src/hg/hgTracks/hapmapTrack.c 1.48
1.48 2010/05/11 01:43:27 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/hapmapTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/hapmapTrack.c,v
retrieving revision 1.47
retrieving revision 1.48
diff -b -B -U 4 -r1.47 -r1.48
--- src/hg/hgTracks/hapmapTrack.c 9 Mar 2009 21:17:52 -0000 1.47
+++ src/hg/hgTracks/hapmapTrack.c 11 May 2010 01:43:27 -0000 1.48
@@ -201,16 +201,16 @@
char orthoTable[HDB_MAX_TABLE_STRING];
for (i = 0; i < HAP_ORTHO_COUNT; i++)
{
- if (endsWith(tg->mapName, "PhaseII"))
+ if (endsWith(tg->table, "PhaseII"))
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%sPhaseII", hapmapOrthoSpecies[i]);
else
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%s", hapmapOrthoSpecies[i]);
- if (sameString(tg->mapName, orthoTable))
+ if (sameString(tg->table, orthoTable))
{
struct hapmapAllelesOrtho *orthoLoadItem, *orthoItemList = NULL;
- sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, NULL, &rowOffset);
+ sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
orthoLoadItem = hapmapAllelesOrthoLoad(row+rowOffset);
slAddHead(&orthoItemList, orthoLoadItem);
@@ -223,9 +223,9 @@
}
}
struct hapmapSnps *simpleLoadItem, *simpleItemList = NULL;
-sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, NULL, &rowOffset);
+sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
simpleLoadItem = hapmapSnpsLoad(row+rowOffset);
slAddHead(&simpleItemList, simpleLoadItem);
@@ -607,17 +607,17 @@
int i;
char orthoTable[HDB_MAX_TABLE_STRING];
for (i = 0; i < HAP_ORTHO_COUNT; i++)
{
- if (endsWith(tg->mapName, "PhaseII"))
+ if (endsWith(tg->table, "PhaseII"))
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%sPhaseII", hapmapOrthoSpecies[i]);
else
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%s", hapmapOrthoSpecies[i]);
- if (sameString(tg->mapName, orthoTable))
+ if (sameString(tg->table, orthoTable))
{
struct hapmapAllelesOrtho *orthoLoadItem, *orthoItemList = NULL;
struct hapmapAllelesOrtho *orthoItemsFiltered = NULL;
- sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, NULL, &rowOffset);
+ sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
orthoLoadItem = hapmapAllelesOrthoLoad(row+rowOffset);
slAddHead(&orthoItemList, orthoLoadItem);
@@ -631,9 +631,9 @@
}
}
struct hapmapSnps *simpleLoadItem, *simpleItemList = NULL, *simpleItemsFiltered = NULL;
-sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, NULL, &rowOffset);
+sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
simpleLoadItem = hapmapSnpsLoad(row+rowOffset);
slAddHead(&simpleItemList, simpleLoadItem);
@@ -733,21 +733,21 @@
return FALSE;
}
boolean loadOrthosPhaseIII(struct track *tg, struct sqlConnection *conn, struct hash *summaryHash)
-/* If tg->mapName is a hapmapAlleles table, load & filter into tg->items and return TRUE. */
+/* If tg->table is a hapmapAlleles table, load & filter into tg->items and return TRUE. */
{
int i;
char orthoTable[HDB_MAX_TABLE_STRING];
for (i = 0; i < HAP_ORTHO_COUNT; i++)
{
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%s", hapmapOrthoSpecies[i]);
- if (sameString(tg->mapName, orthoTable))
+ if (sameString(tg->table, orthoTable))
{
struct hapmapAllelesOrtho *item, *itemList = NULL;
struct hapmapPhaseIIISummary *summary;
int rowOffset;
- struct sqlResult *sr = hRangeQuery(conn, tg->mapName,
+ struct sqlResult *sr = hRangeQuery(conn, tg->table,
chromName, winStart, winEnd, NULL, &rowOffset);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
@@ -777,9 +777,9 @@
return;
struct hapmapSnps *item, *itemList = NULL;
struct hapmapPhaseIIISummary *summary;
-struct sqlResult *sr = hRangeQuery(conn, tg->mapName, chromName, winStart, winEnd, NULL, &rowOffset);
+struct sqlResult *sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
item = hapmapSnpsLoad(row+rowOffset);
summary = (struct hapmapPhaseIIISummary *)hashMustFindVal(summaryHash, item->name);
@@ -830,13 +830,13 @@
int i;
char orthoTable[HDB_MAX_TABLE_STRING];
for (i = 0; i < HAP_ORTHO_COUNT; i++)
{
- if (endsWith(tg->mapName, "PhaseII"))
+ if (endsWith(tg->table, "PhaseII"))
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%sPhaseII", hapmapOrthoSpecies[i]);
else
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%s", hapmapOrthoSpecies[i]);
- if (sameString(tg->mapName, orthoTable))
+ if (sameString(tg->table, orthoTable))
{
struct hapmapAllelesOrtho *thisItem = item;
chromStart = thisItem->chromStart;
chromEnd = thisItem->chromEnd;
@@ -896,13 +896,13 @@
int i;
char orthoTable[HDB_MAX_TABLE_STRING];
for (i = 0; i < HAP_ORTHO_COUNT; i++)
{
- if (endsWith(tg->mapName, "PhaseII"))
+ if (endsWith(tg->table, "PhaseII"))
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%sPhaseII", hapmapOrthoSpecies[i]);
else
safef(orthoTable, sizeof(orthoTable), "hapmapAlleles%s", hapmapOrthoSpecies[i]);
- if (sameString(tg->mapName, orthoTable))
+ if (sameString(tg->table, orthoTable))
{
struct hapmapAllelesOrtho *thisItem = item;
gradient = grayInRange(thisItem->score, 0, 100);
col = shadesOfBrown[gradient];