/* domains - do protein domains section. */
/* This module is adopted from the domains module of hgGene. */

/* 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 "linefile.h"
#include "dystring.h"
#include "spDb.h"
#include "hdb.h"
#include "pbTracks.h"


char *samGenomeDb(char *proteinId)
/* Determin if a protein belongs to a genome DB that has SAM results */
/* This function will be updated as SAM applies to more genomes */
{
char condStr[128];
char *taxon;

sqlSafef(condStr, sizeof(condStr), "acc='%s'", proteinId);
taxon = sqlGetField(UNIPROT_DB_NAME, "accToTaxon", "taxon", condStr);
if (taxon == NULL) return(NULL);

if (sameWord(taxon, "4932")) 
    {
    return(strdup("sacCer1"));
    }
else
    {
    return(NULL);
    }
}

void modBaseAnchor(char *swissProtAcc)
/* Print out anchor to modBase. */
{
hPrintf("<A HREF=\"http://salilab.org/modbase/search?databaseID=%s\" TARGET=_blank>", swissProtAcc);
}

void domainsPrint(struct sqlConnection *spConn, char *swissProtAcc)
/* Print out protein domains. */
{
struct slName *el, *list;
char *samDb;
char condStr[128];
char *parentId;
char *kgId = NULL;

/* Use parent protein ID for domain links */

/* There may be cases that a specific variant may have some domain spliced out */
/* But, it is better to cover most of them, than none at all */

sqlSafef(condStr, sizeof(condStr), "variant='%s'", swissProtAcc);
parentId = sqlGetField(PROTEOME_DB_NAME, "spVariant", "parent", condStr);

list = spExtDbAcc1List(spConn, parentId, "Interpro");
if (list != NULL)
    {
    char query[256], **row;
    struct sqlResult *sr;
    hPrintf("<B>InterPro Domains: </B>");
    hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/ISpy?mode=single&ac=%s\" TARGET=_blank>",
    	swissProtAcc);
    hPrintf("Graphical view of domain structure</A><BR>\n<UL>");fflush(stdout);
    sqlSafef(query, sizeof(query),
    	"select extAcc1,extAcc2 from extDbRef,extDb"
	" where extDbRef.acc = '%s'"
	" and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb"
	, parentId);
	
    sr = sqlGetResult(spConn, query);
    while ((row = sqlNextRow(sr)) != NULL)
        {
	hPrintf("<LI><A HREF=\"http://www.ebi.ac.uk/interpro/IEntry?ac=%s\" TARGET=_blank>", row[0]);
	hPrintf("%s</A> - %s</LI>\n", row[0], row[1]);
	}
    hPrintf("</UL>\n");
    slFreeList(&list);
    }

if (kgVersion == KG_III)
    {
    struct sqlConnection *hgConn;   /* Connection to genome database. */
    hgConn = sqlConnect(database);
   
    sqlSafef(condStr, sizeof(condStr), "spId='%s'", swissProtAcc);
    kgId = sqlGetField(database, "kgXref", "kgId", condStr);
   
    /* Do Pfam domains here. */
    list = NULL;
    if (kgId != NULL) list = getPfamDomainList(hgConn, kgId);
    if (list != NULL)
    	{
    	hPrintf("<B>Pfam Domains:</B><BR>");
    	for (el = list; el != NULL; el = el->next)
	    {
	    char query[256];
	    char *description;
	    sqlSafef(query, sizeof(query), 
	          "select description from %s.pfamDesc where pfamAC='%s'", database, el->name);
	    description = sqlQuickString(hgConn, query);
	    if (description == NULL)
	    	description = cloneString("n/a");
	    hPrintf("<A HREF=\"http://pfam.sanger.ac.uk/family?acc=%s\" TARGET=_blank>", 
	    	    el->name);
	    hPrintf("%s</A> - %s<BR>\n", el->name, description);
	    freez(&description);
	    }
        slFreeList(&list);
        hPrintf("<BR>\n");
	}
    
    /* Do SCOP domains here */
    list = NULL;
    if (kgId != NULL) list = getDomainList(hgConn, kgId,  "Scop");
    if (list != NULL)
    	{
    	hPrintf("<B>SCOP Domains:</B><BR>");
    	for (el = list; el != NULL; el = el->next)
	    {
	    char query[256];
	    char *description;
	    sqlSafef(query, sizeof(query), 
	          "select description from %s.scopDesc where acc='%s'", database, el->name);
	    description = sqlQuickString(hgConn, query);
	    if (description == NULL)
	    	description = cloneString("n/a");
	    hPrintf("<A HREF=\"http://scop.berkeley.edu/search.cgi?sunid=%s\" TARGET=_blank>", 
	    	    el->name);
	    hPrintf("%s</A> - %s<BR>\n", el->name, description);
	    freez(&description);
	    }
        slFreeList(&list);
        hPrintf("<BR>\n");
	}
    }
else
    {
    list = spExtDbAcc1List(spConn, parentId, "Pfam");
    if (list != NULL)
    	{
    	hPrintf("<B>Pfam Domains:</B>\n<UL>");fflush(stdout);
    	for (el = list; el != NULL; el = el->next)
	    {
	    char query[256];
	    char *description;
            sqlSafef(query, sizeof(query), "select description from %s.pfamDesc where pfamAC='%s'", 
		  protDbName, el->name);
	    description = sqlQuickString(spConn, query);
	    if (description == NULL)
	    	description = cloneString("n/a");
	    hPrintf("<LI><A HREF=\"http://pfam.sanger.ac.uk/family?acc=%s\" TARGET=_blank>", 
	    	    el->name);
	    hPrintf("%s</A> - %s</LI>\n", el->name, description);
	    freez(&description);
	    }
    	slFreeList(&list);
    	hPrintf("</UL>\n");
    	}
    }

/* do not use parent protein, since 3D structure is determined by specific protein sequence */
list = spExtDbAcc1List(spConn, swissProtAcc, "PDB");
if (list != NULL)
    {
    char query[256], **row;
    struct sqlResult *sr;
    int column = 0, maxColumn=4, rowCount=0;
    hPrintf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>");
    sqlSafef(query, sizeof(query),
    	"select extAcc1,extAcc2 from extDbRef,extDb"
	" where extDbRef.acc = '%s'"
	" and extDb.val = 'PDB' and extDb.id = extDbRef.extDb"
	, swissProtAcc);
    sr = sqlGetResult(spConn, query);
    hPrintf("<TABLE><TR>\n");
    while ((row = sqlNextRow(sr)) != NULL)
        {
	if (++column > maxColumn)
	    {
	    hPrintf("</TR><TR>");
	    column = 1;
	    if (rowCount == 0)
	        {
		hPrintf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn);
		hPrintf("</TR><TR>");
		}
	    ++rowCount;
	    }
	hPrintf("<TD>");
	hPrintf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]);
	if (rowCount < 1)
	    hPrintf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_asym_r_250.jpe\"><BR>", row[0]);
	hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
	hPrintf("</TD>");
	}
    hPrintf("</TR></TABLE>\n");
    hPrintf("<BR>\n");
    slFreeList(&list);
    }

/* if this protein belongs to a genome having SAM-T02 results, show the sub-section */
samDb = samGenomeDb(swissProtAcc);
if (samDb != NULL)
    {
    doSamT02(swissProtAcc, samDb);
    }
    
/* do not use parent ID, again 3D structure is dependent on specific sequence */    
/* Do modBase link. */
    {
    hPrintf("<B>ModBase Predicted Comparative 3D Structure on ");
    modBaseAnchor(swissProtAcc);
    hPrintf("%s", swissProtAcc);
    hPrintf("</A></B><BR>\n");
    hPrintf("<TABLE><TR>");
    hPrintf("<TD>");
    modBaseAnchor(swissProtAcc);
    hPrintf("<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", swissProtAcc);
    hPrintf("<TD>");
    modBaseAnchor(swissProtAcc);
    hPrintf("<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x&degree=90\"></A></TD>", swissProtAcc);
    hPrintf("<TD>");
    modBaseAnchor(swissProtAcc);
    hPrintf("<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y&degree=90\"></A></TD>", swissProtAcc);
    hPrintf("</TR><TR>\n");
    hPrintf("<TD ALIGN=CENTER>Front</TD>");
    hPrintf("<TD ALIGN=CENTER>Top</TD>");
    hPrintf("<TD ALIGN=CENTER>Side</TD>");
    hPrintf("</TR></TABLE>\n");
    hPrintf("<I>The pictures above may be empty if there is no "
            "ModBase structure for the protein.  The ModBase structure "
	    "frequently covers just a fragment of the protein.  You may "
	    "be asked to log onto ModBase the first time you click on the "
	    "pictures. It is simplest after logging in to just click on "
	    "the picture again to get to the specific info on that model.</I>");
    }
}