b2387705edc15aa154101bca5f0b786537958886
galt
  Fri Sep 16 08:23:51 2011 -0700
fixing peptideMapping - use name-and-position based query instead of just position to prevent picking up nearby peptides that are different, show all peptide mapping details, pull out peptideRepeatCount since it does not vary, show only unique alternate locations
diff --git src/hg/hgc/encodeClick.c src/hg/hgc/encodeClick.c
index b1950dc..4edf210 100644
--- src/hg/hgc/encodeClick.c
+++ src/hg/hgc/encodeClick.c
@@ -1,246 +1,279 @@
 /* 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"
 #include "peptideMapping.h"
 
 #ifdef UNUSED
 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);
 }
 #endif//def UNUSED
 
 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("<B>Name:</B> %s<BR>\n", rowPastOffset[3]);
     /* Position */
     printf("<B>Position:</B> "
        "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\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("<B>Peak point:</B> %d<BR>\n", start + peak + 1); // one based
 	}
     /* Strand, score */
     if (rowPastOffset[5][0] != '.')
 	    printf("<B>Strand:</B> %c<BR>\n", rowPastOffset[5][0]);
     printf("<B>Score:</B> %d<BR>\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("<B>Signal value:</B> %.3f<BR>\n", signal);
     if (pValue >= 0)
 	printf("<B>P-value (-log10):</B> %.3f<BR>\n", pValue);
     if (qValue >= 0)
 	printf("<B>Q-value (FDR): </B> %.3f<BR>\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("<B>Position:</B> "
        "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\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), "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
        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);
 }
 
 void doPeptideMapping(struct sqlConnection *conn, struct trackDb *tdb, char *item)
 /* Print details for a peptideMapping track.  */
 {
 char *chrom = cartString(cart,"c");
 int start = cgiInt("o");
 int end = cgiInt("t");
+char query[256];
 char **row;
 struct sqlResult *sr;
-struct peptideMapping *pos = NULL;
-int rowOffset;
+struct peptideMapping pos;
+int rowOffset = 0;  // skip bin field
+int found = 0;
 genericHeader(tdb, NULL);
+
 /* Just get the current item. */
-sr = hOrderedRangeQuery(conn, tdb->track, chrom, start, end, NULL, &rowOffset);
-if ((row = sqlNextRow(sr)) != NULL)
+safef(query, sizeof(query), "select * from %s where name='%s' and chrom='%s' and chromStart=%d and chromEnd=%d", 
+    tdb->track, item, chrom, start, end);
+sr = sqlGetResult(conn, query);
+
+if (sqlFieldColumn(sr, "bin") == 0)
+    rowOffset = 1;
+    
+while ((row = sqlNextRow(sr)) != NULL)
     {
-    pos = peptideMappingLoad(row + rowOffset);
-    sqlFreeResult(&sr);
-    }
-else
+    ++found;
+    peptideMappingStaticLoad(row + rowOffset, &pos);
+    if (found == 1)
     {
-    errAbort("No items in range");
+	printf("<B>Item:</B> %s<BR>\n", pos.name);
+	printPos(pos.chrom, pos.chromStart, pos.chromEnd, pos.strand, TRUE, item);
+
+	printf("<BR>\n");
+	printf("Additional details for all peptide mappings of %s:<BR>\n", item);
+
+	webPrintLinkTableStart();
+	webPrintLabelCell("Score");
+	webPrintLabelCell("Raw Score");
+	webPrintLabelCell("Spectrum ID");
+	webPrintLabelCell("Peptide Rank");
+	}
+    webPrintLinkTableNewRow();
+    webPrintIntCell(pos.score);
+    webPrintDoubleCell(pos.rawScore);
+    webPrintLinkCell(pos.spectrumId);
+    webPrintIntCell(pos.peptideRank);
     }
-printf("<B>Item:</B> %s<BR>\n", pos->name);
-printf("<B>Score:</B> %d<BR>\n", pos->score);
-printPos(pos->chrom, pos->chromStart, pos->chromEnd, pos->strand, TRUE, item);
-printf("<B>Raw Score:</B> %f<BR>\n", pos->rawScore);
-printf("<B>Peptide Rank:</B> %d<BR>\n", pos->peptideRank);
-printf("<B>Peptide Repeat Count:</B> %d<BR>\n", pos->peptideRepeatCount);
-printf("<B>Spectrum ID:</B> %s<BR>\n", pos->spectrumId);
-if (pos->peptideRepeatCount > 1)
+if (found == 0)
+    errAbort("No items in range");
+
+webPrintLinkTableEnd();
+sqlFreeResult(&sr);
+
+/* Draw table of other locations */
+printf("<BR>\n");
+printf("<B>Peptide Repeat Count:</B> %d<BR>\n", pos.peptideRepeatCount);
+if (pos.peptideRepeatCount > 1)
     {
-    char query[256];
+    struct hash *hash = hashNew(8);
     struct peptideMapping anotherPos;
-    safef(query, sizeof(query), "select * from %s where name=\'%s\' and not (chrom=\'%s\' and chromStart=%d and chromEnd=%d)", 
-	  tdb->track, pos->name, pos->chrom, pos->chromStart, pos->chromEnd);
+    safef(query, sizeof(query), "select * from %s where name='%s' and not (chrom='%s' and chromStart=%d and chromEnd=%d)", 
+	  tdb->track, item, chrom, start, end);
     printf("<BR>\n");
     webPrintLinkTableStart();
     webPrintLabelCell("Other genomic loci");
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	char s[1024];
 	peptideMappingStaticLoad(row + rowOffset, &anotherPos);
+	char k[1024];
+	safef(k, sizeof k, "%s.%d.%d", anotherPos.chrom, anotherPos.chromStart, anotherPos.chromEnd);
+	if (!hashLookup(hash, k))
+	    {
+	    hashAdd(hash, k, NULL);
 	safef(s, sizeof(s), "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
 	      hgTracksPathAndSettings(), database, anotherPos.chrom, anotherPos.chromStart+1, 
 	      anotherPos.chromEnd, anotherPos.chrom, anotherPos.chromStart+1, anotherPos.chromEnd);
 	webPrintLinkTableNewRow();
 	webPrintLinkCell(s);
 	}
+	}
     webPrintLinkTableEnd();
     sqlFreeResult(&sr);
+    freeHash(&hash);
     }    
-peptideMappingFree(&pos);
+
 }