Esempio n. 1
0
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;
sqlSafefFrag(cond_str, sizeof(cond_str),"accession='%s'", proteinID);
answer = sqlGetField(PROTEOME_DB_NAME, "spXref3", "division", cond_str);
if (answer != NULL)
    {
    sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s and nameType='scientific name'", answer);
    sciName = sqlGetField(PROTEOME_DB_NAME, "taxonNames", "name", cond_str);

    sqlSafefFrag(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);
}
static void rgdGene2SynonymPrint(struct section *section,
        struct sqlConnection *conn, char *rgdGeneId)
{
char *geneSym = NULL, *geneName = NULL;
char query[256], **row;
struct sqlResult *sr;
if (rgdGeneId != NULL)
    {
    safef(query, sizeof(query), 
	    "select old_symbol, old_name from genes_rat where gene_rgd_id = '%s'", 
	    rgdGeneId+4L);
    sr = sqlGetResult(conn, query);
    if ((row = sqlNextRow(sr)) != NULL)
	{
	if (row[0][0] != 0 && !sameString(row[0], "n/a"))
	    {
	    geneSym = cloneString(row[0]);
	    hPrintf("<B>Symbol:</B> %s ", addComma(row[0]));
	    //hPrintf("<BR>\n");
	    }
	if (row[1][0] != 0 && !sameString(row[0], "n/a"))
	    {
	    geneName = cloneString(row[1]);
	    hPrintf("<BR><B>Name:</B> %s ", addComma(geneName));
	    hPrintf("<BR>\n");
	    }
	}
    sqlFreeResult(&sr);

    safef(query, sizeof(query), 
	    "select value from rgdGene2ToRefSeq where name= '%s'", rgdGeneId);
    sr = sqlGetResult(conn, query);
    if ((row = sqlNextRow(sr)) != NULL)
	{
        hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
	printOurRefseqUrl(stdout, row[0]);
	hPrintf("\">%s</A><BR>\n", row[0]);
	}
    sqlFreeResult(&sr);
    
    safef(query, sizeof(query), 
	    "select value from rgdGene2ToUniProt where name= '%s'", rgdGeneId);
    sr = sqlGetResult(conn, query);
    if ((row = sqlNextRow(sr)) != NULL)
    	{
	char *spId, *spDisplayId, *oldDisplayId;
	spId = row[0];
	hPrintf("<B>Protein: </B>");
        hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
	    "TARGET=_blank>%s</A>\n",
	    spId, spId);
    
        /* show SWISS-PROT display ID if it is different than the accession ID */
        /* but, if display name is like: Q03399 | Q03399_HUMAN, then don't show display name */
        spDisplayId = spAnyAccToId(spConn, spId);
        if (spDisplayId == NULL) 
    	    {
	    errAbort("<br>The corresponding protein %s of this gene is not found in our current UniProtKB DB.", spId);
	    }   
	
        if (strstr(spDisplayId, spId) == 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)
                    && !sameWord(spId, oldDisplayId))
	    	    {
	    	    hPrintf(" or %s", oldDisplayId);
	    	    }  
	        }	
	    hPrintf(")<BR>\n");
	    }  
   	}
    sqlFreeResult(&sr);
    }
}
static void synonymPrint(struct section *section, 
	struct sqlConnection *conn, char *id)
/* Print out SwissProt comments - looking up typeId/commentVal. */
{
char *protAcc = getSwissProtAcc(conn, spConn, id);
char *spDisplayId;
char *refSeqAcc = "";
char *mrnaAcc = "";
char *oldDisplayId;
char condStr[255];
char *kgProteinID;
char *parAcc; /* parent accession of a variant splice protein */
char *chp;

if (isRgdGene(conn))
    {
    rgdGene2SynonymPrint(section,conn, id);
    return;
    }
if (sqlTablesExist(conn, "kgAlias"))
    printAlias(id, conn);
if (sameWord(genome, "Zebrafish"))
    {
    char *xrefTable = "ensXRefZfish";
    char *geneIdCol = "ensGeneId";
    /* get Gene Symbol and RefSeq accession from Zebrafish-specific */
    /* cross-reference table */
    printGeneSymbol(id, xrefTable, geneIdCol, conn);
    refSeqAcc = getRefSeqAcc(id, xrefTable, geneIdCol, conn);
    hPrintf("<B>ENSEMBL ID:</B> %s", id);
    }
else
    {
    char query[256];
    char *toRefTable = genomeOptionalSetting("knownToRef");
    if (toRefTable != NULL && sqlTableExists(conn, toRefTable))
        {
	safef(query, sizeof(query), "select value from %s where name='%s'", toRefTable,
		id);
	refSeqAcc = emptyForNull(sqlQuickString(conn, query));
	}
    if (sqlTableExists(conn, "kgXref"))
	{
	safef(query, sizeof(query), "select mRNA from kgXref where kgID='%s'", id);
	mrnaAcc = emptyForNull(sqlQuickString(conn, query));
	}
    if (sameWord(genome, "C. elegans"))
	hPrintf("<B>WormBase ID:</B> %s<BR>", id);
    else
	hPrintf("<B>UCSC ID:</B> %s<BR>", id);
    }
    
if (refSeqAcc[0] != 0)
    {
    hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
    printOurRefseqUrl(stdout, refSeqAcc);
    hPrintf("\">%s</A><BR>\n", refSeqAcc);
    }
else if (mrnaAcc[0] != 0)
    {
    safef(condStr, sizeof(condStr), "acc = '%s'", mrnaAcc);
    if (sqlGetField(database, "gbCdnaInfo", "acc", condStr) != NULL)
        {
    	hPrintf("<B>Representative RNA: </B> <A HREF=\"");
    	printOurMrnaUrl(stdout, mrnaAcc);
    	hPrintf("\">%s</A><BR>\n", mrnaAcc);
    	}
    else
    /* do not show URL link if it is not found in gbCdnaInfo */
    	{
    	hPrintf("<B>Representative RNA: %s </B>", mrnaAcc);
    	}
    }
if (protAcc != NULL)
    {
    kgProteinID = cloneString("");
    if (hTableExists(sqlGetDatabase(conn), "knownGene")
        && (isNotEmpty(cartOptionalString(cart, hggChrom)) &&
	      differentWord(cartOptionalString(cart, hggChrom),"none")))
    	{
    	safef(condStr, sizeof(condStr), "name = '%s' and chrom = '%s' and txStart=%s and txEnd=%s", 
	        id, cartOptionalString(cart, hggChrom), 
    	        cartOptionalString(cart, hggStart), 
		cartOptionalString(cart, hggEnd));
    	kgProteinID = sqlGetField(database, "knownGene", "proteinID", condStr);
    	}

    hPrintf("<B>Protein: ");
    if (strstr(kgProteinID, "-") != NULL)
        {
	parAcc = cloneString(kgProteinID);
	chp = strstr(parAcc, "-");
	*chp = '\0';
	
        /* show variant splice protein and the UniProt link here */
	hPrintf("<A HREF=\"http://www.uniprot.org/uniprot%s\" "
	    "TARGET=_blank>%s</A></B>, splice isoform of ",
	    kgProteinID, kgProteinID);
        hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
	    "TARGET=_blank>%s</A></B>\n",
	    parAcc, parAcc);
	}
    else
        {
        hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
	    "TARGET=_blank>%s</A></B>\n",
	    protAcc, protAcc);
	}
    /* show SWISS-PROT display ID if it is different than the accession ID */
    /* but, if display name is like: Q03399 | Q03399_HUMAN, then don't show display name */
    spDisplayId = spAnyAccToId(spConn, protAcc);
    if (spDisplayId == NULL) 
    	{
	errAbort("<br>%s seems to no longer be a valid protein ID in our latest UniProtKB DB.", protAcc);
	}
	
    if (strstr(spDisplayId, protAcc) == 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)
                && !sameWord(protAcc, oldDisplayId))
	    	{
	    	hPrintf(" or %s", oldDisplayId);
	    	}
	    }
	hPrintf(")<BR>\n");
	}
    }
printCcds(id, conn);

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

struct sqlConnection *conn;
char query[256];
struct sqlResult *sr;
char **row;

int  iypos;
char *spDisplayId;
char *oldDisplayId;
conn  = sqlConnect(UNIPROT_DB_NAME);
printf("<BR>");
hPrintf("<BR><font size=4><B>Protein: ");
hPrintf("%s</B>", proteinID);

/* Please note the hiv database name is hard wired here.*/
safef(query, sizeof(query), 
"select subjId from hivVax003Vax004.gsIdXref where aaSeqId = '%s'", proteinID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
    {
    printf("<BR>");
    hPrintf("<font size=4><B>Subject: ");
    hPrintf("<A HREF=\"../cgi-bin/gsidSubj?hgs_subj=%s&submit=Go!\">", row[0]);
    hPrintf("%s</A></B><BR>", row[0]);
    }
sqlFreeResult(&sr);

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("</font><br>");

protSeq = getAA(proteinID);
if (protSeq == NULL)
    {
    errAbort("%s is not a current valid entry in UniProt(SWISS-PROT/TrEMBL)\n", proteinID);
    }
protSeqLen = strlen(protSeq);

fflush(stdout);

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

pbScale = 3;
pixWidth = 520;
insideWidth = pixWidth-gfxBorder;

pixHeight = 350;

if (psOutput2)
    {
    vg2 = vgOpenPostScript(pixWidth, pixHeight, psOutput2);
    }
else
    {
    trashDirFile(&gifTn2, "pbt", "pbt", ".gif");
    vg2 = vgOpenGif(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/pbGsid/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
    }

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

hPrintf("<P>");

histDone:

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

printFASTA(proteinID, protSeq);
}