/* pbTracks.c - UCSC 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 "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*/ boolean IAmPbTracks = TRUE; int kgVersion = KG_UNKNOWN; boolean proteinInSupportedGenome=TRUE; /* The protein is in supported genome DB */ /* This is a new variable necessary for PB V1.0 and PB V1.1 sharing the same PB library */ struct cart *cart; /* The cart where we keep persistent variables. */ struct hash *oldVars = NULL; /* The cart vars before new cgi stuff added. */ /* 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]; 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; struct sqlConnection *conn; int iypos; char *spDisplayId; hPrintf("
"); hPrintf("%s protein: ", organism); hPrintf("%s\n", proteinID, proteinID); /* 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 = spAccToId(spConn, proteinID); if (strstr(spDisplayId, proteinID) == NULL) { hPrintf(" (aka %s", spDisplayId); /* don't show 2nd aka if the new and old displayId are the same */ if (oldSpDisplayId(spDisplayId) != NULL) { if (!sameWord(spDisplayId, oldSpDisplayId(spDisplayId))) { hPrintf(" or %s", oldSpDisplayId(spDisplayId)); } } hPrintf(") ", oldSpDisplayId(spDisplayId)); } hPrintf(" %s\n", description); hPrintf("

"); protSeq = getAA(proteinID); if (protSeq == NULL) { hUserAbort("%s is not a current valid entry in UniProtKB\n", proteinID); } protSeqLen = strlen(protSeq); 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", mapName); vgSetClip(vg2, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder); iypos = 15; /* Draw stamps. */ doStamps(proteinID, mrnaID, protSeq, vg2, &iypos); /* Finish map. */ hPrintf("\n"); /* Save out picture and tell html file about it. */ vgClose(&vg2); hPrintf("

"); hPrintf("\n
", gifTn2.forCgi, pixWidth, pixHeight, mapName); hPrintf("\n"); hPrintf("Explanation of Protein Property Histograms
"); hPrintf("

"); histDone: hPrintf("\nUCSC Links:
\n "); hPrintf("

"); conn = sqlConnect(UNIPROT_DB_NAME); domainsPrint(conn, proteinID); hPrintf("

"); doPathwayLinks(protDisplayID, 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("

\n\n", "../cgi-bin/pbTracks"); cartSaveSession(cart); hPrintf("\n"); hPrintf("", wrapWhiteFont("Home")); hPrintf("", "UCSC Proteome Browser"); hPrintf("\n", cartSessionVarName(), cartSessionId(cart), wrapWhiteFont("PDF/PS")); hPrintf("", wrapWhiteFont("Help")); hPrintf("
%s%s%s%s
"); fflush(stdout); /* Make clickable image and map. */ makeActiveImagePB(psOutput, psOutput2); if (psOutput == NULL) 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 *answer; /* 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); } */ getDbAndGenome(cart, &database, &organism, oldVars); /* if kgProtMap2 table exists, this means we are doing KG III */ if (hTableExists(database, "kgProtMap2")) { kgVersion = KG_III; strcpy(kgProtMapTableName, "kgProtMap2"); } protDbName = hPdbFromGdb(database); spConn = sqlConnect(UNIPROT_DB_NAME); 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, ""); } proteinID = cartOptionalString(cart, "proteinID"); /* 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 UniProtKB protein ID.", proteinID); } else { protDisplayID = proteinID; proteinID = proteinAC; } } else { sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", proteinID); protDisplayID = sqlGetField(protDbName, "spXref3", "displayID", cond_str); } if (spFindAcc(spConn, proteinID) == NULL) { sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", proteinID); answer = sqlGetField(protDbName, "spXref3", "biodatabaseID", cond_str); if (sameWord(answer, "3")) { hUserAbort("The corresponding protein %s is no longer available from UniProtKB.", proteinID); } else { hUserAbort("%s seems not to be a valid protein ID.", proteinID); } } else { if (!sameWord(proteinID, spFindAcc(spConn, proteinID))) { hPrintf("%s seems to be an outdated protein ID.", proteinID); printf("

Please try "); hPrintf(" %s instead.\n", spFindAcc(spConn, proteinID), spFindAcc(spConn, proteinID));fflush(stdout); hUserAbort(" "); } } 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); } sqlSafef(cond_str, sizeof(cond_str), "accession='%s'", proteinID); description = sqlGetField(protDbName, "spXref3", "description", cond_str); /* obtain previous genome position range selected by the Genome Browser user */ positionStr = cloneString(cartOptionalString(cart, "position")); 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); oldVars = hashNew(10); if (cgiVarExists("pbt.reset")) resetVars(); cartHtmlShellPB("UCSC Proteome Browser", doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }