/* pbTracksGlobal.c - UCSC Global Proteome Browser main cgi script. */
#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), "
%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("
\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("
Protein ");
hPrintf("%s\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("
");
hPrintf("Organism: ");
/* get scientific and Genbank common name of this organism */
sciName = NULL;
commonName = NULL;
safef(cond_str, sizeof(cond_str),"accession='%s'", proteinID);
answer = sqlGetField(PROTEOME_DB_NAME, "spXref3", "division", cond_str);
if (answer != NULL)
{
safef(cond_str, sizeof(cond_str), "id=%s and nameType='scientific name'", answer);
sciName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);
safef(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("
");
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\n");
/* Save out picture and tell html file about it. */
vgClose(&vg2);
hPrintf("");
hPrintf("\n![](\"%s\")
",
gifTn2.forCgi, pixWidth, pixHeight, mapName);
if (proteinInSupportedGenome)
{
hPrintf("\n");
}
else
{
hPrintf("\n");
}
hPrintf("Explanation of Protein Property Histograms
");
hPrintf("
");
histDone:
hPrintf("
");
fflush(stdout);
/* See if a UCSC Genome Browser exist for this organism. If so, display BLAT link. */
connCentral = hConnectCentral();
safef(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("\nUCSC Links:
\n ");
hPrintf("
\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("
");
}
/* This section shows various types of domains */
conn = sqlConnect(UNIPROT_DB_NAME);
domainsPrint(conn, proteinID);
hPrintf("
");
/* 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("
");
}
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("PostScript/PDF Output
\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.
\n");
doTrackForm(psTn.forCgi, psTn2.forCgi);
printf("Click here to download "
"the current protein tracks graphic in PostScript. ", psTn.forCgi);
pdfFile = convertEpsToPdf(psTn.forCgi);
if (pdfFile != NULL)
{
printf("
Click here to download "
"the current protein tracks graphic in PDF", pdfFile);
}
else
printf("
PDF format not available");
printf("
Click here to download "
"the current protein histograms graphic in PostScript. ", psTn2.forCgi);
pdfFile = convertEpsToPdf(psTn2.forCgi);
if (pdfFile != NULL)
{
printf("
Click here to download "
"the current protein histograms graphic in PDF", pdfFile);
}
else
printf("
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.
Click here "
"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);
safef(cond_str, sizeof(cond_str), "alias='%s'", queryID);
proteinID = sqlGetField(database, "kgSpAlias", "spID", cond_str);
safef(cond_str, sizeof(cond_str), "spID='%s'", proteinID);
answer = sqlGetField(database, "kgXref", "spDisplayID", cond_str);
safef(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("
before enter main section:
proteinInSupportedGenome=%d
proteinID=%s
database=%s
organism=%s
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 */
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
proteinAC = sqlGetField(protDbName, "spXref3", "accession", cond_str);
if (proteinAC == NULL)
{
safef(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.
Click here to start another query."
, proteinID);
}
else
{
protDisplayID = proteinID;
proteinID = proteinAC;
}
}
else
{
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
protDisplayID = sqlGetField(protDbName, "spXref3", "displayID", cond_str);
}
if (proteinInSupportedGenome)
{
if (kgVersion == KG_III)
{
safef(cond_str, sizeof(cond_str), "spId='%s'", proteinID);
mrnaID = sqlGetField(database, "kgXref", "kgId", cond_str);
}
else
{
safef(cond_str, sizeof(cond_str), "proteinID='%s'", protDisplayID);
mrnaID = sqlGetField(database, "knownGene", "name", cond_str);
}
}
else
{
mrnaID = NULL;
positionStr = NULL;
}
safef(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("The Browser is Being Updated
\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;
}