struct sqlConnection *conn;
char query[256];
struct sqlResult *sr;
char **row;
char *chp;
int i=0;
conn = hAllocConn(database);
@@ -12711,34 +12930,34 @@
registerTrackHandler("pgTest", pgSnpMethods);
registerTrackHandler("protVarPos", protVarMethods);
registerTrackHandler("oreganno", oregannoMethods);
registerTrackHandler("encodeDless", dlessMethods);
transMapRegisterTrackHandlers();
retroRegisterTrackHandlers();
registerTrackHandler("retroposons", dbRIPMethods);
registerTrackHandlerOnFamily("kiddEichlerDisc", kiddEichlerMethods);
registerTrackHandlerOnFamily("kiddEichlerValid", kiddEichlerMethods);
registerTrackHandler("dgv", dgvMethods);
registerTrackHandlerOnFamily("hapmapSnps", hapmapMethods);
registerTrackHandlerOnFamily("hapmapSnpsPhaseII", hapmapMethods);
registerTrackHandlerOnFamily("omicia", omiciaMethods);
registerTrackHandler("omimGene", omimGeneMethods);
-registerTrackHandler("omimGeneClass3", omimGeneClass3Methods);
+registerTrackHandler("omimGene2", omimGene2Methods);
registerTrackHandler("omimAvSnp", omimAvSnpMethods);
registerTrackHandler("omimLocation", omimLocationMethods);
-registerTrackHandler("omimComposite", omimGeneClass3Methods);
+registerTrackHandler("omimComposite", omimGene2Methods);
registerTrackHandler("rest", restMethods);
#endif /* GBROWSE */
}
void createHgFindMatchHash()
/* Read from the cart the string assocated with matches and
put the matching items into a hash for highlighting later. */
{
char *matchLine = NULL;
struct slName *nameList = NULL, *name = NULL;
matchLine = cartOptionalString(cart, "hgFind.matches");
if(matchLine == NULL)
return;
nameList = slNameListFromString(matchLine,',');
hgFindMatches = newHash(5);