/* colKnownGene - columns having to do with knownGene and closely tables. */

/* 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 "linefile.h"
#include "hash.h"
#include "obscure.h"
#include "dystring.h"
#include "jksql.h"
#include "cheapcgi.h"
#include "cart.h"
#include "hdb.h"
#include "hCommon.h"
#include "hgNear.h"
#include "kgAlias.h"
#include "findKGAlias.h"


static char *posFromRow3(char **row)
/* Convert chrom/start/end row to position. */
{
char buf[128];
char *chrom;
int start,end;

chrom = row[0];
start = sqlUnsigned(row[1]);
end = sqlUnsigned(row[2]);
safef(buf, sizeof(buf), "%s:%d-%d", chrom, start+1, end);
return cloneString(buf);
}


static char *genePredPosFromTable(char *table, struct genePos *gp, 
	struct sqlConnection *conn)
/* Get genePred position from table.  Well, actually just get it from gp. */
{
if (gp->chrom != NULL)
    {
    char pos[256];
    safef(pos, sizeof(pos), "%s:%d-%d", gp->chrom, gp->start+1, gp->end);
    return cloneString(pos);
    }
else
    {
    char query[256];
    struct sqlResult *sr;
    char *pos = NULL;
    char **row;

    sqlSafef(query, sizeof(query), 
    	"select chrom,txStart,txEnd from %s where name = '%s'",
	table, gp->name);
    sr = sqlGetResult(conn, query);
    if ((row = sqlNextRow(sr)) != NULL)
        pos = posFromRow3(row);
    sqlFreeResult(&sr);
    return pos;
    }
}

static char *genePredPosVal(struct column *col, struct genePos *gp, 
	struct sqlConnection *conn)
/* Get genome position of genePred type table. */
{
return genePredPosFromTable(col->table, gp, conn);
}

static void genePredPosPrint(struct column *col, struct genePos *gp, 
	struct sqlConnection *conn)
/* Print genome position with hyperlink to browser. */
{
char *pos = col->cellVal(col, gp, conn);
char *chrom;
int start, end;

hPrintf("<TD>");
if (pos == NULL)
    hPrintf("n/a");
else
    {
    char numBuf[32];
    hgParseChromRange(database, pos, &chrom, &start, &end);
    sprintLongWithCommas(numBuf, (start+end+1)/2);
    hPrintf("<A HREF=\"%s?db=%s&position=%s&%s&%s=full\">",
	    hgTracksName(), database, pos, cartSidUrlString(cart), genomeSetting("geneTable"));
    hPrintf("%s&nbsp;%s</A>", chrom, numBuf);
    freeMem(pos);
    }
hPrintf("</TD>");
}

static void genePredPosFilterControls(struct column *col, struct sqlConnection *conn)
/* Print out controls for advanced filter. */
{
hPrintf("chromosome: ");
advFilterRemakeTextVar(col, "chr", 8);
hPrintf(" start: ");
advFilterRemakeTextVar(col, "start", 8);
hPrintf(" end: ");
advFilterRemakeTextVar(col, "end", 8);
}

static struct genePos *genePredPosAdvFilter(struct column *col, 
	struct sqlConnection *conn, struct genePos *list)
/* Do advanced filter on position. */
{
char *chrom = advFilterVal(col, "chr");
char *startString = advFilterVal(col, "start");
char *endString = advFilterVal(col, "end");
if (chrom != NULL)
    {
    struct genePos *newList = NULL, *gp, *next;
    for (gp = list; gp != NULL; gp = next)
	{
	next = gp->next;
	if (sameWord(chrom, gp->chrom))
	    {
	    slAddHead(&newList, gp);
	    }
	}
    slReverse(&newList);
    list = newList;
    }
if (startString != NULL)
    {
    int start = atoi(startString)-1;
    struct genePos *newList = NULL, *gp, *next;
    for (gp = list; gp != NULL; gp = next)
	{
	next = gp->next;
	if (gp->end > start)
	    {
	    slAddHead(&newList, gp);
	    }
	}
    slReverse(&newList);
    list = newList;
    }
if (endString != NULL)
    {
    int end = atoi(endString);
    struct genePos *newList = NULL, *gp, *next;
    for (gp = list; gp != NULL; gp = next)
	{
	next = gp->next;
	if (gp->start < end)
	    {
	    slAddHead(&newList, gp);
	    }
	}
    slReverse(&newList);
    list = newList;
    }
return list;
}

static void genePredPosMethods(struct column *col, char *table)
/* Put in methods for genePred based positions. */
{
col->table = table;
col->exists = simpleTableExists;
col->cellVal = genePredPosVal;
col->cellPrint = genePredPosPrint;
col->filterControls = genePredPosFilterControls;
col->advFilter = genePredPosAdvFilter;
}

static char *knownPosCellVal(struct column *col, struct genePos *gp, 
	struct sqlConnection *conn)
/* Get genome position of knownPos table.  Ok to have col NULL. */
{
char *pos = genePredPosFromTable("knownGene", gp, conn);
if (pos == NULL)
    {
    /* As a backup plan, try to find accession in all_mrna table. */
    char query[256];
    struct sqlResult *sr;
    char **row;
    sqlSafef(query, sizeof(query), "select tName, tStart, tEnd from %s where qName = '%s'",
	"all_mrna", gp->name);
    sr = sqlGetResult(conn, query);
    if ((row = sqlNextRow(sr)) != NULL)
	pos = posFromRow3(row);
    sqlFreeResult(&sr);
    }
return pos;
}

static struct genePos *genePosFromQuery(struct sqlConnection *conn, char *query, boolean oneOnly)
/* Get all positions from a query that returns 5 columns. */
{
struct sqlResult *sr;
char **row;
struct genePos *gpList = NULL, *gp;
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
    {
    AllocVar(gp);
    genePosFillFrom5(gp, row);
    slAddHead(&gpList, gp);
    if (oneOnly)
        break;
    }
sqlFreeResult(&sr);
return gpList;
}

struct genePos *knownPosAll(struct sqlConnection *conn)
/* Get all positions in knownGene table. */
{
char query[1024];
// These sql querys are safe since it is from an .ra file on disk.
if (showOnlyCanonical())
    sqlSafef(query, sizeof query, genomeSetting("allGeneQuery"),NULL);       
else
    sqlSafef(query, sizeof query, genomeSetting("allTranscriptQuery"),NULL);
return genePosFromQuery(conn, query, FALSE);
}

struct genePos *knownPosOne(struct sqlConnection *conn, char *name)
/* Get all positions of named gene. */
{
char query[1024];
sqlSafef(query, sizeof(query), genomeSetting("oneGeneQuery"), name);
return genePosFromQuery(conn, query, FALSE);
}

struct genePos *knownPosFirst(struct sqlConnection *conn)
/* Get first gene in known gene table. */
{
char query[1024];
sqlSafef(query, sizeof query, genomeSetting("allGeneQuery"), NULL); 
struct genePos *gp = genePosFromQuery(conn, query, TRUE);
return gp;
}

void setupColumnKnownPos(struct column *col, char *parameters)
/* Set up column that links to genome browser based on known gene
 * position. */
{
genePredPosMethods(col, genomeSetting("geneTable"));
col->cellVal = knownPosCellVal;
}

static void linkToDetailsCellPrint(struct column *col, struct genePos *gp, 
	struct sqlConnection *conn)
/* Print a link to known genes details page. */
{
char *s = col->cellVal(col, gp, conn);
fillInKnownPos(gp, conn);
hPrintf("<TD>");
hPrintf("<A HREF=\"../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d&%s=%s\">", 
	cartSidUrlString(cart), 
	"db", database,
	"hgg_gene", gp->name,
	"hgg_chrom", gp->chrom,
	"hgg_start", gp->start,
	"hgg_end", gp->end,
        "hgg_type", genomeSetting("geneTable"));
if (s == NULL) 
    {
    hPrintf("n/a");
    }
else
    {
    hPrintEncodedNonBreak(s);
    freeMem(s);
    }
hPrintf("</A></TD>");
}

void fillInKnownPos(struct genePos *gp, struct sqlConnection *conn)
/* If gp->chrom is not filled in go look it up. */
{
if (gp->chrom == NULL)
    {
    char *pos = knownPosCellVal(NULL, gp, conn);
    char *chrom;
    hgParseChromRange(database, pos, &chrom, &gp->start, &gp->end);
    gp->chrom = cloneString(chrom);
    }
}

struct searchResult *knownGeneSearchResult(struct sqlConnection *conn, 
	char *kgID, char *alias)
/* Return a searchResult for a known gene. */
{
struct searchResult *sr;
struct dyString *dy = dyStringNew(1024);
char query[256];
char name[64];
char *description = NULL;

/* Allocate and fill in with geneID. */
AllocVar(sr);
sr->gp.name = cloneString(kgID);

/* Get gene symbol into short label if possible. */
sqlSafef(query, sizeof(query),
	"select geneSymbol from kgXref where kgID = '%s'", kgID);
if (sqlQuickQuery(conn, query, name, sizeof(name)))
    sr->shortLabel = cloneString(name);
else
    sr->shortLabel = cloneString(kgID);

/* Add alias to long label if need be */
if (alias != NULL && !sameWord(name, alias))
    dyStringPrintf(dy, "(aka %s) ", alias);

/* Add description to long label. */
sqlSafef(query, sizeof(query), 
    "select description from kgXref where kgID = '%s'", kgID);
description = sqlQuickString(conn, query);
if (description != NULL)
    dyStringAppend(dy, description);
sr->longLabel = cloneString(dy->string);

/* Cleanup and go home. */
dyStringFree(&dy);
return sr;
}

static struct searchResult *knownNameSimpleSearch(struct column *col, 
    struct sqlConnection *conn, char *search)
/* Look for matches to known genes. */
{
struct kgAlias *ka, *kaList;
struct searchResult *srList = NULL, *sr;
kaList = findKGAlias(sqlGetDatabase(conn), search, "F");
for (ka = kaList; ka != NULL; ka = ka->next)
    {
    sr = knownGeneSearchResult(conn, ka->kgID, ka->alias);
    slAddHead(&srList, sr);
    }
return srList;
}

void setupColumnKnownDetails(struct column *col, char *parameters)
/* Set up a column that links to details page for known genes. */
{
setupColumnLookup(col, parameters);
col->cellPrint = linkToDetailsCellPrint;
}

void setupColumnKnownName(struct column *col, char *parameters)
/* Set up a column that looks up name to display, and selects on a click. */
{
setupColumnLookup(col, parameters);
col->cellPrint = cellSelfLinkPrint;
col->simpleSearch = knownNameSimpleSearch;
}