bd0b0a42ee56a2e20728a1e4d5002127c724e72d
tdreszer
  Mon Jun 25 17:08:25 2012 -0700
Next batch of many checkins as dictated by Jim.  Formatting space after if and limiting lines to 100 chars.  Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history.  None of these changes should affect executables in any way.  Only affect is to my sanity and Jim's.
diff --git src/hg/hgc/encodeClick.c src/hg/hgc/encodeClick.c
index 4edf210..22e7c9f 100644
--- src/hg/hgc/encodeClick.c
+++ src/hg/hgc/encodeClick.c
@@ -1,279 +1,281 @@
 /* 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;
 int rowOffset = 0;  // skip bin field
 int found = 0;
 genericHeader(tdb, NULL);
 
 /* Just get the current item. */
-safef(query, sizeof(query), "select * from %s where name='%s' and chrom='%s' and chromStart=%d and chromEnd=%d", 
+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)
     {
     ++found;
     peptideMappingStaticLoad(row + rowOffset, &pos);
     if (found == 1)
 	{
 	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);
     }
 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)
     {
     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)", 
+    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);
     }    
 
 }