/* probePage - put up page of info on probe. */

/* Copyright (C) 2013 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

#include "common.h"
#include "hash.h"
#include "dystring.h"
#include "jksql.h"
#include "cart.h"
#include "htmshell.h"
#include "dnautil.h"
#include "web.h"
#include "hdb.h"
#include "visiGene.h"
#include "hgVisiGene.h"
#include "probePage.h"

static char *orgName(struct sqlConnection *conn, int taxon)
/* Return organism name associated with taxon. */
{
char *binomial;
char query[256];
sqlSafef(query, sizeof(query), 
	"select binomial from uniProt.taxon where id=%d", taxon);
binomial = sqlQuickString(conn, query);
return shortOrgName(binomial);
}

static void labeledText(char *label, char *text)
/* Print out labeled text */
{
printf("<B>%s</B>: %s ", label, naForEmpty(text));
}

static void labeledResult(char *label, struct sqlConnection *conn, char *query)
/* Put up labeled query result. */
{
labeledText(label, sqlQuickString(conn, query));
}

static void rnaProbeInfo(struct sqlConnection *conn, int probeId)
/* Print out info on RNA/DNA based probe */
{
char query[256];
char *seq;
printf("<BR>\n");
sqlSafef(query, sizeof(query), 
    "select fPrimer from probe where id=%d", probeId);
labeledResult("forward primer", conn, query);
printf("<BR>\n");
sqlSafef(query, sizeof(query), 
    "select rPrimer from probe where id=%d", probeId);
labeledResult("reverse primer", conn, query);
printf("<BR>\n");
sqlSafef(query, sizeof(query),
    "select seq from probe where id=%d", probeId);
seq = naForEmpty(sqlQuickString(conn, query));
printf("<BR><B>sequence:</B>\n");
if (sameWord(seq, "n/a"))
   printf("%s<BR>", seq);
else
    {
    printf("<TT><PRE>");
    writeSeqWithBreaks(stdout, seq, strlen(seq), 60);
    printf("</PRE></TT>");
    }
}

static void bacProbeInfo(struct sqlConnection *conn, int probeId, int taxon)
/* Print out information about BAC probe. */
{
char query[256];
int bacId;
char *name = NULL;
char *genomeDb = hDbForTaxon(taxon);
boolean gotMapping = FALSE;

/* Start new line. */
printf("<BR>\n");

/* Lookup bacId and print name associated with it. */
sqlSafef(query, sizeof(query), "select bac from probe where id=%d", probeId);
bacId = sqlQuickNum(conn, query);
if (bacId != 0)
    {
    sqlSafef(query, sizeof(query), "select name from bac where id=%d", bacId);
    name = sqlQuickString(conn, query);
    }

/* Find where bac lands in genome and print hyperlink to genome browser. */
if (genomeDb != NULL && name != NULL && name[0] != 0)
    {
    struct sqlConnection *gConn = sqlConnect(genomeDb);
    if (sqlTableExists(gConn, "bacEndPairs"))
        {
	char query[256];
	int count;
	sqlSafef(query, sizeof(query), 
	    "select count(*) from bacEndPairs where name = '%s'", name);
	count = sqlQuickNum(gConn, query);
	if (count > 0)
	    gotMapping = TRUE;
	}
    sqlDisconnect(&gConn);
    }

/* Print out BAC name, hyperlinked to genome browser if possible. */
printf("<B>BAC name:</B> ");
if (gotMapping)
    {
    printf("<A HREF=\"");
    printf("../cgi-bin/hgTracks?db=%s&position=%s", genomeDb, name);
    printf("\">");
    }
printf("%s", naForEmpty(name));
if (gotMapping)
   printf("</A>");
}

static void antibodyProbeInfo(struct sqlConnection *conn, 
    int probeId, int submissionSourceId)
/* Print out info on antibody based probe */
{
char query[256];
int abId;
int taxon;
char *species = "n/a";
char *abUrl = NULL;

/* Lookup antibody id and taxon. */
sqlSafef(query, sizeof(query), "select antibody from probe where id=%d", 
	probeId);
abId = sqlQuickNum(conn, query);
sqlSafef(query, sizeof(query), "select taxon from antibody where id=%d", abId);
taxon = sqlQuickNum(conn, query);

sqlSafef(query, sizeof(query), "select name from antibody where id=%d", abId);
labeledResult("name", conn, query);
if (taxon != 0)
    species = orgName(conn, taxon);
labeledText("species", species);
printf("<BR>\n");
sqlSafef(query, sizeof(query), "select description from antibody where id=%d", abId);
labeledResult("description", conn, query);
printf("<BR>\n");

sqlSafef(query, sizeof(query), "select abUrl from submissionSource where id=%d", submissionSourceId);
abUrl = sqlQuickString(conn, query);
if (abUrl != NULL && abUrl[0] != 0)
    {
    char *abSubmitId = NULL;
    sqlSafef(query, sizeof(query), "select abSubmitId from antibodySource"
	" where antibody=%d and submissionSource=%d", abId, submissionSourceId);
    abSubmitId = sqlQuickString(conn, query);
    if (abSubmitId != NULL && abSubmitId[0] != 0)
	{
	printf("<B>source:</B> ");
	printf("<A HREF=\"");
	printf(abUrl, abSubmitId);
	printf("\" target=_blank>%s</A> ", "MGI");
	freez(&abSubmitId);
	}
    }

freez(&abUrl);
}

void probePage(struct sqlConnection *conn, int probeId, int submissionSourceId)
/* Put up a page of info on probe. */
{
char query[256];
int geneId, taxon;
char *probeType;

webStartWrapperDetailedNoArgs(cart, NULL, "", "Probe Information",
        FALSE, FALSE, FALSE, TRUE);

/* Get gene ID. */
sqlSafef(query, sizeof(query), "select gene from probe where id=%d", probeId);
geneId = sqlQuickNum(conn, query);

/* Print gene symbol. */
sqlSafef(query, sizeof(query), "select name from gene where id=%d", geneId);
labeledResult("gene symbol", conn, query);

/* Print organism. */
sqlSafef(query, sizeof(query), "select taxon from gene where id=%d", geneId);
taxon = sqlQuickNum(conn, query);
labeledText("organism", orgName(conn, taxon));

/* Print synonyms if any. */
sqlSafef(query, sizeof(query), 
	"select name from geneSynonym where gene=%d", geneId);
printf("<B>synonyms: </B> %s<BR>\n", 
	makeCommaSpacedList(sqlQuickList(conn, query)));

/* Print refSeq, genbank, uniProt */
sqlSafef(query, sizeof(query), "select refSeq from gene where id=%d", geneId);
labeledResult("RefSeq", conn, query);
sqlSafef(query, sizeof(query), "select genbank from gene where id=%d", geneId);
labeledResult("GenBank", conn, query);
sqlSafef(query, sizeof(query), "select uniProt from gene where id=%d", geneId);
labeledResult("UniProt", conn, query);

/* Now print probe information. */
sqlSafef(query, sizeof(query),
	"select probeType.name from probe,probeType "
	"where probe.id = %d and probe.probeType = probeType.id"
	, probeId);
probeType = sqlQuickString(conn, query);
labeledText("probe type", probeType);
if (sameWord(probeType, "antibody"))
    antibodyProbeInfo(conn, probeId, submissionSourceId);
else if (sameWord(probeType, "BAC"))
    bacProbeInfo(conn, probeId, taxon);
else
    rnaProbeInfo(conn, probeId);

webEnd();
}