f4424a364948c3f69cf55d42ea04ae15eb71e476 kent Fri Jul 2 18:56:59 2010 -0700 Removing unused routine. diff --git src/hg/hgc/encodeClick.c src/hg/hgc/encodeClick.c index 70accbb..9e07798 100644 --- src/hg/hgc/encodeClick.c +++ src/hg/hgc/encodeClick.c @@ -1,204 +1,188 @@ /* Handle details page for ENCODE tracks. */ #include "common.h" #include "cart.h" #include "hgc.h" #include "hCommon.h" #include "hgColors.h" #include "customTrack.h" #include "web.h" #include "encode/encodePeak.h" static boolean pairInList(struct slPair *pair, struct slPair *list) /* Return TRUE if pair is in list. */ { struct slPair *el; for (el = list; el != NULL; el = el->next) if (sameString(pair->name, el->name) && sameString(pair->val, el->val)) return TRUE; return FALSE; } static boolean selGroupListMatch(struct trackDb *tdb, struct slPair *selGroupList) /* Return TRUE if tdb has match to every item in selGroupList */ { char *subGroups = trackDbSetting(tdb, "subGroups"); if (subGroups == NULL) return FALSE; struct slPair *groupList = slPairFromString(subGroups); struct slPair *selGroup; for (selGroup = selGroupList; selGroup != NULL; selGroup = selGroup->next) { if (!pairInList(selGroup, groupList)) return FALSE; } return TRUE; } static void rAddMatching(struct trackDb *tdb, struct slPair *selGroupList, struct slName **pList) /* Add track and any descendents that match selGroupList to pList */ { if (selGroupListMatch(tdb, selGroupList)) slNameAddHead(pList, tdb->track); struct trackDb *sub; for (sub = tdb->subtracks; sub != NULL; sub = sub->next) rAddMatching(sub, selGroupList, pList); } -struct slName *encodeFindMatchingSubtracks(struct slName *inTrackList, struct slPair *selGroupList) -/* Look at a list of tracks, and their descendents for tracks with groups that match all - * name/value pairs in selGroupList */ -{ -struct slName *matchList = NULL; -struct slName *inTrack; -for (inTrack = inTrackList; inTrack != NULL; inTrack = inTrack->next) - { - struct trackDb *tdb = hashFindVal(trackHash, inTrack->name); - if (tdb == NULL) - errAbort("Can't find track %s which is in inputTracks", inTrack->name); - rAddMatching(tdb, selGroupList, &matchList); - } -return matchList; -} - void doEncodePeak(struct trackDb *tdb, struct customTrack *ct) /* details for encodePeak type tracks. */ { struct sqlConnection *conn; struct sqlResult *sr; enum encodePeakType peakType; char **row; char *db; char *table = tdb->table; char *chrom = cartString(cart,"c"); int start = cgiInt("o"); int end = cgiInt("t"); int rowOffset; /* connect to DB */ if (ct) { db = CUSTOM_TRASH; table = ct->dbTableName; } else db = database; conn = hAllocConn(db); peakType = encodePeakInferTypeFromTable(db, table, tdb->type); if (peakType == 0) errAbort("unrecognized peak type from table %s", tdb->table); genericHeader(tdb, NULL); sr = hOrderedRangeQuery(conn, table, chrom, start, end, NULL, &rowOffset); while((row = sqlNextRow(sr)) != NULL) { char **rowPastOffset = row + rowOffset; if ((sqlUnsigned(rowPastOffset[1]) != start) || (sqlUnsigned(rowPastOffset[2]) != end)) continue; float signal = -1; float pValue = -1; float qValue = -1; /* Name */ if (rowPastOffset[3][0] != '.') printf("Name: %s
\n", rowPastOffset[3]); /* Position */ printf("Position: " "%s:%d-%d
\n", hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end); /* Print peak base */ if ((peakType == narrowPeak) || (peakType == encodePeak)) { int peak = sqlSigned(rowPastOffset[9]); if (peak > -1) printf("Peak point: %d
\n", start + peak + 1); // one based } /* Strand, score */ if (rowPastOffset[5][0] != '.') printf("Strand: %c
\n", rowPastOffset[5][0]); printf("Score: %d
\n", sqlUnsigned(rowPastOffset[4])); /* signalVal, pVal */ if (peakType != gappedPeak) { signal = sqlFloat(rowPastOffset[6]); pValue = sqlFloat(rowPastOffset[7]); qValue = sqlFloat(rowPastOffset[8]); } else { signal = sqlFloat(rowPastOffset[12]); pValue = sqlFloat(rowPastOffset[13]); qValue = sqlFloat(rowPastOffset[14]); } if (signal >= 0) printf("Signal value: %.3f
\n", signal); if (pValue >= 0) printf("P-value (-log10): %.3f
\n", pValue); if (qValue >= 0) printf("Q-value (FDR): %.3f
\n", qValue); } sqlFreeResult(&sr); hFreeConn(&conn); } int encodeFiveCInterCmp(const void *va, const void *vb) /* reverse sort on bed nine's reserved field which in this */ /* case is the where the strength of the interaction is stored */ { const struct bed *a = *((struct bed **)va); const struct bed *b = *((struct bed **)vb); return b->itemRgb - a->itemRgb; } void doEncodeFiveC(struct sqlConnection *conn, struct trackDb *tdb) /* Print details for 5C track */ { char *interTable = trackDbRequiredSetting(tdb, "interTable"); char *interTableKind = trackDbRequiredSetting(tdb, "interTableKind"); char **row; char *chrom = cartString(cart,"c"); int start = cgiInt("o"); int end = cgiInt("t"); int rowOffset; int outCount = 0; struct sqlResult *sr; struct bed *interList = NULL, *inter; genericHeader(tdb, NULL); sr = hOrderedRangeQuery(conn, interTable, chrom, start, end, NULL, &rowOffset); printf("Position: " "%s:%d-%d
\n", hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end); while ((row = sqlNextRow(sr)) != NULL) { inter = bedLoadN(row + rowOffset, 9); slAddHead(&interList, inter); } slSort(&interList, encodeFiveCInterCmp); webNewSection("Top %s interations", interTableKind); webPrintLinkTableStart(); webPrintLabelCell("Position"); webPrintLabelCell("5C signal"); webPrintLabelCell("Distance"); webPrintLinkTableNewRow(); for (inter = interList; inter != NULL; inter = inter->next) { char s[1024]; int distance = 0; safef(s, sizeof(s), "%s:%d-%d", hgTracksPathAndSettings(), database, chrom, inter->thickStart+1, inter->thickEnd, chrom, inter->thickStart+1, inter->thickEnd); webPrintLinkCell(s); safef(s, sizeof(s), "%d", inter->itemRgb); webPrintLinkCell(s); if (start > inter->thickStart) distance = inter->thickEnd - start; else distance = inter->thickStart - end; safef(s, sizeof(s), "%d", distance); webPrintLinkCell(s); if (++outCount == 50) break; if (inter->next != NULL) webPrintLinkTableNewRow(); } webPrintLinkTableEnd(); sqlFreeResult(&sr); }