e19de49c3685111d42c4e5cf7a8be2130d2ef3d8
markd
  Wed Dec 28 09:31:19 2011 -0800
added annotation level to gencode details page
diff --git src/hg/hgc/gencodeClick.c src/hg/hgc/gencodeClick.c
index 973c429..099c211 100644
--- src/hg/hgc/gencodeClick.c
+++ src/hg/hgc/gencodeClick.c
@@ -1,639 +1,654 @@
 /* gencodeClick - click handling for GENCODE tracks */
 #include "common.h"
 #include "hgc.h"
 #include "gencodeClick.h"
 #include "genePred.h"
 #include "genePredReader.h"
 #include "ensFace.h"
 #include "htmshell.h"
 #include "jksql.h"
 #include "encode/wgEncodeGencodeAttrs.h"
 #include "encode/wgEncodeGencodeGeneSource.h"
 #include "encode/wgEncodeGencodePdb.h"
 #include "encode/wgEncodeGencodePubMed.h"
 #include "encode/wgEncodeGencodeRefSeq.h"
 #include "encode/wgEncodeGencodeTag.h"
 #include "encode/wgEncodeGencodeTranscriptSource.h"
 #include "encode/wgEncodeGencodeTranscriptSupport.h"
 #include "encode/wgEncodeGencodeExonSupport.h"
 #include "encode/wgEncodeGencodeUniProt.h"
 #include "encode/wgEncodeGencodeAnnotationRemark.h"
 
 /*
  * General notes:
  *  - this will be integrated into hgGene at some point, however this was
  *    done as part of hgc for timing reasons and to allow more time to design
  *    the hgGene part.
  *  - Tables below will output at least one row even if no data is available.
  *    
  */
 
 /* size for buffering URL strings */
 static const int urlBufSize = 512;
 
 static char *getGencodeTable(struct trackDb *tdb, char *tableBase)
 /* get a table name from the settings. */
 {
 return trackDbRequiredSetting(tdb, tableBase);
 }
 
 static int transAnnoCmp(const void *va, const void *vb)
 /* Compare genePreds, sorting to keep select gene first.  The only cases
  * that annotations will be duplicated is if they are in the PAR and thus
  * on different chroms. */
 {
 const struct genePred *a = *((struct genePred **)va);
 const struct genePred *b = *((struct genePred **)vb);
 if (sameString(a->name, seqName))
     return -1;
 else if (sameString(b->name, seqName))
     return 1;
 else
     return strcmp(a->name, b->name);
 }
 
 static struct genePred *transAnnoLoad(struct sqlConnection *conn, struct trackDb *tdb, char *gencodeId)
 /* load the gencode annotations and sort the one corresponding to the one that was clicked on is
  * first.  Should only have one or two. */
 {
 // must check chrom due to PAR
 char where[256];
 safef(where, sizeof(where), "(chrom = \"%s\") and (name = \"%s\")", seqName, gencodeId);
 struct genePred *transAnno = genePredReaderLoadQuery(conn, tdb->track, where);
 slSort(&transAnno, transAnnoCmp);
 return transAnno;
 }
 
 static struct wgEncodeGencodeAttrs *transAttrsLoad(struct trackDb *tdb, struct sqlConnection *conn, char *gencodeId)
 /* load the gencode class information */
 {
 return sqlQueryObjs(conn, (sqlLoadFunc)wgEncodeGencodeAttrsLoad, sqlQuerySingle|sqlQueryMust,
                     "select * from %s where transcriptId = \"%s\"",
                     getGencodeTable(tdb, "wgEncodeGencodeAttrs"), gencodeId);
 }
 
 static void getGeneBounds(struct trackDb *tdb, struct sqlConnection *conn, struct genePred *transAnno,
                           int *geneChromStart, int *geneChromEnd)
 /* find bounds for the gene */
 {
 // must check chrom due to PAR
 char where[256];
 safef(where, sizeof(where), "(chrom = \"%s\") and (name2 = \"%s\")", seqName, transAnno->name2);
 struct genePred *geneAnnos = genePredReaderLoadQuery(conn, tdb->track, where);
 struct genePred *geneAnno;
 *geneChromStart = transAnno->txStart;
 *geneChromEnd = transAnno->txEnd;
 for (geneAnno = geneAnnos; geneAnno != NULL; geneAnno = geneAnno->next)
     {
     *geneChromStart = min(*geneChromStart, geneAnno->txStart);
     *geneChromEnd = max(*geneChromEnd, transAnno->txEnd);
     }
 genePredFreeList(&geneAnnos);
 }
 
 static void *metaDataLoad(struct trackDb *tdb, struct sqlConnection *conn, char *gencodeId, char *tableBase, char *keyCol, unsigned queryOpts, sqlLoadFunc loadFunc)
 /* load autoSql objects for gencode meta data. */
 {
 return sqlQueryObjs(conn, loadFunc, queryOpts, "select * from %s where %s = \"%s\"",
                     getGencodeTable(tdb, tableBase), keyCol, gencodeId);
 }
 
 static int uniProtDatasetCmp(const void *va, const void *vb)
 /* Compare wgEncodeGencodeUniProt by dateset */
 {
 const struct wgEncodeGencodeUniProt *a = *((struct wgEncodeGencodeUniProt **)va);
 const struct wgEncodeGencodeUniProt *b = *((struct wgEncodeGencodeUniProt **)vb);
 return a->dataset - b->dataset;
 }
 
 static char *getMethodDesc(char *source)
 /* return the annotation method name based gene or transcript source */
 {
 // looks for being havana and/or ensembl
 // classifies other sources as automatic (mt_genbank_import ncrna ncrna_pseudogene)
 bool hasHav = containsStringNoCase(source, "havana") != NULL;
 bool hasEns = containsStringNoCase(source, "ensembl") != NULL;
 if (hasHav && hasEns)
     return "manual & automatic";
 else if (hasHav)
     return "manual";
 else
     return "automatic";
 }
 
+static char *getLevelDesc(int level)
+/* return english description for level */
+{
+if (level == 1)
+    return "validated";
+else if (level == 2)
+    return "manual";
+else if (level == 3)
+    return "automatic";
+else
+    return "unknown";
+}
+
 static char *mkExtIdUrl(struct trackDb *tdb,  char *id, char *settingName, char *urlBuf)
 /* generate a url to a external database given an id and the name of a setting
  * containing the sprintf URL template.*/
 {
 safef(urlBuf, urlBufSize, trackDbRequiredSetting(tdb, settingName), id);
 return urlBuf;
 }
 
 static void prExtIdAnchor(struct trackDb *tdb,  char *id, char *settingName)
 /* if an id to an external database is not empty, print an HTML anchor to it */
 {
 char urlBuf[urlBufSize];
 if (!isEmpty(id))
     printf("<a href=\"%s\" target=_blank>%s</a>", mkExtIdUrl(tdb, id, settingName, urlBuf), id);
 }
 
 static void prTdExtIdAnchor(struct trackDb *tdb,  char *id, char *settingName)
 /* print a table data element with an anchor for a id */
 {
 printf("<td>");
 prExtIdAnchor(tdb, id, settingName);
 }
 
+
 static void writePosLink(char *chrom, int chromStart, int chromEnd)
 /* write link to a genomic position */
 {
 printf("<a href=\"%s&db=%s&position=%s%%3A%d-%d\" target=_blank>%s:%d-%d</A>",
        hgTracksPathAndSettings(), database,
        chrom, chromStart, chromEnd, chrom, chromStart+1, chromEnd);
 }
 
 static void writeBasicInfoHtml(struct trackDb *tdb, char *gencodeId, struct genePred *transAnno, struct wgEncodeGencodeAttrs *transAttrs,
                                int geneChromStart, int geneChromEnd,
                                struct wgEncodeGencodeGeneSource *geneSource, struct wgEncodeGencodeTranscriptSource *transcriptSource)
 /* write basic HTML info for all genes */
 {
 /*
  * notes:
  *   - According to Steve: `status' is not the same for ensembl and havana.  So either avoid displaying it
  *     or display it as `automatic status' or `manual status'.
  */
 
 // basic gene and transcript information
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th><th>Transcript<th>Gene</tr>\n");
 printf("</thead><tbody>\n");
 
 printf("<tr><th>Gencode id");
 prTdExtIdAnchor(tdb, transAttrs->transcriptId, "ensemblTranscriptIdUrl");
 prTdExtIdAnchor(tdb, transAttrs->geneId, "ensemblGeneIdUrl");
 printf("</tr>\n");
 
 printf("<tr><th>HAVANA manual id");
 prTdExtIdAnchor(tdb, transAttrs->havanaTranscriptId, "vegaTranscriptIdUrl");
 prTdExtIdAnchor(tdb, transAttrs->havanaGeneId, "vegaGeneIdUrl");
 printf("</tr>\n");
 
 // FIXME: white-space style should be in CCS, but don't want to risk breaking
 // other things.
 printf("<tr><th>Position");
 printf("<td style=\"white-space: nowrap;\">");
 writePosLink(transAnno->chrom, transAnno->txStart, transAnno->txEnd);
 printf("<td style=\"white-space: nowrap;\">");
 writePosLink(transAnno->chrom, geneChromStart, geneChromEnd);
 printf("</tr>\n");
 
 printf("<tr><th>Strand<td>%s<td></tr>\n", transAnno->strand);
 
 printf("<tr><th><a href=\"http://www.gencodegenes.org/gencode_biotypes.html\">Biotype</a><td>%s<td>%s</tr>\n", transAttrs->transcriptType, transAttrs->geneType);
 /* FIXME: add href o */
 printf("<tr><th>Status<td>%s<td>%s</tr>\n", transAttrs->transcriptStatus, transAttrs->geneStatus);
-printf("<tr><th>Method<td>%s<td>%s</tr>\n", getMethodDesc(transcriptSource->source), getMethodDesc(geneSource->source));
+printf("<tr><th>Annotation Level<td>%s (%d)<td></tr>\n", getLevelDesc(transAttrs->level), transAttrs->level);
+printf("<tr><th>Annotation Method<td>%s<td>%s</tr>\n", getMethodDesc(transcriptSource->source), getMethodDesc(geneSource->source));
 printf("<tr><th>HUGO gene<td colspan=2>%s</tr>\n", transAttrs->geneName);
 printf("<tr><th>CCDS<td>%s<td></tr>\n", transAttrs->ccdsId);
 // FIXME: add sequence here??
 printf("</tbody></table>\n");
 }
 
 static void writeSequenceHtml(struct trackDb *tdb, char *gencodeId, struct genePred *transAnno)
 /* write links to get sequences */
 {
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=\"2\">Sequences</tr>\n");
 printf("</thead><tbody>\n");
 if (transAnno->cdsStart < transAnno->cdsEnd)
     {
     // protein coding
     printf("<tr><td>");
     hgcAnchorSomewhere("htcGeneMrna", gencodeId, tdb->table, seqName);
     printf("Predicted mRNA</a>");
     printf("<td>");
     hgcAnchorSomewhere("htcTranslatedPredMRna", gencodeId, "translate", seqName);
     printf("Predicted protein</a></tr>\n");
     }
 else
     {
     // non-protein coding
     printf("<tr><td>");
     hgcAnchorSomewhere("htcGeneMrna", gencodeId, tdb->table, seqName);
     printf("Predicted mRNA</a><td></tr>\n");
     }
 printf("</tbody></table>\n");
 }
 
 static void writeAnnotationRemarkHtml(struct wgEncodeGencodeAnnotationRemark *remarks)
 /* write HTML links to remarks */
 {
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=\"1\">Annotation Remarks</tr>\n");
 printf("</thead><tbody>\n");
 struct wgEncodeGencodeAnnotationRemark *remark;
 for (remark = remarks; remark != NULL; remark = remark->next)
     {
     char *encRemark = htmlEncode(remark->remark);
     printf("<tr><td>%s</td></tr>\n", encRemark);
     freeMem(encRemark);
     }
 printf("</tbody></table>\n");
 }
 
 static void writePdbLinkHtml(struct wgEncodeGencodePdb *pdbs)
 /* write HTML links to PDB */
 {
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=\"3\">Protein Data Bank</tr>\n");
 printf("</thead><tbody>\n");
 struct wgEncodeGencodePdb *pdb = pdbs;
 int i, rowCnt = 0;
 while ((pdb != NULL) || (rowCnt == 0))
     {
     printf("<tr>");
     for (i = 0; i < 3; i++)
         {
         printf("<td>");
         if (pdb != NULL)
             {
             printf("<a href=\"http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=%s\" target=_blank>%s</a>", pdb->pdbId, pdb->pdbId);
             pdb = pdb->next;
             }
         }
     printf("</tr>\n");
     rowCnt++;
     }
 printf("</tbody></table>\n");
 }
 
 static void writePubMedEntry(struct wgEncodeGencodePubMed *pubMed)
 /* write HTML table entry for a pubMed */
 {
 printf("<td><a href=\"");
 printEntrezPubMedUidUrl(stdout, pubMed->pubMedId);
 printf("\" target=_blank>%d</a>", pubMed->pubMedId);
 }
 
 static void writePubMedLinkHtml(struct wgEncodeGencodePubMed *pubMeds)
 /* write HTML links to PubMed */
 {
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=\"3\">PubMed</tr>\n");
 printf("</thead><tbody>\n");
 struct wgEncodeGencodePubMed *pubMed = pubMeds;
 int i, rowCnt = 0;
 while ((pubMed != NULL) || (rowCnt == 0))
     {
     printf("<tr>");
     for (i = 0; i < 3; i++)
         {
         if (pubMed != NULL)
             {
             writePubMedEntry(pubMed);
             pubMed = pubMed->next;
             }
         else
             printf("<td>");
         }
     printf("</tr>\n");
     rowCnt++;
     }
-printf("</thead></table>\n");
+printf("</tbody></table>\n");
 }
 
 static void writeRefSeqEntry(struct wgEncodeGencodeRefSeq *refSeq)
 /* write HTML table entry for a RefSeq */
 {
 printf("<td><a href=\"");
 printEntrezNucleotideUrl(stdout, refSeq->rnaAcc);
 printf("\" target=_blank>%s</a>", refSeq->rnaAcc);
 printf("<td>");
 if (!isEmpty(refSeq->pepAcc))
     {
     printf("<a href=\"");
     printEntrezProteinUrl(stdout, refSeq->pepAcc);
     printf("\" target=_blank>%s</a>", refSeq->pepAcc);
     }
 }
 
 static void writeRefSeqLinkHtml(struct wgEncodeGencodeRefSeq *refSeqs)
 /* write HTML links to RefSeq */
 {
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=\"2\">RefSeq</tr>\n");
 printf("<tr><th>RNA<th>Protein</tr>\n");
 printf("</thead><tbody>\n");
 struct wgEncodeGencodeRefSeq *refSeq = refSeqs;
 int rowCnt = 0;
 while ((refSeq != NULL) || (rowCnt == 0))
     {
     printf("<tr>");
     if (refSeq != NULL)
         {
         writeRefSeqEntry(refSeq);
         refSeq = refSeq->next;
         }
     else
         printf("<td><td>");
     printf("</tr>\n");
     rowCnt++;
     }
 printf("</tbody></table>\n");
 }
 
 static void writeUniProtEntry(struct wgEncodeGencodeUniProt *uniProt)
 /* write HTML table entry for a UniProt */
 {
 printf("<td>%s", (uniProt->dataset == wgEncodeGencodeUniProtSwissProt) ? "SwissProt" : "TrEMBL");
 printf("<td><a href=\"");
 printSwissProtAccUrl(stdout, uniProt->acc);
 printf("\" target=_blank>%s</a>", uniProt->acc);
 printf("<td><a href=\"");
 printSwissProtAccUrl(stdout, uniProt->name);
 printf("\" target=_blank>%s</a>", uniProt->name);
 }
 
 static void writeUniProtLinkHtml(struct wgEncodeGencodeUniProt *uniProts)
 /* write HTML links to UniProt */
 {
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=\"6\">UniProt</tr>\n");
 printf("<tr><th>Data set<th>Accession<th>Name<th>Data set<th>Accession<th>Name</tr>\n");
 printf("</thead><tbody>\n");
 int i, rowCnt = 0;
 struct wgEncodeGencodeUniProt *uniProt = uniProts;
 while ((uniProt != NULL) || (rowCnt == 0))
     {
     printf("<tr>");
     for (i = 0; i < 2; i++)
         {
         if (uniProt != NULL)
             {
             writeUniProtEntry(uniProt);
             uniProt = uniProt->next;
             }
         else
             printf("<td colspan=3>");
         }
     printf("</tr>\n");
     rowCnt++;
     }
 printf("</tbody></table>\n");
 }
 
 struct supportEvid
 /* temporary struct for subset of supporting information displayed */
 {
     struct supportEvid *next;
     char *seqId;              /* sequence id (memory not owned) */
     char *seqSrc;             /* evidence source database (memory not owned) */
 };
 
 static int supportEvidCmp(const void *va, const void *vb)
 /* Compare two supportEvid objects. */
 {
 const struct supportEvid *a = *((struct supportEvid **)va);
 const struct supportEvid *b = *((struct supportEvid **)vb);
 int diff = strcmp(a->seqSrc, b->seqSrc);
 if (diff == 0)
     diff = strcmp(a->seqId, b->seqId);
 return diff;
 }
 
 static void transcriptSupportToSupportEvid(struct supportEvid **supportEvids, struct wgEncodeGencodeTranscriptSupport *transcriptSupports)
 /* convert transcriptSupport to common structure */
 {
 struct wgEncodeGencodeTranscriptSupport *transcriptSupport;
 for (transcriptSupport = transcriptSupports; transcriptSupport != NULL; transcriptSupport = transcriptSupport->next)
     {
     struct supportEvid *supportEvid;
     AllocVar(supportEvid);
     supportEvid->seqId = transcriptSupport->seqId;
     supportEvid->seqSrc = transcriptSupport->seqSrc;
     slAddHead(supportEvids, supportEvid);
     }
 }
 
 static void exonSupportToSupportEvid(struct supportEvid **supportEvids, struct wgEncodeGencodeExonSupport *exonSupports)
 /* convert exonSupport to common structure */
 {
 struct wgEncodeGencodeExonSupport *exonSupport;
 for (exonSupport = exonSupports; exonSupport != NULL; exonSupport = exonSupport->next)
     {
     struct supportEvid *supportEvid;
     AllocVar(supportEvid);
     supportEvid->seqId = exonSupport->seqId;
     supportEvid->seqSrc = exonSupport->seqSrc;
     slAddHead(supportEvids, supportEvid);
     }
 }
 
 static void sortUniqSupportExidence(struct supportEvid **supportEvids)
 /* sort support evidence and make unique */
 {
 struct supportEvid *supportEvid, *supportEvids2 = NULL;
 slSort(supportEvids, supportEvidCmp);
 // make unique
 while ((supportEvid = slPopHead(supportEvids)) != NULL)
     {
     if ((supportEvids2 == NULL) || (supportEvidCmp(&supportEvid, &supportEvids2) != 0))
         slAddHead(&supportEvids2, supportEvid);
     else
         freeMem(supportEvid);
     }
 slReverse(&supportEvids2);
 *supportEvids = supportEvids2;
 }
 
 static struct supportEvid *loadSupportEvid(struct wgEncodeGencodeTranscriptSupport *transcriptSupports,
                                            struct wgEncodeGencodeExonSupport *exonSupports)
 /* load transcript and supporting evidence into a common structure */
 {
 struct supportEvid *supportEvids = NULL;
 transcriptSupportToSupportEvid(&supportEvids, transcriptSupports);
 exonSupportToSupportEvid(&supportEvids, exonSupports);
 sortUniqSupportExidence(&supportEvids);
 return supportEvids;
 }
 
 static void writeSupportExidenceEntry(struct supportEvid *supportEvid)
 /* write HTML table entry  for a supporting evidence */
 {
 // FIXME: should link to sources when possible
 printf("<td>%s", supportEvid->seqSrc);
 printf("<td>%s", supportEvid->seqId);
 }
 
 static void writeSupportingEvidenceLinkHtml(struct wgEncodeGencodeTranscriptSupport *transcriptSupports,
                                             struct wgEncodeGencodeExonSupport *exonSupports)
 /* write HTML links to supporting evidence */
 {
 struct supportEvid *supportEvids = loadSupportEvid(transcriptSupports, exonSupports);
 
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=\"4\">Supporting Evidence</tr>\n");
 printf("<tr><th>Source<th>Sequence<th>Source<th>Sequence</tr>\n");
 printf("</thead><tbody>\n");
 struct supportEvid *supportEvid = supportEvids;
 int i, rowCnt = 0;
 while ((supportEvid != NULL) || (rowCnt == 0))
     {
     printf("<tr>");
     for (i = 0; i < 2; i++)
         {
         if (supportEvid != NULL)
             {
             writeSupportExidenceEntry(supportEvid);
             supportEvid = supportEvid->next;
             }
         else
             printf("<td colspan=\"2\">");
         }
     printf("</tr>\n");
     rowCnt++;
     }
 printf("</tbody></table>\n");
 slFreeList(&supportEvids);
 }
 
 static void writeTagEntry(struct wgEncodeGencodeTag *tag)
 /* write HTML table entry for a Tag */
 {
 // FIXME: link to help
 printf("<td>%s", tag->tag);
 }
 
 static void writeTagLinkHtml(struct wgEncodeGencodeTag *tags)
 /* write HTML links to Tag */
 {
 printf("<table class=\"hgcCcds\"><thead>\n");
 printf("<tr><th colspan=3>Tags</tr>\n");
 printf("</thead><tbody>\n");
 int i, rowCnt = 0;
 struct wgEncodeGencodeTag *tag = tags;
 while ((tag != NULL) || (rowCnt == 0))
     {
     printf("<tr>");
     for (i = 0; i < 3; i++)
         {
         if (tag != NULL)
             {
             writeTagEntry(tag);
             tag = tag->next;
             }
         else
             printf("<td>");
         }
     printf("</tr>\n");
     rowCnt++;
     }
 printf("</tbody></table>\n");
 }
 
 static void doGencodeGeneTrack(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *transAnno)
 /* Process click on a GENCODE gene annotation track. */
 {
 struct wgEncodeGencodeAttrs *transAttrs = transAttrsLoad(tdb, conn, gencodeId);
 char * gencodeGeneId = transAttrs->geneId;
 struct wgEncodeGencodeGeneSource *geneSource = metaDataLoad(tdb, conn, gencodeGeneId, "wgEncodeGencodeGeneSource", "geneId", sqlQueryMust|sqlQuerySingle, (sqlLoadFunc)wgEncodeGencodeGeneSourceLoad);
 struct wgEncodeGencodeTranscriptSource *transcriptSource = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTranscriptSource", "transcriptId", sqlQueryMust|sqlQuerySingle, (sqlLoadFunc)wgEncodeGencodeTranscriptSourceLoad);
 bool haveRemarks = (trackDbSetting(tdb, "wgEncodeGencodeAnnotationRemark") != NULL);
 struct wgEncodeGencodeAnnotationRemark *remarks = haveRemarks ? metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeAnnotationRemark", "transcriptId", 0, (sqlLoadFunc)wgEncodeGencodeAnnotationRemarkLoad) : NULL;
 struct wgEncodeGencodePdb *pdbs = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodePdb", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodePdbLoad);
 struct wgEncodeGencodePubMed *pubMeds = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodePubMed", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodePubMedLoad);
 struct wgEncodeGencodeRefSeq *refSeqs = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeRefSeq", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeRefSeqLoad);
 struct wgEncodeGencodeTag *tags = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTag", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeTagLoad);
 struct wgEncodeGencodeTranscriptSupport *transcriptSupports = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeTranscriptSupport", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeTranscriptSupportLoad);
 struct wgEncodeGencodeExonSupport *exonSupports = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeExonSupport", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeExonSupportLoad);
 struct wgEncodeGencodeUniProt *uniProts = metaDataLoad(tdb, conn, gencodeId, "wgEncodeGencodeUniProt", "transcriptId", sqlQueryMulti, (sqlLoadFunc)wgEncodeGencodeUniProtLoad);
 slSort(&uniProts, uniProtDatasetCmp);
 int geneChromStart, geneChromEnd;
 getGeneBounds(tdb, conn, transAnno, &geneChromStart, &geneChromEnd);
 
 char *title = "GENCODE Transcript Annotation";
 char header[256];
 safef(header, sizeof(header), "%s %s", title, gencodeId);
 if (!isEmpty(transAttrs->geneName))
     safef(header, sizeof(header), "%s %s (%s)", title, gencodeId, transAttrs->geneName);
 else
     safef(header, sizeof(header), "%s %s", title, gencodeId);
 cartWebStart(cart, database, "%s", header);
 printf("<H2> %s</H2>\n", header);
 
 writeBasicInfoHtml(tdb, gencodeId, transAnno, transAttrs, geneChromStart, geneChromEnd, geneSource, transcriptSource);
 writeTagLinkHtml(tags);
 writeSequenceHtml(tdb, gencodeId, transAnno);
 if (haveRemarks)
     writeAnnotationRemarkHtml(remarks);
 writePdbLinkHtml(pdbs);
 writePubMedLinkHtml(pubMeds);
 writeRefSeqLinkHtml(refSeqs);
 writeUniProtLinkHtml(uniProts);
 writeSupportingEvidenceLinkHtml(transcriptSupports, exonSupports);
 wgEncodeGencodeAttrsFree(&transAttrs);
 wgEncodeGencodeAnnotationRemarkFreeList(&remarks);
 wgEncodeGencodeGeneSourceFreeList(&geneSource);
 wgEncodeGencodeTranscriptSourceFreeList(&transcriptSource);
 wgEncodeGencodePdbFreeList(&pdbs);
 wgEncodeGencodePubMedFreeList(&pubMeds);
 wgEncodeGencodeRefSeqFreeList(&refSeqs);
 wgEncodeGencodeTranscriptSupportFreeList(&transcriptSupports);
 wgEncodeGencodeExonSupportFreeList(&exonSupports);
 wgEncodeGencodeUniProtFreeList(&uniProts);
 }
 
 static void doGencodeGene2WayPseudo(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *pseudoAnno)
 /* Process click on a GENCODE two-way pseudogene annotation track. */
 {
 char header[256];
 safef(header, sizeof(header), "GENCODE 2-way consensus pseudogene %s", gencodeId);
 cartWebStart(cart, database, "%s", header);
 printf("<H2>%s</H2>\n", header);
 printf("<b>Yale id:</b> ");
 prExtIdAnchor(tdb, gencodeId, "yalePseudoUrl");
 printf("<br>");
 printPos(pseudoAnno->chrom, pseudoAnno->txStart, pseudoAnno->txEnd, pseudoAnno->strand, FALSE, NULL);
 }
 
 static void doGencodeGenePolyA(struct trackDb *tdb, char *gencodeId, struct sqlConnection *conn, struct genePred *polyAAnno)
 /* Process click on a GENCODE poly-A annotation track. */
 {
 char header[256];
 safef(header, sizeof(header), "GENCODE PolyA Annotation %s (%s)", polyAAnno->name2, gencodeId);
 cartWebStart(cart, database, "%s", header);
 printf("<H2>%s</H2>\n", header);
 printf("<b>Annotation id:</b> %s<br>", gencodeId);
 printf("<b>Annotation Type:</b> %s<br>",polyAAnno->name2);
 printPos(polyAAnno->chrom, polyAAnno->txStart, polyAAnno->txEnd, polyAAnno->strand, FALSE, NULL);
 }
 
 void doGencodeGene(struct trackDb *tdb, char *gencodeId)
 /* Process click on a GENCODE annotation. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct genePred *anno = transAnnoLoad(conn, tdb, gencodeId);
 if (startsWith("wgEncodeGencodeBasic", tdb->track)
     || startsWith("wgEncodeGencodeComp", tdb->track)
     || startsWith("wgEncodeGencodePseudoGene", tdb->track))
     doGencodeGeneTrack(tdb, gencodeId, conn, anno);
 else if (startsWith("wgEncodeGencode2wayConsPseudo", tdb->track))
     doGencodeGene2WayPseudo(tdb, gencodeId, conn, anno);
 else if (startsWith("wgEncodeGencodePolya", tdb->track))
     doGencodeGenePolyA(tdb, gencodeId, conn, anno);
 else
     errAbort("doGencodeGene: track not handled: \"%s\"", tdb->track);
 
 htmlHorizontalLine();
 printTrackHtml(tdb);
 
 genePredFreeList(&anno);
 hFreeConn(&conn);
 }
 
 bool isNewGencodeGene(struct trackDb *tdb)
 /* is this a new-style gencode (>= V7) track, as indicated by
  * the presence of the wgEncodeGencodeVersion setting */
 {
 return trackDbSetting(tdb, "wgEncodeGencodeVersion") != NULL;
 }