src/hg/hgc/transMapClick.c 1.14
1.14 2010/05/24 20:19:22 kent
Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
Index: src/hg/hgc/transMapClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/transMapClick.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/hg/hgc/transMapClick.c 11 May 2010 01:43:29 -0000 1.13
+++ src/hg/hgc/transMapClick.c 24 May 2010 20:19:22 -0000 1.14
@@ -1,259 +1,259 @@
/* transMapClick - transMap click handling */
/*
* Per-genome tables associated with transMap:
* transMapAliXxx - mapped PSLs alignments
* transMapInfoXxx - information for mapped alignments
* hgFixed tables associated with transMap:
* transMapSrcXxx - information about source alignments
* transMapGeneXxx - gene information
* transMapSeqXxx - seq table for accessing sequence
* transMapExtFileXxx - extFile table
*
* Xxx is:
* - UcscGene - UCSC genes
* - RefSeq - RefSeq mRNAs
* - MRna - GenBank mRNAs
* - SplicedEst - GenBank spliced ESTs
*/
#include "common.h"
#include "hgc.h"
#include "hui.h"
#include "hCommon.h"
#include "transMapClick.h"
#include "transMapStuff.h"
#include "transMapInfo.h"
#include "transMapSrc.h"
#include "transMapGene.h"
#include "genbank.h"
struct transMapBag
/* object contain collected information on a specific transMap mapping */
{
struct psl *psl; // transMap alignment
struct transMapInfo *info; // addition information about mapping
struct transMapSrc *src; // source information
struct transMapGene *gene; // gene information
boolean srcDbIsActive; // source database is active
};
static struct transMapBag *transMapBagLoad(struct sqlConnection *conn,
struct trackDb *tdb, char *mappedId,
boolean getSrcRec)
/* load information from various tables */
{
struct transMapBag *bag;
AllocVar(bag);
bag->psl = getAlignments(conn, tdb->table, mappedId);
char *transMapInfoTbl = trackDbRequiredSetting(tdb, transMapInfoTblSetting);
bag->info = transMapInfoQuery(conn, transMapInfoTbl, mappedId);
if (getSrcRec)
{
char *transMapSrcTbl = trackDbRequiredSetting(tdb, transMapSrcTblSetting);
bag->src = transMapSrcQuery(conn, transMapSrcTbl, bag->info->srcDb, bag->info->srcId);
}
char *transMapGeneTbl = trackDbSetting(tdb, transMapGeneTblSetting);
if (transMapGeneTbl != NULL)
bag->gene = transMapGeneQuery(conn, transMapGeneTbl,
bag->info->srcDb, transMapIdToAcc(bag->info->srcId));
bag->srcDbIsActive = hDbIsActive(bag->info->srcDb);
return bag;
}
static void transMapBagFree(struct transMapBag **bagPtr)
/* free the bag */
{
struct transMapBag *bag = *bagPtr;
if (bag != NULL)
{
pslFree(&bag->psl);
transMapInfoFree(&bag->info);
transMapSrcFree(&bag->src);
transMapGeneFree(&bag->gene);
freez(bagPtr);
}
}
static void prOrgScientific(char *db)
/* print organism and scientific name for a database. */
{
char *org = hOrganism(db);
char *sciName = hScientificName(db);
if ((org != NULL) && (sciName != NULL))
printf("%s (%s)", org, sciName);
else
printf("n/a");
freeMem(org);
freeMem(sciName);
}
static char *chainSubsetDesc(enum transMapInfoChainSubset cs)
/* get description for chain subset */
{
switch (cs)
{
case transMapInfoUnknown:
return "unknown";
case transMapInfoAll:
return "all";
case transMapInfoSyn:
return "syntenic";
case transMapInfoRbest:
return "reciprocal best";
}
return NULL;
}
static void displayMapped(struct transMapBag *bag)
/* display information about the mapping alignment */
{
printf("<TABLE class=\"transMap\">\n");
printf("<CAPTION>TransMap Alignment</CAPTION>\n");
printf("<TBODY>\n");
// organism/assembly
printf("<TR CLASS=\"transMapLeft\"><TD>Organism<TD>");
prOrgScientific(database);
printf("</TR>\n");
printf("<TR CLASS=\"transMapLeft\"><TD>Genome<TD>%s</TR>\n", database);
// position
printf("<TR CLASS=\"transMapLeft\">");
printf("<TD>Position<TD CLASS=\"transMapNoWrap\">");
printf("<A HREF=\"%s&position=%s:%d-%d\">",
hgTracksPathAndSettings(),
bag->psl->tName, bag->psl->tStart, bag->psl->tEnd);
printf("%s:%d-%d</A>", bag->psl->tName, bag->psl->tStart, bag->psl->tEnd);
printf("</TR>\n");
// % identity and % aligned
printf("<TR CLASS=\"transMapLeft\"><TD>Identity<TD>%0.1f%%</TR>\n",
100.0*pslIdent(bag->psl));
printf("<TR CLASS=\"transMapLeft\"><TD>Aligned<TD>%0.1f%%</TR>\n",
100.0*pslQueryAligned(bag->psl));
// chain used in mapping
printf("<TR CLASS=\"transMapLeft\"><TD>Chain ID<TD>%s</TR>\n",
bag->info->mappingId);
printf("<TR CLASS=\"transMapLeft\"><TD>Chain subset<TD>%s</TR>\n",
chainSubsetDesc(bag->info->chainSubset));
printf("</TBODY></TABLE>\n");
}
static void displaySource(struct transMapBag *bag)
/* display information about the source gene that was mapped */
{
printf("<TABLE class=\"transMap\">\n");
printf("<CAPTION>Source Alignment</CAPTION>\n");
printf("<TBODY>\n");
// organism/assembly
printf("<TR CLASS=\"transMapLeft\"><TD>Organism<TD>");
prOrgScientific(bag->info->srcDb);
printf("</TR>\n");
printf("<TR CLASS=\"transMapLeft\"><TD>Genome<TD>%s</TR>\n", bag->info->srcDb);
// position
printf("<TR CLASS=\"transMapLeft\"><TD>Position\n");
printf("<TD CLASS=\"transMapNoWrap\">");
if (bag->srcDbIsActive)
printf("<A HREF=\"%s?db=%s&position=%s:%d-%d\" target=_blank>"
"%s:%d-%d</A>",
hgTracksName(), bag->src->db,
bag->src->chrom, bag->src->chromStart, bag->src->chromEnd,
bag->src->chrom, bag->src->chromStart, bag->src->chromEnd);
else
printf("%s:%d-%d", bag->src->chrom, bag->src->chromStart, bag->src->chromEnd);
printf("</TR>\n");
// % identity and % aligned
printf("<TR CLASS=\"transMapLeft\"><TD>Identity<TD>%0.1f%%</TR>\n",
100.0*bag->src->ident);
printf("<TR CLASS=\"transMapLeft\"><TD>Aligned<TD>%0.1f%%</TR>\n",
100.0*bag->src->aligned);
// gene and CDS
printf("<TR CLASS=\"transMapLeft\"><TD>Gene<TD>%s</TR>\n",
(((bag->gene != NULL) && (strlen(bag->gene->geneName) > 0))
? bag->gene->geneName : " "));
printf("<TR CLASS=\"transMapLeft\"><TD>CDS<TD>%s</TR>\n",
(((bag->gene != NULL) && (strlen(bag->gene->cds) > 0))
? bag->gene->cds : " "));
printf("</TBODY></TABLE>\n");
}
static void displayAligns(struct trackDb *tdb, struct transMapBag *bag)
/* display cDNA alignments */
{
int start = cartInt(cart, "o");
printf("<H3>mRNA/Genomic Alignments</H3>");
-printAlignmentsSimple(bag->psl, start, "hgcTransMapCdnaAli", tdb->track, bag->info->mappedId);
+printAlignmentsSimple(bag->psl, start, "hgcTransMapCdnaAli", tdb->table, bag->info->mappedId);
}
void transMapClickHandler(struct trackDb *tdb, char *mappedId)
/* Handle click on a transMap tracks */
{
struct sqlConnection *conn = hAllocConn(database);
struct transMapBag *bag = transMapBagLoad(conn, tdb, mappedId, TRUE);
genericHeader(tdb, mappedId);
printf("<TABLE class=\"transMapLayout\">\n");
printf("<TR><TD>\n");
displayMapped(bag);
printf("<TD>\n");
displaySource(bag);
printf("<TD> \n");
printf("</TR>\n");
printf("<TR><TD COLSPAN=3>\n");
displayAligns(tdb, bag);
printf("</TR>\n");
printf("</TABLE>\n");
printTrackHtml(tdb);
transMapBagFree(&bag);
hFreeConn(&conn);
}
static struct dnaSeq *getCdnaSeq(struct trackDb *tdb, char *name)
/* look up sequence name in seq and extFile tables specified
* for base coloring. */
{
/* FIXME: this is really a rip off of some of the code in
* hgTracks/cds.c; really need to centralize it somewhere */
char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE);
char *specCopy = cloneString(spec);
// value is: extFile seqTbl extFileTbl
char *words[3];
int nwords = chopByWhite(specCopy, words, ArraySize(words));
if ((nwords != ArraySize(words)) || !sameString(words[0], "extFile"))
errAbort("invalid %s track setting: %s", BASE_COLOR_USE_SEQUENCE, spec);
struct dnaSeq *seq = hDnaSeqGet(NULL, name, words[1], words[2]);
freeMem(specCopy);
return seq;
}
void transMapShowCdnaAli(struct trackDb *tdb, char *mappedId)
/* Show alignment for mappedId, mostly ripped off from htcCdnaAli */
{
struct sqlConnection *conn = hAllocConn(database);
struct transMapBag *bag = transMapBagLoad(conn, tdb, mappedId, FALSE);
struct genbankCds cds;
if ((bag->gene == NULL) || (strlen(bag->gene->cds) == 0)
|| !genbankCdsParse(bag->gene->cds, &cds))
ZeroVar(&cds); /* can't get or parse cds */
struct dnaSeq *seq = getCdnaSeq(tdb, transMapIdToAcc(mappedId));
writeFramesetType();
puts("<HTML>");
printf("<HEAD>\n<TITLE>%s vs Genomic</TITLE>\n</HEAD>\n\n", mappedId);
showSomeAlignment(bag->psl, seq, gftDna, 0, seq->size, NULL, cds.start, cds.end);
dnaSeqFree(&seq);
transMapBagFree(&bag);
hFreeConn(&conn);
}