1a38d91ca5503a0560b19596417156b978cc53b7
markd
  Fri Dec 2 16:11:29 2011 -0800
display gencode annotation remarks
diff --git src/hg/hgc/gencodeClick.c src/hg/hgc/gencodeClick.c
index e7ae23d..973c429 100644
--- src/hg/hgc/gencodeClick.c
+++ src/hg/hgc/gencodeClick.c
@@ -5,30 +5,31 @@
 #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. */
@@ -212,30 +213,46 @@
     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)
@@ -509,60 +526,65 @@
             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);