2c4c813bcb91cf575584d868a1d145f3a3bc6416
kate
  Mon Nov 17 00:28:14 2014 -0800
Add peptide table with sequence and other info for details page.  refs #25054
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index dd3c9fc..9b6ba86 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -40,30 +40,31 @@
 #include "agpGap.h"
 #include "ctgPos.h"
 #include "contigAcc.h"
 #include "ctgPos2.h"
 #include "clonePos.h"
 #include "bactigPos.h"
 #include "rmskOut.h"
 #include "xenalign.h"
 #include "isochores.h"
 #include "simpleRepeat.h"
 #include "cpgIsland.h"
 #include "cpgIslandExt.h"
 #include "genePred.h"
 #include "genePredReader.h"
 #include "pepPred.h"
+#include "peptideAtlasPeptide.h"
 #include "wabAli.h"
 #include "genomicDups.h"
 #include "est3.h"
 #include "rnaGene.h"
 #include "tRNAs.h"
 #include "gbRNAs.h"
 #include "encode/encodeRna.h"
 #include "hgMaf.h"
 #include "maf.h"
 #include "stsMarker.h"
 #include "stsMap.h"
 #include "rhMapZfishInfo.h"
 #include "recombRate.h"
 #include "recombRateRat.h"
 #include "recombRateMouse.h"
@@ -20816,30 +20817,101 @@
           "select * from sgdOtherDescription where name = '%s'", item);
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	sgdDescriptionStaticLoad(row, &sgd);
 	dyStringPrintf(dy, "<B>Description:</B> %s<BR>\n", sgd.description);
 	dyStringPrintf(dy, "<B>Type:</B> %s<BR>\n", sgd.type);
 	}
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 genericClickHandlerPlus(tdb, item, NULL, dy->string);
 dyStringFree(&dy);
 }
 
+
+void doPeptideAtlas(struct trackDb *tdb, char *item)
+/* PeptideAtlas item details display. Peptide details are in hgFixed.<table>Peptides */
+{
+char query[512];
+struct sqlResult *sr;
+char **row;
+
+int start = cartInt(cart, "o");
+int end = cartInt(cart, "t");
+
+genericHeader(tdb, item);
+printCustomUrl(tdb, item, FALSE);
+struct sqlConnection *conn = hAllocConn(database);
+char peptideTable[128];
+safef(peptideTable, sizeof(peptideTable), "%sPeptides", tdb->table);
+
+// peptide info
+struct sqlConnection *connFixed= hAllocConn("hgFixed");
+if (sqlTableExists(connFixed, peptideTable))
+    {
+    sqlSafef(query, sizeof(query), "select * from %s where accession = '%s'", peptideTable, item);
+    sr = sqlGetResult(connFixed, query);
+    row = sqlNextRow(sr);
+    if (row != NULL)
+        {
+        struct peptideAtlasPeptide *peptideInfo;
+        AllocVar(peptideInfo);
+        peptideAtlasPeptideStaticLoad(row, peptideInfo);
+        printf("<b>Peptide sequence:</b> %s<br>\n", peptideInfo->sequence);
+        printf("<b>Peptide size:</b> %d<br>\n", (int)strlen(peptideInfo->sequence));
+        printf("<b>Samples where observed:</b> %d<br>\n", peptideInfo->sampleCount);
+        printf("<b>Proteotypic score:</b> %.3f<br>\n", peptideInfo->proteotypicScore);
+        printf("<b>Hydrophobicity:</b> %.3f<br><br>\n", peptideInfo->hydrophobicity);
+        }
+    sqlFreeResult(&sr);
+    }
+hFreeConn(&connFixed);
+
+// peptide mappings
+sqlSafef(query, sizeof(query), "select * from %s where name = '%s' order by chrom, chromStart, chromEnd", 
+        tdb->table, item);
+sr = sqlGetResult(conn, query);
+row = sqlNextRow(sr);
+struct bed *bed = NULL, *beds = NULL;
+int rowOffset = hOffsetPastBin(database, seqName, tdb->table);
+while (row != NULL)
+    {
+    bed = bedLoadN(row + rowOffset, 12);
+    if (sameString(bed->chrom, seqName) && bed->chromStart == start && bed->chromEnd == end)
+        bedPrintPos(bed, 12, tdb);
+    else
+        slAddHead(&beds, bed);
+    row = sqlNextRow(sr);
+    }
+if (beds != NULL)
+    {
+    slSort(&beds, bedCmp);
+    printf("<br><b>Other mappings of this peptide:</b> %d<br>\n", slCount(beds));
+    for (bed = beds; bed != NULL; bed = bed->next)
+        {
+        printf("&nbsp;&nbsp;&nbsp;&nbsp;"
+               "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">",
+               hgTracksPathAndSettings(), database, bed->chrom, bed->chromStart+1, bed->chromEnd);
+        printf("%s:%d-%d</A><BR>\n", bed->chrom, bed->chromStart+1, bed->chromEnd);
+        }
+    }
+hFreeConn(&conn);
+printTrackHtml(tdb);
+}
+
 static void doSgdClone(struct trackDb *tdb, char *item)
 /* Display information about other Sacchromyces Genome Database
  * other (not-coding gene) info. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct dyString *dy = dyStringNew(1024);
 
 if (sqlTableExists(conn, "sgdClone"))
     {
     /* print out url with ATCC number */
     struct sgdClone sgd;
     struct sqlResult *sr;
     char query[256], **row;
     sqlSafef(query, sizeof(query),
           "select * from sgdClone where name = '%s'", item);
@@ -21984,30 +22056,31 @@
 if (hTableExists(database, "anoEstExpressed"))
     {
     char query[512];
 
     sqlSafef(query, sizeof(query),
 	  "select 1 from anoEstExpressed where name = '%s'", item);
     if (sqlQuickNum(conn, query))
 	puts("<B>Expressed:</B> yes<BR>");
     else
 	puts("<B>Expressed:</B> no<BR>");
     }
 hFreeConn(&conn);
 printTrackHtml(tdb);
 }
 
+
 void mammalPsgTableRow(char *test, char *description, float pVal, unsigned isFdrSignificant)
 /* print single row of the overview table for mammal PSG track */
 {
 char *start = "";
 char *end = "";
 
 if (isFdrSignificant)
     {
     start = "<b>";
     end = "</b>";
     }
 
 if (pVal<=1)
     {
     printf("<tr><td>%s%s%s</td><td>%s%s%s</td><td>%s%.02g%s</tr>\n",
@@ -25599,45 +25672,48 @@
     {
     doQPCRPrimers(tdb, item);
     }
 else if (sameString("lrg", table))
     {
     doLrg(tdb, item);
     }
 else if (sameString("lrgTranscriptAli", table))
     {
     doLrgTranscriptPsl(tdb, item);
     }
 else if (sameWord(table, "htcLrgCdna"))
     {
     htcLrgCdna(item);
     }
+else if (startsWith("peptideAtlas", table))
+    {
+    doPeptideAtlas(tdb, item);
+    }
 else if (isHubTrack(table) && startsWith("snake", trackHubSkipHubName(table)))
     {
     doSnakeClick(tdb, item);
     }
 #ifdef USE_TABIX
 else if (tdb != NULL && startsWithWord("vcfTabix", tdb->type))
     {
     doVcfTabixDetails(tdb, item);
     }
 #endif // USE_TABIX
 else if (tdb != NULL && startsWithWord("vcf", tdb->type))
     {
     doVcfDetails(tdb, item);
     }
-
 else if (tdb != NULL)
     {
     genericClickHandler(tdb, item, NULL);
     }
 else
     {
     cartWebStart(cart, database, "%s", track);
     printf("Sorry, clicking there doesn't do anything yet (%s).", track);
     }
 /* End of 1000+ line dispatch on table involving 100+ if/elses. */
 
 cartHtmlEnd();
 }
 
 struct hash *orgDbHash = NULL;