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);
}
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);
}
