e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/hgc/mgcClick.c src/hg/hgc/mgcClick.c
index 88304bd..6a9f3d5 100644
--- src/hg/hgc/mgcClick.c
+++ src/hg/hgc/mgcClick.c
@@ -1,859 +1,862 @@
 /* mgcClick - click handling for MGC and ORFEome related tracks */
+
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "hgc.h"
 #include "mgcClick.h"
 #include "ccdsClick.h"
 #include "ccdsGeneMap.h"
 #include "gbMiscDiff.h"
 #include "web.h"
 #include "genbank.h"
 #include "htmshell.h"
 #include "genePred.h"
 #include "geneSimilarities.h"
 
 
 static char *findRefSeqSummary(struct sqlConnection *conn,
                                struct geneSimilarities *refSeqs,
                                char **sumAccv)
 /* Given similar refseq genes, find the first one with a RefSeq
  * summary and return that summary, or NULL if not found.  Also returns
  * accv of matched */
 {
 char buf[GENBANK_ACC_BUFSZ];
 struct geneSim *rs;
 for (rs = refSeqs->genes; rs != NULL; rs = rs->next)
     {
     char *sum = getRefSeqSummary(conn, genbankDropVer(buf, rs->gene->name));
     if (sum != NULL)
         {
         *sumAccv = cloneString(rs->gene->name);
         return sum;
         }
     }
 *sumAccv = NULL;
 return NULL;
 }
 
 static char *getAccVersion(struct sqlConnection *conn, char *acc)
 /* given a accession, get acc.ver */
 {
 char query[256], accver[64];
 sqlSafef(query, sizeof(query), "SELECT version FROM gbCdnaInfo WHERE acc=\"%s\"", acc);
 safef(accver, sizeof(accver), "%s.%d", acc, sqlNeedQuickNum(conn, query));
 return cloneString(accver);
 }
 
 struct mgcDb
 /* information about an MGC databases */
 {
     char *name;       /* collection name */
     char *title;      /* collection title */
     char *organism;   /* organism name for URL, case-sensitive */
     char *server;     /* MGC server */
 };
 
 static struct mgcDb getMgcDb()
 /* get the mgc database info for the current host */
 {
 struct mgcDb mgcDb;
 mgcDb.name = "MGC";
 mgcDb.title = "Mammalian Gene Collection";
 mgcDb.server = "mgc";
 mgcDb.organism = NULL;
 /* NOTE: mgc server likes first letter of organism capitalized */
 if (startsWith("hg", database) || startsWith("braNey", database))
     mgcDb.organism = "Hs";
 else if (startsWith("mm", database))
     mgcDb.organism = "Mm";
 else if (startsWith("rn", database))
     mgcDb.organism = "Rn";
 else if (startsWith("bosTau", database))
     mgcDb.organism = "Bt";
 else if (startsWith("danRer", database))
     {
     mgcDb.name = "ZGC";
     mgcDb.title = "Zebrafish Gene Collection";
     mgcDb.organism = "Dr";
     mgcDb.server = "zgc";
     }
 else if (startsWith("xenTro", database))
     {
     mgcDb.name = "XGC";
     mgcDb.title = "Xenopus Gene Collection";
     mgcDb.organism = "Str";
     mgcDb.server = "xgc";
     }
 else
     errAbort("can't map database \"%s\" to an MGC organism", database);
 return mgcDb;
 }
 
 char *mgcDbName()
 /* get just the MGC collection name for the current ucsc database */
 {
 return getMgcDb().name;
 }
 
 void printMgcHomeUrl(struct mgcDb *mgcDb)
 /* print out an URL to link to the MGC site */
 {
 printf("http://%s.nci.nih.gov/", mgcDb->server);
 }
 
 void printMgcUrl(int imageId)
 /* print out an URL to link to the MGC site for a full-length MGC clone */
 {
 struct mgcDb mgcDb = getMgcDb();
 printf("http://%s.nci.nih.gov/Reagents/CloneInfo?ORG=%s&IMAGE=%d",
        mgcDb.server, mgcDb.organism, imageId);
 }
 
 static void printOrderUrl(int gi)
 /* print out an URL to link to the NCBI order CGI for a full-length MGC clone */
 {
 printf("http://www.ncbi.nlm.nih.gov/genome/clone/orderclone.cgi?db=nucleotide&uid=%d", gi);
 }
 
 static void printImageUrl(int imageId)
 /* print out an URL to link to IMAGE database for a clone */
 {
 printf("http://www.imageconsortium.org/IQ/bin/singleCloneQuery?clone_id=%d", imageId);
 }
 
 void printMgcDetailsUrl(char *acc, int start)
 /* print out an URL to link to MGC details pages from another details page in
  * the browser.*/
 {
 // pass zero coordiates for window to indicate this isn't a browser click
 printf("../cgi-bin/hgc?%s&g=mgcGenes&o=%d&i=%s&l=0&r=0&db=%s",
        cartSidUrlString(cart), start, acc, database);
 }
 
 static void printMBLabValidDbUrl(char *acc)
 /* print out an URL to link to Brent lab validation database */
 {
 printf("http://mblab.wustl.edu/cgi-bin/mgc.cgi?acc=%s&action=cloneRpt&alignment=Submit", acc);
 }
 
 struct cloneInfo
 /* Information on a MGC or ORFeome clone collected from various tables */
 {
     boolean isMgc;    // is this MGC or ORFeome
     char *acc;
     int start;
     char *pslTbl;     // psl-format table
     char *gpTbl;      // genePred format table
     char *desc;       // genbank info
     char *organism;
     char *tissue;
     char *library;
     char *development;
     char *geneName;
     char *productName;
     char *moddate;
     char *clone;
     char *cds;
     char *keyword;
     int version;
     int imageId;
     int mgcId;
     int gi;
     char *refSeqAccv;     // best RefSeq acc.version, or NULL
     char *refSeqSum;      // RefSeq from best matching RefSeq with summary, or NULL.
     char *refSeqSumAccv;  // accv for summary, maybe different than best match
     struct geneSimilarities *refSeqs;  // most similar RefSeqs, with name set to acc.version
 };
 
 static boolean isInMBLabValidDb(char *acc)
 /* check if an accession is in the Brent lab validation database */
 {
 boolean inMBLabValidDb = FALSE;
 struct sqlConnection *fconn = sqlMayConnect("hgFixed");
 if ((fconn != NULL) && sqlTableExists(fconn, "mgcMBLabValid"))
     {
     char query[64], buf[32];
     sqlSafef(query, sizeof(query), "select acc from mgcMBLabValid where acc=\"%s\"",
           acc);
     if (sqlQuickQuery(fconn, query, buf, sizeof(buf)) != NULL)
         inMBLabValidDb = TRUE;
     sqlDisconnect(&fconn);
     }
 return inMBLabValidDb;
 }
 
 static void cdnaInfoLoad(struct cloneInfo *ci, struct sqlConnection *conn)
 /* Loading clone information from gbCdnaInfo relational tables. */
 {
 // data from gbCdnaInfo and friends
 char query[1024];
 sqlSafef(query, sizeof(query),
       "select "
       "description.name, organism.name, tissue.name, library.name,"
       "development.name, geneName.name, productName.name, mrnaClone.name,"
       "cds.name,keyword.name,gbCdnaInfo.moddate,gbCdnaInfo.version,"
       "gbCdnaInfo.gi"
       " from "
       "gbCdnaInfo,description,organism,tissue,library,development,"
       "geneName,productName,mrnaClone,cds,keyword"
       " where "
       "(acc = \"%s\") and"
       "(description = description.id) and (organism = organism.id) and"
       "(tissue = tissue.id) and (library = library.id) and"
       "(development = development.id) and (geneName = geneName.id) and"
       "(productName = productName.id) and (mrnaClone = mrnaClone.id) and"
       "(cds = cds.id) and (keyword = keyword.id)", ci->acc);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = sqlNextRow(sr);
 if (row == NULL)
     errAbort("can't find %s in gbCdnaInfo", ci->acc);
 int i = 0;
 ci->desc = cloneString(row[i++]);
 ci->organism = cloneString(row[i++]);
 ci->tissue = cloneString(row[i++]);
 ci->library = cloneString(row[i++]);
 ci->development = cloneString(row[i++]);
 ci->geneName = cloneString(row[i++]);
 ci->productName = cloneString(row[i++]);
 ci->clone = cloneString(row[i++]);
 ci->cds = cloneString(row[i++]);
 ci->keyword = cloneString(row[i++]);
 ci->moddate = cloneString(row[i++]);
 ci->version = sqlUnsigned(row[i++]);
 ci->gi = sqlUnsigned(row[i++]);
 sqlFreeResult(&sr);
 }
 
 static char *cdnaInfoDbName(struct cloneInfo *ci)
 /* get the name to use in describing this gene collection */
 {
 return (ci->isMgc ? mgcDbName() : "ORFeome");
 }
 
 static void getRefSeqInfo(struct sqlConnection *conn, struct cloneInfo *ci)
 /* fill in refSeq info */
 {
 ci->refSeqs = geneSimilaritiesBuildAt(conn, TRUE, ci->acc, seqName, ci->start,
                                       ci->gpTbl, "refGene");
 // replace accession in gene names with accession.version
 struct geneSim *gs;
 for (gs = ci->refSeqs->genes; gs != NULL; gs = gs->next)
     {
     char *accv ;
 
     // add version number if it's not already there
     if (strchr(gs->gene->name, '.'))
 	accv = cloneString(gs->gene->name);
     else
 	accv = getAccVersion(conn, gs->gene->name);
     freeMem(gs->gene->name);
     gs->gene->name = accv;
     }
 
 if ((ci->refSeqs != NULL) && (ci->refSeqs->genes != NULL))
     {
     // use first one (highest similarity)
     ci->refSeqAccv = cloneString(ci->refSeqs->genes->gene->name);
     // get summary for first one with summary
     ci->refSeqSum = findRefSeqSummary(conn, ci->refSeqs, &ci->refSeqSumAccv);
     }
 }
 
 static void parseCloneField(struct cloneInfo *ci)
 /* parse the mrnaClone field to get IMAGE and MGC fields, if available */
 {
 /* MGC:135061 IMAGE:40080529
  * or
  * IMAGE:100005038; FLH186078.01X; RZPDo839A0971D
  */
 char buf[1024], *words[64];
 safecpy(buf, sizeof(buf), ci->clone);
 int nwords = chopByWhite(buf, words, ArraySize(words));
 if (nwords == ArraySize(words))
     errAbort("more words in mrnaClone file than can be parsed, most likely data corruption: %s",
              ci->clone);
 int i;
 for (i = 0; i < nwords; i++)
     {
     char *word = words[i];
     int l = strlen(word);
     if ((l > 0) && (word[l-1] == ';'))
         word[l-1] = '\0';  // wack trailing `;'
     if (startsWith("MGC:", word))
         ci->mgcId = sqlUnsigned(word+4);
     else if (startsWith("IMAGE:", word))
         ci->imageId = sqlUnsigned(word+6);
     }
 }
 
 static struct cloneInfo *cloneInfoLoad(struct sqlConnection *conn, char *acc,
                                        int start, char *pslTbl, char *gpTbl)
 /* Load clone information tables. */
 {
 struct cloneInfo *ci;
 AllocVar(ci);
 ci->acc = cloneString(acc);
 ci->start = start;
 ci->pslTbl = cloneString(pslTbl);
 ci->gpTbl = cloneString(gpTbl);
 cdnaInfoLoad(ci, conn);
 parseCloneField(ci);
 if (sqlTableExists(conn, "refGene"))
     getRefSeqInfo(conn, ci);
 return ci;
 }
 
 static void cloneInfoFree(struct cloneInfo **ciPtr)
 /* free a cloneInfo object */
 {
 struct cloneInfo *ci = *ciPtr;
 if (ci != NULL)
     {
     freeMem(ci->acc);
     freeMem(ci->pslTbl);
     freeMem(ci->gpTbl);
     freeMem(ci->desc);
     freeMem(ci->organism);
     freeMem(ci->tissue);
     freeMem(ci->library);
     freeMem(ci->development);
     freeMem(ci->geneName);
     freeMem(ci->productName);
     freeMem(ci->moddate);
     freeMem(ci->clone);
     freeMem(ci->cds);
     freeMem(ci->keyword);
     freeMem(ci->refSeqAccv);
     freeMem(ci->refSeqSum);
     geneSimilaritiesFree(&ci->refSeqs);
     freeMem(ci);
     *ciPtr = NULL;
     }
 }
 
 static struct cloneInfo *mgcCloneInfoLoad(struct sqlConnection *conn, char *acc,
                                           int start)
 /* Load MGC clone information */
 {
 struct cloneInfo *ci = cloneInfoLoad(conn, acc, start, "mgcFullMrna", "mgcGenes");
 ci->isMgc = TRUE;
 if (ci->mgcId == 0)
     errAbort("no MGC:nnnn entry in mrnaClone table for MGC clone %s", acc);
 if (ci->imageId == 0)
     errAbort("no IMAGE:nnnn entry in mrnaClone table for MGC clone %s", acc);
 return ci;
 }
 
 static struct cloneInfo *orfeomeCloneInfoLoad(struct sqlConnection *conn, char *acc,
                                               int start)
 /* Load ORFeome clone information */
 {
 struct cloneInfo *ci = cloneInfoLoad(conn, acc, start, "orfeomeMrna", "orfeomeGenes");
 ci->isMgc = FALSE;
 return ci;
 }
 
 
 static void prCellLabelVal(char *label, char *val)
 /* print label and value as adjacent cells  */
 {
 webPrintLabelCell(label);
 webPrintLinkCell(val);
 }
 
 static void prInitialSection(struct cloneInfo *ci, char *collection)
 /* start page and print initial section */
 {
 cartWebStart(cart, database, "%s Clone %s.%d", collection, ci->acc, ci->version);
 printf("<B>%s</B>\n", ci->geneName);
 printf("<BR>%s\n", ci->desc);
 if (ci->refSeqAccv != NULL)
     printf("<BR><B>RefSeq</B>: %s\n", ci->refSeqAccv);
 if (ci->refSeqSum != NULL)
     {
     printf("<BR><B>RefSeq Summary</B>:");
     if (!sameString(ci->refSeqSumAccv, ci->refSeqAccv))
         printf(" <EM>(summary from %s)</EM>:", ci->refSeqAccv); // no summary for best match
     printf(" %s\n", ci->refSeqSum);
     }
 }
 
 static void prCloneInfo(struct cloneInfo *ci)
 /* print table of clone information */
 {
 webPrintLinkTableStart();
 prCellLabelVal("Gene", ci->geneName);
 webPrintLinkTableNewRow();
 prCellLabelVal("Product", ci->productName);
 webPrintLinkTableNewRow();
 prCellLabelVal("Tissue", ci->tissue);
 webPrintLinkTableNewRow();
 prCellLabelVal("Library", ci->library);
 webPrintLinkTableNewRow();
 prCellLabelVal("Development", ci->development);
 webPrintLinkTableNewRow();
 prCellLabelVal("CDS", ci->cds);
 webPrintLinkTableNewRow();
 prCellLabelVal("Modification date", ci->moddate);
 webPrintLinkTableEnd();
 }
 
 static void prSeqLinks(struct sqlConnection *conn, struct cloneInfo *ci)
 /* print table of sequence links */
 {
 webNewSection("Sequences");
 webPrintLinkTableStart();
 
 webPrintLinkCellStart();
 hgcAnchorSomewhere("htcDisplayMrna", ci->acc, ci->pslTbl, seqName);
 printf("mRNA</a>");
 webPrintLinkCellEnd();
 
 webPrintLinkCellStart();
 hgcAnchorSomewhere("htcTranslatedMRna", ci->acc, ci->pslTbl, seqName);
 printf("Protein</A><br>");
 webPrintLinkCellEnd();
 
 webPrintLinkCellStart();
 hgcAnchorSomewhere("htcGeneInGenome", ci->acc, ci->gpTbl, seqName);
 printf("Genomic</A>");
 webPrintLinkCellEnd();
 
 webPrintLinkTableNewRow();
 
 webPrintLinkCellStart();
 hgcAnchorSomewhere("htcDisplayMrna", ci->acc, ci->gpTbl, seqName);
 printf("Reference genome mRNA</A>");
 webPrintLinkCellEnd();
 
 #if BROKEN
 // FIXME: doesn't work when genePred table is not the track; not that important
 webPrintLinkCellStart();
 hgcAnchorSomewhereTbl("htcTranslatedPredMRna", ci->acc, ci->pslTbl, seqName, ci->gpTbl);
 printf("Reference genome protein</A>");
 webPrintLinkCellEnd();
 webFinishPartialLinkTable(1, 2, 3);
 #else
 webFinishPartialLinkTable(1, 1, 3);
 #endif
 
 webPrintLinkTableEnd();
 }
 
 static void prAlign(struct sqlConnection *conn, char *pslTbl, struct psl *psl)
 /* print an alignment */
 {
 // genomic location
 webPrintLinkCellStart();
 printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
        hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd,
        psl->tName, psl->tStart+1, psl->tEnd);
 webPrintLinkCellEnd();
 
 // genomic span
 webPrintLinkCellRightStart();
 printf("%d", psl->tEnd-psl->tStart);
 webPrintLinkCellEnd();
 
 // strand
 webPrintLinkCell(psl->strand);
 
 // mRNA location, linked to aligment viewer
 webPrintLinkCellStart();
 char other[128];
 safef(other, sizeof(other), "%d&aliTable=%s", psl->tStart, pslTbl);
 hgcAnchorSomewhere("htcCdnaAli", psl->qName, other, psl->tName);
 printf("%s:%d-%d</A>", psl->qName, psl->qStart+1, psl->qEnd);
 webPrintLinkCellEnd();
 
 // identity
 webPrintLinkCellRightStart();
 printf("%.2f%%", 100.0 * pslIdent(psl));
 webPrintLinkCellEnd();
 
 // fraction aligned
 webPrintLinkCellRightStart();
 int aligned = psl->match + psl->misMatch + psl->repMatch;
 printf("%.2f%%", 100.0*aligned/((float)psl->qSize));
 webPrintLinkCellEnd();
 }
 
 static void prAligns(struct sqlConnection *conn, struct cloneInfo *ci)
 /* print table of alignments */
 {
 struct psl* pslList = getAlignments(conn, ci->pslTbl, ci->acc);
 assert(pslList != NULL);
 slSort(&pslList, pslCmpMatch);
 
 // header, print note about order only if we have multiple alignments and didn't
 // come from another details page
 webNewSection("Alignments");
 if ((pslList->next != NULL) && (winStart < winEnd))
     printf("<span style='font-size:smaller;'><em>The alignment you clicked on is shown first.</em></span>\n");
 
 webPrintLinkTableStart();
 webPrintLabelCell("genomic (browser)");
 webPrintLabelCell("span");
 webPrintLabelCell("&nbsp;");
 webPrintLabelCell("mRNA (alignment details)");
 webPrintLabelCell("identity");
 webPrintLabelCell("aligned");
 
 // print with clicked alignment first
 struct psl* psl;
 int pass;
 for (pass = 1; pass <= 2; pass++)
     {
     for (psl = pslList; psl != NULL; psl = psl->next)
         if ((pass == 1) == (psl->tStart == ci->start))
             {
             webPrintLinkTableNewRow();
             prAlign(conn, ci->pslTbl, psl);
             }
     }
 webPrintLinkTableEnd();
 }
 
 enum gbMiscDiffFields
 /* optional fields in gbMiscDiff table */
 {
     gbMiscDiffNotes = 0x01,
     gbMiscDiffGene = 0x02,
     gbMiscDiffReplace = 0x04
 };
 
 static unsigned getMiscDiffFields(struct gbMiscDiff *gmds)
 /* find which fields are present */
 {
 struct gbMiscDiff *gmd;
 unsigned flds = 0;
 for (gmd = gmds; gmd != NULL; gmd = gmd->next)
     {
     if (gmd->notes != NULL)
         flds |= gbMiscDiffNotes;
     if (gmd->gene != NULL)
         flds |=gbMiscDiffGene;
     if (gmd->replacement != NULL)
         flds |= gbMiscDiffReplace;
     }
 return flds;
 }
 
 static void prMiscDiffHdr(unsigned miscDiffFlds)
 /* print a header row for miscDiffs table */
 {
 webPrintLabelCell("mRNA start");
 webPrintLabelCell("mRNA end");
 if (miscDiffFlds & gbMiscDiffGene)
     webPrintLabelCell("Gene");
 if (miscDiffFlds & gbMiscDiffReplace)
     webPrintLabelCell("Replace");
 if (miscDiffFlds & gbMiscDiffNotes)
     webPrintLabelCell("Notes");
 }
 
 static void prMiscDiff(struct gbMiscDiff *gmd, unsigned miscDiffFlds)
 /* print any gbMiscDiff row */
 {
 webPrintLinkTableNewRow();
 webPrintIntCell(gmd->mrnaStart);
 webPrintIntCell(gmd->mrnaEnd);
 if (miscDiffFlds & gbMiscDiffGene)
     webPrintLinkCell(gmd->gene);
 if (miscDiffFlds & gbMiscDiffReplace)
     webPrintLinkCell(gmd->replacement);
 if (miscDiffFlds & gbMiscDiffNotes)
     webPrintLinkCell(gmd->notes);
 }
 
 static void prMiscDiffs(struct sqlConnection *conn, char *acc)
 /* print any gbMiscDiff rows for the accession */
 {
 struct gbMiscDiff *gmds = NULL, *gmd;
 if (sqlTableExists(conn, "gbMiscDiff"))
     gmds = sqlQueryObjs(conn, (sqlLoadFunc)gbMiscDiffLoad, sqlQueryMulti,
                         "select * from gbMiscDiff where acc=\"%s\"", acc);
 webNewSection("NCBI Clone Validation");
 if (gmds != NULL)
     {
     unsigned miscDiffFlds = getMiscDiffFields(gmds);
     webPrintLinkTableStart();
     prMiscDiffHdr(miscDiffFlds);
     for (gmd = gmds; gmd != NULL; gmd = gmd->next)
         prMiscDiff(gmd, miscDiffFlds);
     webPrintLinkTableEnd();
     }
 else
     printf("<EM>No clone discrepancies annotated</EM><BR><BR>\n");
 }
 
 static void prMethodsLink(struct sqlConnection *conn, char *track)
 /* generate link to methods page */
 {
 webNewSection("Description and Methods");
 printf("Click <A HREF=\"%s&g=htcTrackHtml&table=%s&c=%s&l=%d&r=%d\">here</A> for details",
        hgcPathAndSettings(), track, seqName, winStart, winEnd);
 }
 
 static void prOrderLink(char *name, struct cloneInfo *ci)
 /* create link to NCBI clone order CGI */
 {
 webPrintLinkTableNewRow();
 webPrintLinkCellStart();
 printf("<a href=\"");
 printOrderUrl(ci->gi);
 printf("\" TARGET=_blank>Order %s clone</a>", name);
 webPrintLinkCellEnd();
 }
 
 static void prImageLink(struct cloneInfo *ci)
 /* create link to IMAGE database */
 {
 webPrintLinkTableNewRow();
 webPrintLinkCellStart();
 printf("<a href=\"");
 printImageUrl(ci->imageId);
 printf("\" TARGET=_blank>IMAGE clone %d</a>", ci->imageId);
 webPrintLinkCellEnd();
 }
 
 static void prGenbankLink(struct cloneInfo *ci)
 /* create link to Genbank database */
 {
 webPrintLinkTableNewRow();
 webPrintLinkCellStart();
 printf("<a href=\"");
 printEntrezNucleotideUrl(stdout, ci->acc);
 printf("\" TARGET=_blank>Genbank %s</a>", ci->acc);
 webPrintLinkCellEnd();
 }
 
 static void prRefSeqLinks(struct cloneInfo *ci)
 /* print link to RefSeq */
 {
 webPrintLinkTableNewRow();
 webPrintLinkCellStart();
 printf("<a href=\"");
 printEntrezNucleotideUrl(stdout, ci->refSeqAccv);
 printf("\" TARGET=_blank>RefSeq %s</a>", ci->refSeqAccv);
 webPrintLinkCellEnd();
 }
 
 static void prCcdsLinks(struct sqlConnection *conn, struct cloneInfo *ci)
 /* generate links to CCDS gene */
 {
 struct geneSimilarities *ccdsGenes
     = geneSimilaritiesBuildAt(conn, TRUE, ci->acc, seqName, ci->start,
                               ci->gpTbl, "ccdsGene");
 if (ccdsGenes->genes != NULL)
     {
     /* just use cloest one */
     char *ccdsId = ccdsGenes->genes->gene->name;
     webPrintLinkTableNewRow();
     webPrintLinkCellStart();
     printf("<A href=\"");
     printCcdsUrl(conn, ccdsId);
     printf("\">%s</A>", ccdsId);
     webPrintLinkCellEnd();
     }
 geneSimilaritiesFree(&ccdsGenes);
 }
 
 static void prUcscGenesLinks(struct sqlConnection *conn, struct cloneInfo *ci)
 /* generate links to UCSC or known genes */
 {
 struct geneSimilarities *ucscGenes
     = geneSimilaritiesBuildAt(conn, TRUE, ci->acc, seqName, ci->start,
                               ci->gpTbl, "knownGene");
 if (ucscGenes->genes != NULL)
     {
     /* just use cloest one */
     struct genePred *gene = ucscGenes->genes->gene;
     webPrintLinkTableNewRow();
     webPrintLinkCellStart();
     printf("<A href=\"../cgi-bin/hgGene?%s&db=%s&hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=knownGene\">UCSC Gene %s</A>",
            cartSidUrlString(cart), database, gene->name, seqName, gene->txStart, gene->txEnd, gene->name);
     webPrintLinkCellEnd();
     }
 geneSimilaritiesFree(&ucscGenes);
 }
 
 static void prMgcCloneLinks(struct sqlConnection *conn, struct mgcDb *mgcDb, struct cloneInfo *ci)
 /* print table of clone links */
 {
 webPrintLinkTableStart();
 webPrintLabelCell("Links");
 if (ci->gi > 0)
     prOrderLink(mgcDb->name, ci);
 
 // link to MGC database
 webPrintLinkTableNewRow();
 webPrintLinkCellStart();
 printf("<a href=\"");
 printMgcUrl(ci->imageId);
 printf("\" TARGET=_blank>%s clone database</a>", mgcDb->name);
 webPrintLinkCellEnd();
 
 prImageLink(ci);
 prGenbankLink(ci);
 if (ci->refSeqAccv != NULL)
     prRefSeqLinks(ci);
 if (sqlTableExists(conn, "ccdsGene"))
     prCcdsLinks(conn, ci);
 if (sqlTableExists(conn, "knownGene"))
     prUcscGenesLinks(conn, ci);
 
 // Brent lab validation database
 if (isInMBLabValidDb(ci->acc))
     {
     webPrintLinkTableNewRow();
     webPrintLinkCellStart();
     printf("<a href=\"");
     printMBLabValidDbUrl(ci->acc);
     printf("\" TARGET=_blank>Brent Lab Clone Validation</a>");
     webPrintLinkCellEnd();
     }
 webPrintLinkTableEnd();
 }
 
 static void prMgcInfoLinks(struct sqlConnection *conn, char *acc, struct mgcDb *mgcDb,
                            struct cloneInfo *ci)
 /* print clone info and links */
 {
 webNewSection("%s Clone Information and Links", mgcDb->name);
 printf("<table border=0><tr valign=top><td>\n");
 prCloneInfo(ci);
 printf("<td>\n");
 prMgcCloneLinks(conn, mgcDb, ci);
 printf("</tr></table>\n");
 }
 
 static void prRefSeqSim(struct cloneInfo *ci, struct geneSim *gs)
 /* print similarity information for a given RefSeq */
 {
 webPrintLinkTableNewRow();
 // RefSeq acc and link
 webPrintLinkCellStart();
 printf("<a href=\"");
 printEntrezNucleotideUrl(stdout, gs->gene->name);
 printf("\" TARGET=_blank>%s</a>", gs->gene->name);
 webPrintLinkCellEnd();
 
 // link to browser
 webPrintLinkCellStart();
 printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\" target=_blank>%s:%d-%d</A>",
        hgTracksPathAndSettings(), database,
        gs->gene->chrom, gs->gene->txStart+1, gs->gene->txEnd,
        gs->gene->chrom, gs->gene->txStart+1, gs->gene->txEnd);
 webPrintLinkCellEnd();
 
 // similarity
 webPrintLinkCellRightStart();
 printf("%0.2f%%", 100.0*gs->sim);
 webPrintLinkCellEnd();
 }
 
 static void prRefSeqSims(struct cloneInfo *ci)
 /* print similarity information for RefSeqs */
 {
 webNewSection("RefSeq CDS isoform similarity of %s clone %s",
               cdnaInfoDbName(ci), ci->acc);
 webPrintLinkTableStart();
 webPrintLabelCell("RefSeq");
 webPrintLabelCell("Position");
 webPrintLabelCell("Similarity");
 struct geneSim *gs;
 for (gs = ci->refSeqs->genes; gs != NULL; gs = gs->next)
     prRefSeqSim(ci, gs);
 webPrintLinkTableEnd();
 printf("This table compares the similarity of the BLAT genomic alignments of "
        "the CDS of this %s clone with alignment of RefSeq mRNA CDSs.  This is a metric "
        "of the similarity of the exon structure of the mRNAs, rather than a measure of their "
        "nucleotide sequence similarity.", cdnaInfoDbName(ci));
 }
 
 void doMgcGenes(struct trackDb *tdb, char *acc)
 /* Process click on a mgcGenes track. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 int start = cartInt(cart, "o");
 struct mgcDb mgcDb = getMgcDb();
 struct cloneInfo *ci = mgcCloneInfoLoad(conn, acc, start);
 
 prInitialSection(ci, mgcDb.name);
 printf("<BR><B>Clone Source</B>: <A href=\"");
 printMgcHomeUrl(&mgcDb);
 printf("\" TARGET=_blank>%s</A>\n", mgcDb.title);
 
 prMgcInfoLinks(conn, acc, &mgcDb, ci);
 if ((ci->refSeqs != NULL) && (ci->refSeqs->genes != NULL))
     prRefSeqSims(ci);
 prSeqLinks(conn, ci);
 prAligns(conn, ci);
 prMiscDiffs(conn, acc);
 prMethodsLink(conn, tdb->track);
 
 cloneInfoFree(&ci);
 hFreeConn(&conn);
 }
 
 static void prOrfeomeCloneLinks(struct sqlConnection *conn, char *acc, struct cloneInfo *ci)
 /* print table of clone links */
 {
 webPrintLinkTableStart();
 webPrintLabelCell("Links");
 webPrintLinkTableNewRow();
 if (ci->gi > 0)
     prOrderLink("ORFeome", ci);
 
 #if 0
 // link to ORFeome database
 // FIXME: this doesn't appear to work, need to ask Christa
 // http://www.orfeomecollaboration.org/bin/cloneStatus.pl
 #endif
 
 if (ci->imageId > 0)
     prImageLink(ci);
 prGenbankLink(ci);
 if (ci->refSeqAccv != NULL)
     prRefSeqLinks(ci);
 if (sqlTableExists(conn, "ccdsGene"))
     prCcdsLinks(conn, ci);
 if (sqlTableExists(conn, "knownGene"))
     prUcscGenesLinks(conn, ci);
 
 webPrintLinkTableEnd();
 }
 
 static void prOrfeomeInfoLinks(struct sqlConnection *conn, char *acc, struct cloneInfo *ci)
 /* print clone info and links */
 {
 webNewSection("ORFeome Clone Information and Links");
 printf("<table border=0><tr valign=top><td>\n");
 prCloneInfo(ci);
 printf("<td>\n");
 prOrfeomeCloneLinks(conn, acc, ci);
 printf("</tr></table>\n");
 }
 
 void doOrfeomeGenes(struct trackDb *tdb, char *acc)
 /* Process click on a orfeomeGenes track. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 int start = cartInt(cart, "o");
 struct cloneInfo *ci = orfeomeCloneInfoLoad(conn, acc, start);
 
 // initial section
 prInitialSection(ci, "ORFeome");
 printf("<BR><B>Clone Source</B>: <A href=\"http://www.orfeomecollaboration.org/\""
        " TARGET=_blank>ORFeome collaboration</A>\n");
 
 prOrfeomeInfoLinks(conn, acc, ci);
 if ((ci->refSeqs != NULL) && (ci->refSeqs->genes != NULL))
     prRefSeqSims(ci);
 prSeqLinks(conn, ci);
 prAligns(conn, ci);
 prMiscDiffs(conn, acc);
 prMethodsLink(conn, tdb->track);
 cloneInfoFree(&ci);
 hFreeConn(&conn);
 }