97a1917205b8381b4748a142c29dd6bee334f2c5
aamp
  Wed Mar 2 16:01:20 2011 -0800
Reordering the details a bit
diff --git src/hg/hgc/encodeClick.c src/hg/hgc/encodeClick.c
index a8a9f10..b1950dc 100644
--- src/hg/hgc/encodeClick.c
+++ src/hg/hgc/encodeClick.c
@@ -1,245 +1,246 @@
 /* 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 **row;
 struct sqlResult *sr;
 struct peptideMapping *pos = NULL;
 int rowOffset;
 genericHeader(tdb, NULL);
+/* Just get the current item. */
 sr = hOrderedRangeQuery(conn, tdb->track, chrom, start, end, NULL, &rowOffset);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     pos = peptideMappingLoad(row + rowOffset);
     sqlFreeResult(&sr);
     }
 else
     {
     errAbort("No items in range");
     }
 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>Spectrum ID:</B> %s<BR>\n", pos->spectrumId);
 printf("<B>Peptide Rank:</B> %d<BR>\n", pos->peptideRank);
 printf("<B>Peptide Repeat Count:</B> %d<BR>\n", pos->peptideRepeatCount);
-printPos(pos->chrom, pos->chromStart, pos->chromEnd, pos->strand, TRUE, item);
+printf("<B>Spectrum ID:</B> %s<BR>\n", pos->spectrumId);
 if (pos->peptideRepeatCount > 1)
     {
     char query[256];
     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);
     printf("<BR>\n");
     webPrintLinkTableStart();
     webPrintLabelCell("Other genomic loci");
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	char s[1024];
 	peptideMappingStaticLoad(row + rowOffset, &anotherPos);
 	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);
     }    
 peptideMappingFree(&pos);
 }