/* pbTracksGlobal.c - UCSC Global Proteome Browser main cgi script. */

/* 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 "hCommon.h"
#include "portable.h"
#include "jksql.h"
#include "vGfx.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "cart.h"
#include "hdb.h"
#include "web.h"
#include "hgColors.h"
#include "hui.h"
#include "spDb.h"
#include "pbStamp.h"
#include "pbStampPict.h"
#include "pbTracks.h"
#include "trashDir.h"
#include "psGfx.h"


boolean hgDebug = FALSE;      /* Activate debugging code. Set to true by hgDebug=on in command line*/

struct cart *cart;	/* The cart where we keep persistent variables. */

/* These variables persist from one incarnation of this program to the
 * next - living mostly in the cart. */
char *database;			/* Name of database we're using. */
char *organism;			/* Name of organism we're working on. */
char *hgsid;
char hgsidStr[50];

boolean IAmPbTracks = FALSE;

int kgVersion = KG_UNKNOWN;

boolean proteinInSupportedGenome;  /* The protein is in supported genome DB */
int protCntInSupportedGenomeDb; /* The protein count in supported genome DBs */
int protCntInSwissByGene;	/* The protein count from gene search in Swiss-Prot */

int gfxBorder = 1;		/* Width of graphics border. */
int insideWidth;		/* Width of area to draw tracks in in pixels. */

char *protDbName;               /* Name of proteome database for this genome. */

struct tempName gifTn, gifTn2;  /* gifTn for tracks image and gifTn2 for stamps image */
boolean hideControls = FALSE;   /* Hide all controls? */
boolean suppressHtml = FALSE;   /* If doing PostScript output we'll suppress most
                                 * of HTML output. */
char *proteinID;
char *protDisplayID;
char *mrnaID;
char *description;

char *positionStr;

char *prevGBChrom;		/* chrom          previously chosen by Genome Browser */
int  prevGBStartPos;		/* start position previously chosen by Genome Browser */
int  prevGBEndPos;		/* end   position previously chosen by Genome Browser */
int  prevExonStartPos;		/* start position chosen by Genome Browser, converted to exon pos */
int  prevExonEndPos;		/* end   position chosen by Genome Browser, converted to exon pos */

char *ensPepName;		/* Ensembl peptide name, used for Superfamily track */
int sfCount;			/* count of Superfamily domains */

struct sqlConnection *spConn;   /* Connection to SwissProt database. */

char aaAlphabet[30] = {"WCMHYNFIDQKRTVPGEASLXZB"};
char *protSeq;
int  protSeqLen;

char aaChar[20];
float aa_hydro[256];
int aa_attrib[256];
char aa[100000];

struct vGfx *g_vg;
MgFont *g_font;

Color pbRed, pbBlue;

int  currentYoffset;
int  pbScale = {6};
char pbScaleStr[5];

boolean scaleButtonPushed;
double tx[100000], ty[100000];

double xScale = 50.0;
double yScale = 100.0;

struct pbStampPict *stampPictPtr;

double avg[20];
double stddev[20];

int exStart[500], exEnd[500];
int exCount;
int aaStart[500], aaEnd[500];

char kgProtMapTableName[20] = {"kgProtMap"};
int blockSize[500], blockSizePositive[500];
int blockStart[500], blockStartPositive[500];
int blockEnd[500],   blockEndPositive[500];
int blockGenomeStart[500], blockGenomeStartPositive[500];
int blockGenomeEnd[500], blockGenomeEndPositive[500];

int trackOrigOffset = 0;	/* current track display origin offset */
int aaOrigOffset = 0;		/* current track AA base origin offset */
boolean initialWindow = TRUE;
struct vGfx *vg, *vg2;
Color bkgColor;

Color abnormalColor;
Color normalColor;

void dvPrintf(char *format, va_list args)
/* Suppressable variable args hPrintf. */
{
char temp[1000];
safef(temp, sizeof(temp), "<br>%s", format);

vprintf(temp, args);
fflush(stdout);
}

/* used for debugging only */
/* #include "dPrint.c" */

void hvPrintf(char *format, va_list args)
/* Suppressable variable args hPrintf. */
{
if (!suppressHtml)
    vprintf(format, args);
}

void hPrintf(char *format, ...)
/* Printf that can be suppressed if not making
 * html. */
{
va_list(args);
va_start(args, format);
hvPrintf(format, args);
va_end(args);
}

void smallBreak()
/* Draw small horizontal break */
{
hPrintf("<FONT SIZE=1><BR></FONT>\n");
}

void makeActiveImagePB(char *psOutput, char *psOutput2)
/* Make image and image map. */
{
char *mapName = "map";
int pixWidth, pixHeight;

char *answer;
char cond_str[255];
struct sqlConnection *conn;
struct sqlConnection *connCentral;
char query[256];
struct sqlResult *sr;
char **row;
int  iypos;
char *blatGbDb;
char *sciName, *commonName;
char *spDisplayId;
char *oldDisplayId;
conn  = sqlConnect(UNIPROT_DB_NAME);
hPrintf("<br><font size=4>Protein ");

hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" TARGET=_blank><B>%s</B></A>\n",
        proteinID, proteinID);

spDisplayId = spAccToId(conn, spFindAcc(conn, proteinID));
if (strstr(spDisplayId, spFindAcc(conn, proteinID)) == NULL)
    {
    hPrintf(" (aka %s", spDisplayId);
    /* show once if the new and old displayId are the same */
    oldDisplayId = oldSpDisplayId(spDisplayId);
    if (oldDisplayId != NULL)
        {
        if (!sameWord(spDisplayId, oldDisplayId))
            {
            hPrintf(" or %s", oldSpDisplayId(spDisplayId));
            }
        }
    hPrintf(")\n");
    }
hPrintf(" %s\n", description);
hPrintf("</font><br>");

hPrintf("Organism: ");
/* get scientific and Genbank common name of this organism */
sciName    = NULL;
commonName = NULL;
sqlSafef(cond_str, sizeof(cond_str),"accession='%s'", proteinID);
answer = sqlGetField(PROTEOME_DB_NAME, "spXref3", "division", cond_str);
if (answer != NULL)
    {
    sqlSafef(cond_str, sizeof(cond_str), "id=%s and nameType='scientific name'", answer);
    sciName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);

    sqlSafef(cond_str, sizeof(cond_str), "id=%s and nameType='genbank common name'", answer);
    commonName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
    }
if (sciName != NULL)
    {
    hPrintf("%s", sciName);
    }
if (commonName != NULL)
    {
    hPrintf(" (%s)", commonName);
    }
hPrintf("<br>");

protSeq = getAA(proteinID);
if (protSeq == NULL)
    {
    hUserAbort("%s is not a current valid entry in UniProtKB\n", proteinID);
    }
protSeqLen = strlen(protSeq);

fflush(stdout);

iypos = 15;
doTracks(proteinID, mrnaID, protSeq, &iypos, psOutput);
if (!hTableExists(database, "pbStamp")) goto histDone;

pbScale = 3;
pixWidth = 765;
insideWidth = pixWidth-gfxBorder;

pixHeight = 350;

if (psOutput2)
    {
    vg2 = vgOpenPostScript(pixWidth, pixHeight, psOutput2);
    }
else
    {
    trashDirFile(&gifTn2, "pbt", "pbt", ".png");
    vg2 = vgOpenPng(pixWidth, pixHeight, gifTn2.forCgi, FALSE);
    }

g_vg = vg2;

pbRed    = vgFindColorIx(vg2, 0xf9, 0x51, 0x59);
pbBlue   = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0);

normalColor   = pbBlue;
abnormalColor = pbRed;

bkgColor = vgFindColorIx(vg2, 255, 254, 232);
vgBox(vg2, 0, 0, insideWidth, pixHeight, bkgColor);

/* Start up client side map. */
mapName=cloneString("pbStamps");
hPrintf("\n<MAP Name=%s>\n", mapName);

vgSetClip(vg2, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
iypos = 15;

/* Draw stamps. */

doStamps(proteinID, mrnaID, protSeq, vg2, &iypos);

/* Finish map. */
hPrintf("</MAP>\n");

/* Save out picture and tell html file about it. */
vgClose(&vg2);
hPrintf("<P>");

hPrintf("\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>",
            gifTn2.forCgi, pixWidth, pixHeight, mapName);
if (proteinInSupportedGenome)
    {
    hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
    }
else
    {
    hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
    }

hPrintf("Explanation of Protein Property Histograms</A><BR>");

hPrintf("<P>");

histDone:

hPrintf("<P>");
fflush(stdout);

/* See if a UCSC Genome Browser exist for this organism.  If so, display BLAT link. */
connCentral = hConnectCentral();
sqlSafef(query, sizeof(query),
      "select defaultDb.name from dbDb, defaultDb where dbDb.scientificName='%s' and dbDb.name=defaultDb.name",
      sciName);
sr = sqlGetResult(connCentral, query);
row = sqlNextRow(sr);
if (row != NULL)
    {
    blatGbDb = strdup(row[0]);
    }
else
    {
    blatGbDb = NULL;
    }
sqlFreeResult(&sr);
hDisconnectCentral(&connCentral);

if (proteinInSupportedGenome || (blatGbDb != NULL))
    {
    hPrintf("\n<B>UCSC Links:</B><BR>\n ");
    hPrintf("<UL>\n");

    /* Show GB links only if the protein belongs to a supported genome */
    if (proteinInSupportedGenome)
        {
        doGenomeBrowserLink(proteinID, mrnaID, hgsidStr);
        doGeneDetailsLink(proteinID, mrnaID, hgsidStr);
        }

    /* Show Gene Sorter link only if it is valid for this genome */
    if (hgNearOk(database))
        {
        doGeneSorterLink(protDisplayID, mrnaID, hgsidStr);
        }

    /* Show BLAT link if we have UCSC Genome Browser for it */
    if (blatGbDb != NULL)
        {
        doBlatLink(blatGbDb, sciName, commonName, protSeq);
        }

    hPrintf("</UL><P>");
    }

/* This section shows various types of  domains */
conn = sqlConnect(UNIPROT_DB_NAME);
domainsPrint(conn, proteinID);

hPrintf("<P>");

/* Do Pathway section only if the protein belongs to a supported genome */
if (proteinInSupportedGenome);
    {
    doPathwayLinks(proteinID, mrnaID);
    }

printFASTA(proteinID, protSeq);
}

void doTrackForm(char *psOutput, char *psOutput2)
/* Make the tracks display form */
{
if (psOutput != NULL)
    {
    suppressHtml = TRUE;
    hideControls = TRUE;
    }

/* Tell browser where to go when they click on image. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" METHOD=POST>\n\n", "../cgi-bin/pbGlobal");
cartSaveSession(cart);

hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#"HG_COL_HOTLINKS"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"2\"><TR>\n");
hPrintf("<TD ALIGN=LEFT><A HREF=\"../index.html\">%s</A></TD>", wrapWhiteFont("Home"));
hPrintf("<TD style='text-align:center; color:#FFFFFF; font-size:medium;'>%s</TD>",
        "UCSC Proteome Browser");
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/pbGlobal?%s=%u&pbt.psOutput=on\">%s</A></TD>\n",
        cartSessionVarName(), cartSessionId(cart), wrapWhiteFont("PDF/PS"));
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/pbGateway\">%s</A></TD>", wrapWhiteFont("New Query"));
if (proteinInSupportedGenome)
    {
    hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\" TARGET=_blank>%s</A></TD>",
        wrapWhiteFont("Help"));
    }
else
    {
    hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\" TARGET=_blank>%s</A></TD>",
        wrapWhiteFont("Help"));
    }

hPrintf("</TR></TABLE>");
fflush(stdout);

/* Make clickable image and map. */
makeActiveImagePB(psOutput, psOutput2);

if (psOutput == NULL) hPrintf("</FORM>");
}

void handlePostscript()
/* Deal with Postscript output. */
{
struct tempName psTn;
struct tempName psTn2;
char *pdfFile = NULL;

trashDirFile(&psTn, "pbt", "pbt", ".eps");
trashDirFile(&psTn2, "pbt", "pbt2", ".eps");

printf("<H1>PostScript/PDF Output</H1>\n");
printf("PostScript images can be printed at high resolution "
       "and edited by many drawing programs such as Adobe Illustrator.");
printf("  PDF can be viewed with Adobe Acrobat Reader.<BR><BR>\n");

doTrackForm(psTn.forCgi, psTn2.forCgi);

printf("<A HREF=\"%s\">Click here to download</A> "
       "the current protein tracks graphic in PostScript.  ", psTn.forCgi);
pdfFile = convertEpsToPdf(psTn.forCgi);
if (pdfFile != NULL)
    {
    printf("<BR><A HREF=\"%s\">Click here to download</A> "
           "the current protein tracks graphic in PDF", pdfFile);
    }
else
    printf("<BR><BR>PDF format not available");

printf("<BR><BR><A HREF=\"%s\">Click here to download</A> "
       "the current protein histograms graphic in PostScript.  ", psTn2.forCgi);
pdfFile = convertEpsToPdf(psTn2.forCgi);
if (pdfFile != NULL)
    {
    printf("<BR><A HREF=\"%s\">Click here to download</A> "
           "the current protein histograms graphic in PDF", pdfFile);
    }
else
    printf("<BR><BR>PDF format not available");

freez(&pdfFile);
}

void doMiddle(struct cart *theCart)
/* Print the body of an html file.   */
{
char cond_str[255];
struct sqlConnection *conn;
char *proteinAC;
char *chp, *chp1, *chp9;
char *debugTmp = NULL;
char *chromStr, *cdsStartStr, *cdsEndStr, posStr[255];

char *supportedGenomeDatabase;

char *answer;
char *queryID;

/* Initialize layout and database. */
cart = theCart;

/* Uncomment this to see parameters for debugging. */
/* Be careful though, it breaks if custom track
 * is more than 4k */
/*
{ struct dyString *state = cgiUrlString();
  hPrintf("State: %s\n", state->string);
}
*/

queryID = cartOptionalString(cart, "proteinID");
if (sameString(queryID, ""))
    {
    hUserAbort("Please go back and enter a gene symbol or a Swiss-Prot/TrEMBL protein ID.\n");
    }

if (cgiVarExists("db"))
    {
    /* if db is known, get key variables set */
    proteinInSupportedGenome = TRUE;
    database = cgiOptionalString("db");
    organism = hDbOrganism(database);
    protDbName = hPdbFromGdb(database);
    proteinID  = strdup(queryID);
    }
else
    {
    protCntInSwissByGene = searchProteinsInSwissProtByGene(queryID);
    /* no CGI 'db' variable means it did not come in from GB but from pbGateway */
    /* search existing GB databases to see if this protein can be found */
    protCntInSupportedGenomeDb =
        searchProteinsInSupportedGenomes(queryID, &supportedGenomeDatabase);
    if ((protCntInSupportedGenomeDb > 1) || protCntInSwissByGene >= 1)
        {
	/* more than 1 proteins match the query ID, present selection web page */
	proteinInSupportedGenome = 1;
	presentProteinSelections(queryID, protCntInSwissByGene, protCntInSupportedGenomeDb);
	return;
	}
    else
        {
	if (protCntInSupportedGenomeDb == 1)
	    {
	    /* one and only one protein found in a genome DB that support KG and PB */
	    proteinInSupportedGenome = TRUE;
	    database = strdup(supportedGenomeDatabase);
	    organism = hDbOrganism(database);
	    protDbName = hPdbFromGdb(database);
            proteinID=strdup(queryID);
	    }
	else
	    {
	    /* not found in genome DBs that support KG/PB */
	    /* now search PROTEOME_DB_NAMES to see if this protein is there. */

	    answer = uniProtFindPrimAcc(queryID);
	    if (answer == NULL)
		{
	        hUserAbort("'%s' does not seem to be a valid UniProtKB protein ID or a gene "
	                   "symbol.<br><br>Click <A HREF=\"../cgi-bin/pbGateway\">here</A> "
	                   "to start another query.", queryID);
                }

	    proteinInSupportedGenome = FALSE;
	    database = strdup(GLOBAL_PB_DB);
	    organism = strdup("");
            protDbName = strdup(PROTEOME_DB_NAME);
	    proteinID = strdup(answer);
	    }
	}

    if (proteinInSupportedGenome)
        {
        spConn = sqlConnect(database);
        sqlSafef(cond_str, sizeof(cond_str), "alias='%s'", queryID);
        proteinID = sqlGetField(database, "kgSpAlias", "spID", cond_str);

        sqlSafef(cond_str, sizeof(cond_str), "spID='%s'", proteinID);
        answer = sqlGetField(database, "kgXref", "spDisplayID", cond_str);

	sqlSafef(cond_str, sizeof(cond_str), "proteinID='%s'", answer);
        chromStr    = sqlGetField(database, "knownGene", "chrom", cond_str);
	if (chromStr)
	    {
	    cdsStartStr = sqlGetField(database, "knownGene", "cdsStart", cond_str);
	    cdsEndStr   = sqlGetField( database, "knownGene", "cdsEnd", cond_str);
	    safef(posStr, sizeof(posStr), "%s:%s-%s", chromStr, cdsStartStr, cdsEndStr);
	    positionStr = strdup(posStr);
	    cartSetString(cart, "position", positionStr);
	    cartSetString(cart, "organism", organism);
	    }
	}
    }
/* print out key variables for debugging */
/* printf("<br>before enter main section: <br>proteinInSupportedGenome=%d<br>proteinID=%s <br>database=%s <br>organism=%s <br>protDbName=%s\n",
proteinInSupportedGenome, proteinID, database, organism, protDbName);fflush(stdout);
*/

if (hTableExists(database, "kgProtMap2"))
    {
    kgVersion = KG_III;
    strcpy(kgProtMapTableName, "kgProtMap2");
    }

debugTmp = cartUsualString(cart, "hgDebug", "off");
if(sameString(debugTmp, "on"))
    hgDebug = TRUE;
else
    hgDebug = FALSE;
conn  = hAllocConn(database);
hgsid     = cartOptionalString(cart, "hgsid");
if (hgsid != NULL)
    {
    safef(hgsidStr, sizeof(hgsidStr), "&hgsid=%s", hgsid);
    }
else
    {
    strcpy(hgsidStr, "");
    }

/* check proteinID to see if it is a valid SWISS-PROT/TrEMBL accession or display ID */
/* then assign the accession number to global variable proteinID */
sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
proteinAC = sqlGetField(protDbName, "spXref3", "accession", cond_str);
if (proteinAC == NULL)
    {
    sqlSafef(cond_str, sizeof(cond_str), "displayID='%s'", proteinID);
    proteinAC = sqlGetField(protDbName, "spXref3", "accession", cond_str);
    if (proteinAC == NULL)
	{
	hUserAbort("'%s' does not seem to be a valid Swiss-Prot/TrEMBL protein ID or gene symbol.<br><br>Click <A HREF=\"../cgi-bin/pbGateway\">here</A> to start another query."
	, proteinID);
	}
    else
	{
	protDisplayID = proteinID;
	proteinID = proteinAC;
	}
    }
else
    {
    sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
    protDisplayID = sqlGetField(protDbName, "spXref3", "displayID", cond_str);
    }

if (proteinInSupportedGenome)
    {
    if (kgVersion == KG_III)
        {
        sqlSafef(cond_str, sizeof(cond_str), "spId='%s'", proteinID);
        mrnaID = sqlGetField(database, "kgXref", "kgId", cond_str);
	}
    else
        {
        sqlSafef(cond_str, sizeof(cond_str), "proteinID='%s'", protDisplayID);
        mrnaID = sqlGetField(database, "knownGene", "name", cond_str);
        }
    }
else
    {
    mrnaID = NULL;
    positionStr = NULL;
    }

sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
description = sqlGetField(protDbName, "spXref3", "description", cond_str);

if (positionStr != NULL)
    {
    chp = strstr(positionStr, ":");
    *chp = '\0';
    prevGBChrom = cloneString(positionStr);

    chp1 = chp + 1;
    chp9 = strstr(chp1, "-");
    *chp9 = '\0';
    prevGBStartPos = atoi(chp1);
    chp1 = chp9 + 1;
    prevGBEndPos   = atoi(chp1);
    }
else
    {
    prevGBChrom    = NULL;
    prevGBStartPos = -1;
    prevGBEndPos   = -1;
    }

/* Do main display. */
if (cgiVarExists("pbt.psOutput"))
    handlePostscript();
else
    {
    doTrackForm(NULL, NULL);
    }
}

void doDown(struct cart *cart)
{
hPrintf("<H2>The Browser is Being Updated</H2>\n");
hPrintf("The browser is currently unavailable.  We are in the process of\n");
hPrintf("updating the database and the display software.\n");
hPrintf("Please try again later.\n");
}

/* Other than submit and Submit all these vars should start with pbt.
 * to avoid weeding things out of other program's namespaces.
 * Because the browser is a central program, most of it's cart
 * variables are not pbt. qualified.  It's a good idea if other
 * program's unique variables be qualified with a prefix though. */
char *excludeVars[] = { "submit", "Submit", "pbt.reset",
			"pbt.in1", "pbt.in2", "pbt.in3", "pbt.inBase",
			"pbt.out1", "pbt.out2", "pbt.out3",
                        "pbt.left1", "pbt.left2", "pbt.left3",
                        "pbt.right1", "pbt.right2", "pbt.right3",
			"pbt.dinkLL", "pbt.dinkLR", "pbt.dinkRL", "pbt.dinkRR",
			"pbt.tui", "pbt.hideAll", "pbt.psOutput", "hideControls",
			NULL };

void resetVars()
/* Reset vars except for position and database. */
{
static char *except[] = {"db", "position", NULL};
char *cookieName = hUserCookie();
int sessionId = cgiUsualInt(cartSessionVarName(), 0);
char *hguidString = findCookieData(cookieName);
int userId = (hguidString == NULL ? 0 : atoi(hguidString));
struct cart *oldCart = cartNew(userId, sessionId, NULL, NULL);
cartRemoveExcept(oldCart, except);
cartCheckout(&oldCart);
cgiVarExcludeExcept(except);
}

int main(int argc, char *argv[])
{
cgiSpoof(&argc, argv);
if (cgiVarExists("pbt.reset"))
    resetVars();
/* call cartHtmlShellPbGlobal to accomodate situations that PB not entered from GB */
cartHtmlShellPbGlobal("UCSC Proteome Browser V1.1", doMiddle, hUserCookie(), excludeVars, NULL);
return 0;
}