44ccfacbe3a3d4b300f80d48651c77837a4b571e galt Tue Apr 26 11:12:02 2022 -0700 SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix. diff --git src/hg/protein/lib/doTracks.c src/hg/protein/lib/doTracks.c index 9a02242..7abd3b1 100644 --- src/hg/protein/lib/doTracks.c +++ src/hg/protein/lib/doTracks.c @@ -1,1729 +1,1729 @@ /* doTracks.c draw various tracks for Proteome Browser */ /* 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 "memalloc.h" #include "jksql.h" #include "vGfx.h" #include "memgfx.h" #include "htmshell.h" #include "cart.h" #include "hdb.h" #include "web.h" #include "cheapcgi.h" #include "hgColors.h" #include "pbTracks.h" #include "trashDir.h" int prevGBOffsetSav; char trackOffset[20]; int pixWidth, pixHeight; struct tempName gifTn; char *mapName = "map"; char *trackTitle; int trackTitleLen; boolean showPrevGBPos = TRUE; void calxy(int xin, int yin, int *outxp, int *outyp) /* calxy() converts a logical drawing coordinate into an actual drawing coordinate with scaling and minor adjustments */ { *outxp = xin*pbScale + 120 - trackOrigOffset; *outyp = yin + currentYoffset; } /* original calxy without trackOrigOffset, may be useful if track names needed at the left */ void calxy0(int xin, int yin, int *outxp, int *outyp) /* calxy() converts a logical drawing coordinate into an actual drawing coordinate with scaling and minor adjustments */ { *outxp = xin*pbScale + 120; *outyp = yin + currentYoffset; } void relativeScroll(double amount) /* Scroll percentage of visible window. */ { trackOrigOffset = trackOrigOffset + (int)(amount*MAX_PB_PIXWIDTH); /* Make sure don't scroll of ends. */ if (trackOrigOffset > ((pbScale* protSeqLen) - 600)) trackOrigOffset = pbScale*protSeqLen - 700; if (trackOrigOffset < 0) trackOrigOffset = 0; safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale); cgiMakeHiddenVar("pbScaleStr", pbScaleStr); } void mapBoxTrackTitle(int x, int y, int width, int height, char *title, char *tagName) { hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x-1, y-1, x+width+1, y+height+1); if (proteinInSupportedGenome) { hPrintf("HREF=\"../goldenPath/help/pbTracksHelpFiles/pb%s.shtml\"", tagName); } else { if (hIsGsidServer()) { hPrintf("HREF=\"../goldenPath/help/pbTracksHelpFiles/pbGsid/pb%s.shtml\"", tagName); } else { hPrintf("HREF=\"../goldenPath/help/pbTracksHelpFiles/pb%s.shtml\"", tagName); } } hPrintf(" target=_blank ALT=\"Click here for explanation of %c%s%c\">\n", '\'', title, '\''); } void doAnomalies(char *aa, int len, int *yOffp) /* draw the AA Anomalies track */ { char res; int index; char cond_str[255]; char *answer; int xx, yy; int i, j; char *chp; int aaResCnt[20]; double aaResFreqDouble[20]; int abnormal; int ia = -1; double pctLow[20], pctHi[20]; /* count frequency for each residue for current protein */ chp = aa; for (j=0; j<20; j++) { aaResCnt[j] = 0; /* get cutoff threshold value pairs */ - sqlSafefFrag(cond_str, sizeof(cond_str), "AA='%c'", aaAlphabet[j]); + sqlSafef(cond_str, sizeof(cond_str), "AA='%c'", aaAlphabet[j]); answer = sqlGetField(database, "pbAnomLimit", "pctLow", cond_str); pctLow[j] = (double)(atof(answer)); answer = sqlGetField(database, "pbAnomLimit", "pctHi", cond_str); pctHi[j] = (double)(atof(answer)); } for (i=0; i<len; i++) { for (j=0; j<20; j++) { if (*chp == aaChar[j]) { aaResCnt[j] ++; break; } } chp++; } for (j=0; j<20; j++) { aaResFreqDouble[j] = ((double)aaResCnt[j])/((double)len); } currentYoffset = *yOffp; for (index=0; index < len; index++) { res = aa[index]; ia = -1; for (j=0; j<20; j++) { if (res == aaChar[j]) { ia = j; break; } } /* skip non-standard AA alphabets */ if (ia == -1) continue; calxy(index, *yOffp, &xx, &yy); abnormalColor = pbRed; abnormal = chkAnomaly(aaResFreqDouble[ia], pctLow[ia], pctHi[ia]); if (abnormal > 0) { vgBox(g_vg, xx, yy-5, 1*pbScale, 5, abnormalColor); } else { if (abnormal < 0) { vgBox(g_vg, xx, yy, 1*pbScale, 5, abnormalColor); } } vgBox(g_vg, xx, yy, 1*pbScale, 1, MG_BLACK); } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-10, xx, 20, bkgColor); trackTitle = cloneString("AA Anomalies"); vgTextRight(g_vg, xx-25, yy-4, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-6, trackTitleLen*6+12, 14, trackTitle, "pepAnom"); /* update y offset */ *yOffp = *yOffp + 15; } void doCharge(char *aa, int len, int *yOffp) /* draw polarity track */ { char res; int index; int xx, yy; currentYoffset = *yOffp; for (index=0; index < len; index++) { res = aa[index]; calxy(index, *yOffp, &xx, &yy); if (aa_attrib[(int)res] == CHARGE_POS) { vgBox(g_vg, xx, yy-9, 1*pbScale, 9, pbBlue); } else if (aa_attrib[(int)res] == CHARGE_NEG) { vgBox(g_vg, xx, yy, 1*pbScale, 9, pbRed); } else if (aa_attrib[(int)res] == POLAR) { vgBox(g_vg, xx, yy, 1*pbScale, 5, pbRed); } else if (aa_attrib[(int)res] == NEUTRAL) { vgBox(g_vg, xx, yy, 1*pbScale, 1, MG_BLACK); } } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-10, xx, 30, bkgColor); trackTitle = cloneString("Polarity"); vgTextRight(g_vg, xx-25, yy-4, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-6, trackTitleLen*6+12, 14, trackTitle, "polarity"); vgTextRight(g_vg, xx-14, yy-10, 10, 10, pbBlue, g_font, "+"); vgTextRight(g_vg, xx-14, yy, 10, 10, pbRed, g_font, "-"); *yOffp = *yOffp + 15; } void doHydrophobicity(char *aa, int len, int *yOffp) /* draw Hydrophobicity track */ { char res; int index; int xx, yy; int h; int i, i0, i9; int l; int iw = 5; float sum, avg; currentYoffset = *yOffp; for (index=0; index < len; index++) { res = aa[index]; calxy(index, *yOffp, &xx, &yy); { sum = 0; i=index; i0 = index - iw; if (i0 < 0) i0 = 0; i9 = index + iw; if (i9 >= len) i9 = len -1; l = 0; for (i=i0; i <= i9; i++) { sum = sum + aa_hydro[(int)aa[i]]; l++; } avg = sum/(float)l; if (avg> 0.0) { h = 5 * 9 * (100.0 * avg / 9.0) / 100; vgBox(g_vg, xx, yy-h, 1*pbScale, h, pbBlue); } else { h = - 5 * 9 * (100.0 * avg / 9.0) / 100; vgBox(g_vg, xx, yy, 1*pbScale, h, pbRed); } } } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-17, xx, 40, bkgColor); trackTitle = cloneString("Hydrophobicity"); vgTextRight(g_vg, xx-25, yy-4, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-6, trackTitleLen*6+12, 14, trackTitle, "hydroTr"); *yOffp = *yOffp + 15; } void doCysteines(char *aa, int len, int *yOffp) /* draw track for Cysteines and Glycosylation */ { char res; int index; int xx, yy; currentYoffset = *yOffp; for (index=0; index < len; index++) { res = aa[index]; calxy(index, *yOffp, &xx, &yy); if (res == 'C') { vgBox(g_vg, xx, yy-9+1, 1*pbScale, 9, pbBlue); } else { vgBox(g_vg, xx, yy-0, 1, 1, MG_BLACK); } } for (index=1; index < (len-2); index++) { calxy(index-1, *yOffp, &xx, &yy); if (aa[index-1] == 'N') { if ( (aa[index+1] == 'T') || (aa[index+1] == 'S') ) { if ((aa[index+1] != 'C') && (aa[index+2] != 'P')) { vgBox(g_vg, xx-1, yy, 3*pbScale, 9, pbRed); } } } } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-15, xx, 33, bkgColor); trackTitle = cloneString("Cysteines"); vgTextRight(g_vg, xx-25, yy-8, 10, 10, pbBlue, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-10, trackTitleLen*6+12, 12, trackTitle, "cCntTr"); trackTitle = cloneString("Predicted"); vgTextRight(g_vg, xx-25, yy, 10, 10, pbRed, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy, trackTitleLen*6+12, 12, "Glycosylation", "glycosylation"); trackTitle = cloneString("Glycosylation"); vgTextRight(g_vg, xx-25, yy+10, 10, 10, pbRed, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy+8, trackTitleLen*6+12, 12, trackTitle, "glycosylation"); *yOffp = *yOffp + 15; } void doAAScale(int len, int *yOffp, int top_bottom) /* draw the track to show AA scale */ { int index; int tb; /* top or bottom flag */ int xx, yy; int i; int imax; int interval; char scale_str[20]; int markedIndex = -1; tb = 0; if (top_bottom < 0) tb = 1; currentYoffset = *yOffp; imax = len/100 * 100; if ((len % 100) != 0) imax = imax + 100; calxy(1, *yOffp, &xx, &yy); vgBox(g_vg, xx-pbScale/2, yy-tb, (len-1)*pbScale, 1, MG_BLACK); vgText(g_vg, xx-pbScale/2+4, yy+4-12*tb, MG_BLACK, g_font, "1"); interval = 50; if (pbScale >= 18) interval = 10; calxy(1, *yOffp, &xx, &yy); vgBox(g_vg, xx-pbScale/2, yy-9*tb, 1, 9, MG_BLACK); for (i=0; i<len; i++) { index = i+1; if ((index % interval) == 0) { markedIndex = index; if (((index % (interval*2)) == 0) || (index == len)) { calxy(index, *yOffp, &xx, &yy); vgBox(g_vg, xx-pbScale/2, yy-9*tb, 1, 9, MG_BLACK); } else { calxy(index, *yOffp, &xx, &yy); vgBox(g_vg, xx-pbScale/2, yy-5*tb, 1, 5, MG_BLACK); } safef(scale_str, sizeof(scale_str), "%d", index); vgText(g_vg, xx-pbScale/2+4, yy+4-12*tb, MG_BLACK, g_font, scale_str); } } if (markedIndex != len) { calxy(len, *yOffp, &xx, &yy); /* make the end tick a little taller than regular tick */ vgBox(g_vg, xx-pbScale/2, yy-14*tb, 1, 14, MG_BLACK); safef(scale_str, sizeof(scale_str), "%d", len); /* label the end tick with a vertical offset so that it won't overlap with regular ticks */ vgText(g_vg, xx-pbScale/2+4, yy+12-28*tb, MG_BLACK, g_font, scale_str); } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-tb*9-1, xx, 20, bkgColor); trackTitle = cloneString("AA Scale"); vgTextRight(g_vg, xx-25, yy-9*tb, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-9*tb-2, trackTitleLen*6+12, 14, trackTitle, "aaScale"); *yOffp = *yOffp + 15; } void mapBoxExon(int xIn, int y, int width, int height, char *mrnaID, int exonNum, char *chrom, int exonGenomeStartPos, int exonGenomeEndPos) { int x; /* prevent the mapBox spill over to the label */ x = xIn; if (x < 120) x = 120; hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x-1, y-1, x+width+1, y+height+1); hPrintf("HREF=\"../cgi-bin/hgTracks?db=%s&position=%s:%d-%d\"" ,database, chrom, exonGenomeStartPos-1, exonGenomeEndPos+3); hPrintf(" target=_blank ALT=\"Exon %d\">\n", exonNum); } void mapBoxPrevGB(int x, int y, int width, int height, char *posStr) { hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x-1, y-1, x+width+1, y+height+1); hPrintf("HREF=\"../cgi-bin/hgTracks?db=%s&position=%s\"", database, posStr); hPrintf(" target=_blank ALT=\"UCSC Genome Browser %s\">\n", posStr); } int calPrevGB(int exonCount, char *chrom, char strand, int aaLen, int *yOffp, char *proteinID, char *mrnaID) /* calculate the appropriate X offset for the previous Genome Browser position range */ { int xx, yy; int i, j; char exonNumStr[10]; int mrnaLen; int exonStartPos, exonEndPos; int exonGenomeStartPos, exonGenomeEndPos; int exonNumber; int printedExonNumber = -1; int currentPos; int jPrevStart, jPrevEnd; int iPrevExon = -1; int jPrevExonPos = 0; int prevGBOffset; int jcnt = 0; /* The hypothetical mRNA length is 3 times of aaLen */ mrnaLen = aaLen * 3; jPrevStart = mrnaLen-1; jPrevEnd = 0; exonNumber = 1; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; currentYoffset = *yOffp; if (strand == '-') { for (i=0; i<(exonCount-2); i++) { if ((prevGBStartPos < blockGenomeStartPositive[i]) && (prevGBStartPos > blockGenomeEndPositive[i+1]) ) { iPrevExon = i; jPrevExonPos = blockStartPositive[i+1]; } } /* handle special cases at both ends when previous GB position is outside CDS */ if (prevGBStartPos < blockGenomeStartPositive[exonCount-1]) jPrevExonPos = blockEndPositive[exonCount-1] + 3; if (prevGBEndPos > blockGenomeStartPositive[0]) jPrevExonPos = blockStartPositive[0]; } else { for (i=0; i<(exonCount-1); i++) { if ((prevGBStartPos > blockGenomeEndPositive[i]) && (prevGBStartPos < blockGenomeStartPositive[i+1]) ) { iPrevExon = i; jPrevExonPos = blockEndPositive[i]; } } /* handle special cases at both ends when previous GB position is outside CDS */ if (prevGBStartPos < blockGenomeStartPositive[0]) jPrevExonPos = blockStartPositive[0]; if (prevGBEndPos > blockGenomeEndPositive[exonCount-1]) jPrevExonPos = blockEndPositive[exonCount-1]; } for (j = 0; j < mrnaLen; j++) { calxy(j/3, *yOffp, &xx, &yy); if (j > exonEndPos) { if (printedExonNumber != exonNumber) { if ((exonEndPos - exonStartPos)*pbScale/3 > 12) { safef(exonNumStr, sizeof(exonNumStr), "%d", exonNumber); } printedExonNumber = exonNumber; } if (exonNumber < exonCount) { exonNumber++; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; } } if (strand == '-') { currentPos = blockGenomeStartPositive[exonNumber-1] + (blockEndPositive[exonNumber-1]-j)+1; } else { currentPos = blockGenomeStartPositive[exonNumber-1]+(j - blockStartPositive[exonNumber-1])+1; } if ((currentPos >= prevGBStartPos) && (currentPos <= prevGBEndPos)) { jcnt++; if (j < jPrevStart) jPrevStart = j; if (j > jPrevEnd) jPrevEnd = j; } } if (jcnt > 0) { prevGBOffset = jPrevStart/3 * pbScale ; } else { prevGBOffset = jPrevExonPos/3 * pbScale ; } return(prevGBOffset); } void doPrevGB(int exonCount, char *chrom, char strand, int aaLen, int *yOffp, char *proteinID, char *mrnaID) /* draw the previous Genome Browser position range */ { int xx, yy, xx0; int i, j; char prevPosMessage[300]; char exonNumStr[10]; int mrnaLen; Color color; int exonStartPos, exonEndPos; int exonGenomeStartPos, exonGenomeEndPos; int exonNumber; int printedExonNumber = -1; Color exonColor[2]; int currentPos; int jPrevStart, jPrevEnd; int jcnt = 0; int iPrevExon = -1; int jPrevExonPos = 0; Color defaultColor; defaultColor = vgFindColorIx(g_vg, 170, 170, 170); /* The imaginary mRNA length is 3 times of aaLen */ mrnaLen = aaLen * 3; exonColor[0] = pbBlue; exonColor[1] = vgFindColorIx(g_vg, 0, 180, 0); jPrevStart = mrnaLen-1; jPrevEnd = 0; exonNumber = 1; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; currentYoffset = *yOffp; if (strand == '-') { for (i=0; i<(exonCount-2); i++) { if ((prevGBStartPos < blockGenomeStartPositive[i]) && (prevGBStartPos > blockGenomeEndPositive[i+1]) ) { iPrevExon = i; jPrevExonPos = blockStartPositive[i+1]; /*printf("<br>*%d %d %d %d\n",i,blockGenomeEndPositive[i], */ /*prevGBStartPos, blockGenomeStartPositive[i]);fflush(stdout); */ } } /* handle special cases at both ends when previous GB position is outside CDS */ if (prevGBStartPos < blockGenomeStartPositive[exonCount-1]) jPrevExonPos = blockEndPositive[exonCount-1] + 3; if (prevGBEndPos > blockGenomeStartPositive[0]) jPrevExonPos = blockStartPositive[0]; } else { for (i=0; i<(exonCount-1); i++) { if ((prevGBStartPos > blockGenomeEndPositive[i]) && (prevGBStartPos < blockGenomeStartPositive[i+1]) ) { iPrevExon = i; jPrevExonPos = blockEndPositive[i]; } } /* handle special cases at both ends when previous GB position is outside CDS */ if (prevGBStartPos < blockGenomeStartPositive[0]) jPrevExonPos = blockStartPositive[0]; if (prevGBEndPos > blockGenomeEndPositive[exonCount-1]) jPrevExonPos = blockEndPositive[exonCount-1]; } for (j = 0; j < mrnaLen; j++) { color = defaultColor; calxy(j/3, *yOffp, &xx, &yy); if (j > exonEndPos) { if (printedExonNumber != exonNumber) { if ((exonEndPos - exonStartPos)*pbScale/3 > 12) { safef(exonNumStr, sizeof(exonNumStr), "%d", exonNumber); } printedExonNumber = exonNumber; } if (exonNumber < exonCount) { exonNumber++; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; } } if ((j >= exonStartPos) && (j <= exonEndPos)) { color = exonColor[(exonNumber-1) % 2]; } if (strand == '-') { currentPos = blockGenomeStartPositive[exonNumber-1] + (blockEndPositive[exonNumber-1]-j)+1; } else { currentPos = blockGenomeStartPositive[exonNumber-1]+(j - blockStartPositive[exonNumber-1])+1; } if ((currentPos >= prevGBStartPos) && (currentPos <= prevGBEndPos)) { jcnt++; if (j < jPrevStart) jPrevStart = j; if (j > jPrevEnd) jPrevEnd = j; } } positionStr = cloneString(cartOptionalString(cart, "position")); if (jcnt > 0) { calxy(jPrevStart/3, *yOffp, &xx, &yy); if (pbScale > 6) { vgBox(g_vg, xx+(jPrevStart%3)*6, yy-2, (jPrevEnd-jPrevStart+1)*pbScale/3, 2, MG_BLACK); } else { vgBox(g_vg, xx, yy-2, (jPrevEnd-jPrevStart+1)*pbScale/3, 2, MG_BLACK); } mapBoxPrevGB(xx+(jPrevStart%3)*6, yy-2, (jPrevEnd-jPrevStart+1)*pbScale/3, 2, positionStr); safef(prevPosMessage, sizeof(prevPosMessage), "Previous position in UCSC Genome Browser: %s", positionStr); if (strand == '-') safef(prevPosMessage, sizeof(prevPosMessage), "%s (negative strand)", prevPosMessage); vgText(g_vg, xx+(jPrevStart%3)*pbScale/3, yy-10, MG_BLACK, g_font, prevPosMessage); } else { /*calxy(jPrevExonPos/3, *yOffp, &xx, &yy); */ if (jPrevExonPos <= 0) { calxy(jPrevExonPos/3, *yOffp, &xx, &yy); vgBox(g_vg, xx, yy, 1, 5, pbRed); } else { calxy(jPrevExonPos/3+1, *yOffp, &xx, &yy); vgBox(g_vg, xx, yy, 1, 5, pbRed); } mapBoxPrevGB(xx-1, yy-1, 2, 6, positionStr); safef(prevPosMessage, sizeof(prevPosMessage), "Previous position in UCSC Genome Browser: %s (not in a CDS)",positionStr); if (strand == '-') safef(prevPosMessage, sizeof(prevPosMessage), "%s (negative strand)", prevPosMessage); calxy(0, *yOffp, &xx0, &yy); calxy(jPrevExonPos/3, *yOffp, &xx, &yy); if (xx < xx0) { vgText(g_vg, xx0, yy-8, MG_BLACK, g_font, prevPosMessage); } else { if (jPrevExonPos/3 < aaLen/2) { vgText(g_vg, xx, yy-8, MG_BLACK, g_font, prevPosMessage); } else { vgTextRight(g_vg, xx, yy-8, 10, 10, MG_BLACK, g_font, prevPosMessage); } } } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-10, xx, 20, bkgColor); trackTitle = cloneString("Genome Browser"); vgTextRight(g_vg, xx-25, yy-8, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-15, trackTitleLen*6+12, 14, trackTitle, "gb"); *yOffp = *yOffp + 7; } void doExon(int exonCount, char *chrom, int aaLen, int *yOffp, char *proteinID, char *mrnaID) /* draw the track for exons */ { int xx, yy; int j; char exonNumStr[10]; int mrnaLen; Color color; int exonStartPos, exonEndPos; int exonGenomeStartPos, exonGenomeEndPos; int exonNumber; int printedExonNumber = -1; Color exonColor[2]; Color defaultColor; defaultColor = vgFindColorIx(g_vg, 170, 170, 170); /* The hypothetical mRNA length is 3 times of aaLen */ mrnaLen = aaLen * 3; exonColor[0] = pbBlue; exonColor[1] = vgFindColorIx(g_vg, 0, 180, 0); exonNumber = 1; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; currentYoffset = *yOffp; for (j = 0; j < mrnaLen; j++) { color = defaultColor; calxy(j/3, *yOffp, &xx, &yy); if (j > exonEndPos) { if (printedExonNumber != exonNumber) { if ((exonEndPos - exonStartPos)*pbScale/3 > 12) { safef(exonNumStr, sizeof(exonNumStr), "%d", exonNumber); vgTextRight(g_vg, xx-(exonEndPos - exonStartPos)*pbScale/3/2 - 4, yy-9, 10, 10, MG_WHITE, g_font, exonNumStr); } mapBoxExon(xx - (exonEndPos - exonStartPos)*pbScale/3, yy-9, (exonEndPos - exonStartPos)*pbScale/3, 9, mrnaID, exonNumber, chrom, blockGenomeStartPositive[exonNumber-1], blockGenomeEndPositive[exonNumber-1]); printedExonNumber = exonNumber; } if (exonNumber < exonCount) { exonNumber++; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; } } if ((j >= exonStartPos) && (j <= exonEndPos)) { color = exonColor[(exonNumber-1) % 2]; } vgBox(g_vg, xx, yy-9+3*(j-(j/3)*3), pbScale, 3, color); } if ((exonEndPos - exonStartPos)*pbScale/3 > 12) { safef(exonNumStr, sizeof(exonNumStr), "%d", exonNumber); vgTextRight(g_vg, xx-(exonEndPos - exonStartPos)*pbScale/3/2 - 5, yy-9, 10, 10, MG_WHITE, g_font, exonNumStr); } mapBoxExon(xx - (exonEndPos - exonStartPos)*pbScale/3, yy-9, (exonEndPos - exonStartPos)*pbScale/3, 9, mrnaID, exonNumber, chrom, blockGenomeStartPositive[exonNumber-1], blockGenomeEndPositive[exonNumber-1]); calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-10, xx, 12, bkgColor); trackTitle = cloneString("Exons"); vgTextRight(g_vg, xx-25, yy-9, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-12, trackTitleLen*6+12, 14, trackTitle, "exon"); *yOffp = *yOffp + 10; } #define MAX_SF 200 #define MAXNAMELEN 256 int sfId[MAX_SF]; int sfStart[MAX_SF], sfEnd[MAX_SF]; char superfam_name[MAX_SF][256]; struct sqlConnection *conn, *conn2; int getSuperfamilies2(char *proteinID) /* getSuperfamilies2() superceed getSuperfamilies() starting from hg16, it gets Superfamily data of a protein from ensemblXref3, sfAssign, and sfDes from the proteinsXXXXXX database, and placed them in arrays to be used by doSuperfamily().*/ { struct sqlConnection *conn, *conn2, *conn3; char query[MAXNAMELEN], query2[MAXNAMELEN]; struct sqlResult *sr, *sr2; char **row, **row2; char cond_str[255]; char *sfID, *seqID, *sfDesc, *region; int done; int j; char *chp, *chp2; int sfCnt; int int_start, int_end; if (!hTableExists(protDbName, "sfAssign")) return(0); if (!hTableExists(protDbName, "ensemblXref3")) return(0); conn = hAllocConn(database); conn2 = hAllocConn(database); conn3 = hAllocConn(database); sqlSafef(query2, sizeof(query), "select distinct sfID, seqID from %s.ensemblXref3 x, %s.sfAssign a where (swissAcc='%s' or tremblAcc='%s') and seqID=x.protein and protein != '' and evalue <= 0.02", protDbName, protDbName, proteinID, proteinID); sr2 = sqlMustGetResult(conn2, query2); row2 = sqlNextRow(sr2); sfCnt=0; while (row2 != NULL) { sfID = row2[0]; seqID= row2[1]; sqlSafef(query, sizeof(query), "select region from %s.sfAssign where sfID='%s' and seqID='%s' and evalue <=0.02", protDbName, sfID, seqID); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); while (row != NULL) { region = row[0]; for (j=0; j<sfCnt; j++) { if (sfId[j] == atoi(sfID)) goto skip; } - sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s;", sfID); + sqlSafef(cond_str, sizeof(cond_str), "id=%s;", sfID); sfDesc = sqlGetField(protDbName, "sfDes", "description", cond_str); /* !!! refine logic here later to be defensive against illegal syntax */ chp = region; done = 0; while (!done) { chp2 = strstr(chp, "-"); *chp2 = '\0'; chp2++; sscanf(chp, "%d", &int_start); chp = chp2; chp2 = strstr(chp, ","); if (chp2 != NULL) { *chp2 = '\0'; } else { done = 1; } chp2++; sscanf(chp, "%d", &int_end); sfId[sfCnt] = atoi(sfID); sfStart[sfCnt] = int_start; sfEnd[sfCnt] = int_end; strncpy(superfam_name[sfCnt], sfDesc, MAXNAMELEN-1); sfCnt++; chp = chp2; } skip: row = sqlNextRow(sr); } sqlFreeResult(&sr); row2 = sqlNextRow(sr2); } sqlFreeResult(&sr2); hFreeConn(&conn); hFreeConn(&conn2); hFreeConn(&conn3); return(sfCnt); } int getSuperfamilies(char *proteinID) /* preserved here for previous older genomes. Newer genomes should be using getSuperfamilies2(). 6/16/04 Fan*/ { struct sqlConnection *conn, *conn2; char query[MAXNAMELEN]; struct sqlResult *sr; char **row; char cond_str[255]; char *genomeID, *seqID, *modelID, *eValue, *sfID, *sfDesc; char *region; int done; char *ensPep; char *transcriptName; char *chp, *chp2; int ii = 0; int int_start, int_end; if (!hTableExists(database, "sfAssign")) return(0); conn = hAllocConn(database); conn2 = hAllocConn(database); if (hTableExists(database, "ensemblXref3")) { /* use ensemblXref3 for Ensembl data release after ensembl34d */ - sqlSafefFrag(cond_str, sizeof(cond_str), "tremblAcc='%s'", proteinID); + sqlSafef(cond_str, sizeof(cond_str), "tremblAcc='%s'", proteinID); ensPep = sqlGetField(database, "ensemblXref3", "protein", cond_str); if (ensPep == NULL) { - sqlSafefFrag(cond_str, sizeof(cond_str), "swissAcc='%s'", proteinID); + sqlSafef(cond_str, sizeof(cond_str), "swissAcc='%s'", proteinID); ensPep = sqlGetField(database, "ensemblXref3", "protein", cond_str); if (ensPep == NULL) return(0); } } else { if (! (hTableExists(database, "ensemblXref") || hTableExists(database, "ensTranscript") ) ) return(0); /* two steps query needed because the recent Ensembl gene_xref 11/2003 table does not have valid translation_name */ - sqlSafefFrag(cond_str, sizeof(cond_str), "external_name='%s'", protDisplayID); + sqlSafef(cond_str, sizeof(cond_str), "external_name='%s'", protDisplayID); transcriptName = sqlGetField(database, "ensGeneXref", "transcript_name", cond_str); if (transcriptName == NULL) { return(0); } else { - sqlSafefFrag(cond_str, sizeof(cond_str), "transcript_name='%s';", transcriptName); + sqlSafef(cond_str, sizeof(cond_str), "transcript_name='%s';", transcriptName); ensPep = sqlGetField(database, "ensTranscript", "translation_name", cond_str); if (ensPep == NULL) { hFreeConn(&conn); return(0); } } } ensPepName = ensPep; sqlSafef(query, sizeof(query), "select * from %s.sfAssign where seqID='%s' and evalue <= 0.02;", database, ensPep); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row == NULL) return(0); while (row != NULL) { genomeID = row[0]; seqID = row[1]; modelID = row[2]; region = row[3]; eValue = row[4]; sfID = row[5]; /* sfDesc = row[6]; */ /* !!! the recent Suprefamily sfAssign table does not have valid sf description */ - sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s;", sfID); + sqlSafef(cond_str, sizeof(cond_str), "id=%s;", sfID); sfDesc = sqlGetField(database, "sfDes", "description", cond_str); /* !!! refine logic here later to be defensive against illegal syntax */ chp = region; done = 0; while (!done) { chp2 = strstr(chp, "-"); *chp2 = '\0'; chp2++; sscanf(chp, "%d", &int_start); chp = chp2; chp2 = strstr(chp, ","); if (chp2 != NULL) { *chp2 = '\0'; } else { done = 1; } chp2++; sscanf(chp, "%d", &int_end); sfId[ii] = atoi(sfID); sfStart[ii] = int_start; sfEnd[ii] = int_end; strncpy(superfam_name[ii], sfDesc, MAXNAMELEN-1); ii++; chp = chp2; } row = sqlNextRow(sr); } sqlFreeResult(&sr); hFreeConn(&conn); hFreeConn(&conn2); return(ii); } void mapBoxSuperfamily(int x, int y, int width, int height, char *sf_name, int sfID) { hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x-1, y-1, x+width+1, y+height+1); hPrintf("HREF=\"%s?sunid=%d\"", "http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi", sfID); hPrintf(" target=_blank ALT=\"%s\">\n", sf_name); } void vgDrawBox(struct vGfx *vg, int x, int y, int width, int height, Color color) { vgBox(g_vg, x, y, width, height, color); vgBox(vg, x-1, y-1, width+2, 1, MG_BLACK); vgBox(vg, x-1, y+height, width+2, 1, MG_BLACK); vgBox(vg, x-1, y-1, 1, height+2, MG_BLACK); vgBox(vg, x+width, y-1, 1, height+2, MG_BLACK); } void doSuperfamily(char *pepName, int sf_cnt, int *yOffp) /* draw the Superfamily track */ { int xx, yy; int ii, jj; char exonNumStr[10]; int len; int sf_len, name_len; int show_name; Color sfColor; /* sfColor = vgFindColorIx(g_vg, 0xf7, 0xe8, 0xaa); */ sfColor = MG_YELLOW; currentYoffset = *yOffp; calxy(0, *yOffp, &xx, &yy); jj = 0; for (ii=0; ii<sf_cnt; ii++) { if (sfEnd[ii] != 0) { jj++; safef(exonNumStr, sizeof(exonNumStr), "%d", jj); calxy(sfStart[ii], *yOffp, &xx, &yy); sf_len = sfEnd[ii] - sfStart[ii]; name_len = strlen(superfam_name[ii]); if (sf_len*pbScale < name_len*6) { show_name = 0; } else { show_name = 1; } len = strlen(superfam_name[ii]); vgDrawBox(g_vg, xx, yy-9+(jj%4)*5, (sfEnd[ii] - sfStart[ii])*pbScale, 9, sfColor); mapBoxSuperfamily(xx, yy-9+(jj%4)*5, (sfEnd[ii] - sfStart[ii])*pbScale, 9, superfam_name[ii], sfId[ii]); if (show_name) vgTextRight(g_vg, xx+(sfEnd[ii] - sfStart[ii])*pbScale/2 + (len/2)*5, yy-9+(jj%4)*5, 10, 10, MG_BLACK, g_font, superfam_name[ii]); } } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-8, xx, 22, bkgColor); trackTitle = cloneString("Superfamily/SCOP"); vgTextRight(g_vg, xx-25, yy, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-2, trackTitleLen*6+12, 14, trackTitle, "superfam"); *yOffp = *yOffp + 20; } void doResidues(char *aa, int len, int *yOffp) /* draw track for AA residue */ { int index; int xx, yy; char res_str[2]; currentYoffset = *yOffp; calxy(0, *yOffp, &xx, &yy); res_str[1] = '\0'; for (index=0; index < len; index++) { res_str[0] = aa[index]; calxy(index+1, *yOffp, &xx, &yy); /* vgTextRight(g_vg, xx-3-6, yy, 10, 10, MG_BLACK, g_font, res_str); */ if (pbScale >= 18) { vgTextRight(g_vg, xx-3-16, yy, 10, 10, MG_BLACK, g_font, res_str); } else { vgTextRight(g_vg, xx-3-6, yy, 10, 10, MG_BLACK, g_font, res_str); } } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-10, xx, 20, bkgColor); trackTitle = cloneString("AA Sequence"); vgTextRight(g_vg, xx-25, yy, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-2, trackTitleLen*6+12, 14, trackTitle, "aaSeq"); *yOffp = *yOffp + 12; } void doDnaTrack(char *chrom, char strand, int exonCount, int len, int *yOffp) /* draw track for AA residue */ { int xx, yy; int j; int mrnaLen; int exonStartPos, exonEndPos; int exonGenomeStartPos, exonGenomeEndPos; int exonNumber; int printedExonNumber = -1; Color exonColor[2]; Color color; int k; struct dnaSeq *dna; char base[2]; char baseComp[2]; int dnaLen; Color defaultColor; defaultColor = vgFindColorIx(g_vg, 170, 170, 170); /* exonColor[0] = pbBlue; */ exonColor[0] = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0); exonColor[1] = vgFindColorIx(g_vg, 0, 180, 0); base[1] = '\0'; baseComp[1] = '\0'; currentYoffset = *yOffp; calxy(0, *yOffp, &xx, &yy); /* The hypothetical mRNA length is 3 times of aaLen */ mrnaLen = len * 3; exonNumber = 1; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; dna = hChromSeq(database, chrom, exonGenomeStartPos, exonGenomeEndPos+1); dnaLen = strlen(dna->dna); k=0; for (j = 0; j < mrnaLen; j++) { if (j > exonEndPos) { if (printedExonNumber != exonNumber) { printedExonNumber = exonNumber; } if (exonNumber < exonCount) { exonNumber++; exonStartPos = blockStartPositive[exonNumber-1]; exonEndPos = blockEndPositive[exonNumber-1]; exonGenomeStartPos = blockGenomeStartPositive[exonNumber-1]; exonGenomeEndPos = blockGenomeEndPositive[exonNumber-1]; dna = hChromSeq(database, chrom, exonGenomeStartPos, exonGenomeEndPos+1); dnaLen = strlen(dna->dna); k=0; } } if ((j >= exonStartPos) && (j <= exonEndPos)) { if (strand == '+') { base[0] = toupper(*(dna->dna + k)); } else { base[0] = toupper(ntCompTable[(int)*(dna->dna + dnaLen - k -1 )]); baseComp[0] = toupper(*(dna->dna + dnaLen - k -1 )); } k++; color = exonColor[(exonNumber-1) % 2]; calxy(j/3, *yOffp, &xx, &yy); if (strand == '-') { vgTextRight(g_vg, xx-3+(j%3)*6, yy-3, 10, 10, color, g_font, base); vgTextRight(g_vg, xx-3+(j%3)*6, yy+9, 10, 10, color, g_font, baseComp); } else { vgTextRight(g_vg, xx-3+(j%3)*6, yy-3, 10, 10, color, g_font, base); } } color = pbBlue; } calxy0(0, *yOffp, &xx, &yy); vgBox(g_vg, 0, yy-10, xx, 30, bkgColor); if (strand == '-') { trackTitle = cloneString("Coding Sequence"); } else { trackTitle = cloneString("Genomic Sequence"); } vgTextRight(g_vg, xx-25, yy-4, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy-6, trackTitleLen*6+12, 14, trackTitle, "dna"); if (strand == '-') { trackTitle = cloneString("Genomic Sequence"); vgTextRight(g_vg, xx-25, yy+9, 10, 10, MG_BLACK, g_font, trackTitle); trackTitleLen = strlen(trackTitle); mapBoxTrackTitle(xx-25-trackTitleLen*6, yy+7, trackTitleLen*6+12, 14, trackTitle, "dna"); } if (strand == '-') { *yOffp = *yOffp + 20; } else { *yOffp = *yOffp + 12; } } boolean doExonTrack = FALSE; void doTracks(char *proteinID, char *mrnaID, char *aa, int *yOffp, char *psOutput) /* draw various protein tracks */ { int l; char aaOrigOffsetStr[20]; int hasResFreq; char uniProtDbName[50]; char *protDbDate; char *chrom; char strand; char *kgId, *kgPep, *protPep; char cond_str[255]; char *answer; //int i, ll; //char *chp1, *chp2; g_font = mgSmallFont(); safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale); if (psOutput != NULL) { pbScale = atoi(cartOptionalString(cart, "pbt.pbScaleStr")); } if (cgiOptionalString("trackOffset") != NULL) { trackOrigOffset = atoi(cgiOptionalString("trackOffset")); } if (cgiOptionalString("pbScaleStr") != NULL) { pbScale = atoi(cgiOptionalString("pbScaleStr")); } if (cgiOptionalString("pbScale") != NULL) { scaleButtonPushed = TRUE; if (strcmp(cgiOptionalString("pbScale"), "1/6") == 0) pbScale = 1; if (strcmp(cgiOptionalString("pbScale"), "1/2") == 0) pbScale = 3; if (strcmp(cgiOptionalString("pbScale"), "FULL") == 0) pbScale = 6; if (strcmp(cgiOptionalString("pbScale"), "DNA") == 0) pbScale =22; safef(pbScaleStr, sizeof(pbScaleStr), "%d", pbScale); cgiMakeHiddenVar("pbScaleStr", pbScaleStr); } else { scaleButtonPushed = FALSE; } if (psOutput == NULL) { if (cgiVarExists("pbt.left3")) { relativeScroll(-0.95); initialWindow = FALSE; } else if (cgiVarExists("pbt.left2")) { relativeScroll(-0.475); initialWindow = FALSE; } else if (cgiVarExists("pbt.left1")) { relativeScroll(-0.02); initialWindow = FALSE; } else if (cgiVarExists("pbt.right1")) { relativeScroll(0.02); initialWindow = FALSE; } else if (cgiVarExists("pbt.right2")) { relativeScroll(0.475); initialWindow = FALSE; } else if (cgiVarExists("pbt.right3")) { relativeScroll(0.95); initialWindow = FALSE; } } dnaUtilOpen(); l=strlen(aa); /* initialize AA properties */ aaPropertyInit(&hasResFreq); sfCount = getSuperfamilies2(proteinID); if (sfCount == 0) { sfCount = getSuperfamilies(proteinID); } if (mrnaID != NULL) { if (kgVersion == KG_III) { doExonTrack = FALSE; - sqlSafefFrag(cond_str, sizeof(cond_str), "spId='%s'", proteinID); + sqlSafef(cond_str, sizeof(cond_str), "spId='%s'", proteinID); kgId = sqlGetField(database, "kgXref", "kgId", cond_str); if (kgId != NULL) { - sqlSafefFrag(cond_str, sizeof(cond_str), "name='%s'", kgId); + sqlSafef(cond_str, sizeof(cond_str), "name='%s'", kgId); kgPep = sqlGetField(database, "knownGenePep", "seq", cond_str); //printf("<pre><br>%s", kgPep);fflush(stdout); if (kgPep != NULL) { if (strstr(protDbName, "proteins") != NULL) { protDbDate = strstr(protDbName, "proteins") + strlen("proteins"); safef(uniProtDbName, sizeof(uniProtDbName),"sp%s", protDbDate); - sqlSafefFrag(cond_str, sizeof(cond_str), "acc='%s'", proteinID); + sqlSafef(cond_str, sizeof(cond_str), "acc='%s'", proteinID); protPep = sqlGetField(uniProtDbName, "protein", "val", cond_str); //printf("<br>%s\n", protPep);fflush(stdout); if (protPep != NULL) { if (sameWord(kgPep, protPep)) { //printf("<br>MATCH!\n");fflush(stdout); - sqlSafefFrag(cond_str, sizeof(cond_str), "qName='%s'", kgId); + sqlSafef(cond_str, sizeof(cond_str), "qName='%s'", kgId); answer = sqlGetField(database, kgProtMapTableName, "qName", cond_str); if (answer != NULL) { /* NOTE: passing in kgId instead of proteinID because kgProtMap2's qName uses kgId instead of protein display ID */ getExonInfo(kgId, &exCount, &chrom, &strand); assert(exCount > 0); doExonTrack = TRUE; } } /* else { chp1 = kgPep; printf("<br>"); chp2 = protPep; ll = strlen(kgPep); if (strlen(protPep) < ll) ll= strlen(protPep); for (i=0; i<ll; i++) { if (*chp1 != *chp2) { printf("%c", *chp1); } else { printf("."); } chp1++; chp2++; } } //printf("</pre>");fflush(stdout); */ } } } } } else { doExonTrack = TRUE; getExonInfo(proteinID, &exCount, &chrom, &strand); assert(exCount > 0); } /* do the following only if pbTracks called doTracks() */ if (initialWindow && IAmPbTracks) { prevGBOffsetSav = calPrevGB(exCount, chrom, strand, l, yOffp, proteinID, mrnaID); trackOrigOffset = prevGBOffsetSav; if (trackOrigOffset > (protSeqLen*pbScale - 600)) trackOrigOffset = protSeqLen*pbScale - 600; /* prevent negative value */ if (trackOrigOffset < 0) trackOrigOffset = 0; } /* if this if for PDF/Postscript, the trackOrigOffset is already calculated previously, use the saved value */ if (psOutput != NULL) { trackOrigOffset = atoi(cartOptionalString(cart, "pbt.trackOffset")); } } /*printf("<br>%d %d<br>%d %d\n", prevGBStartPos, prevGBEndPos, blockGenomeStartPositive[exCount-1], blockGenomeStartPositive[0]); fflush(stdout); */ if (strand == '-') { if ((prevGBStartPos <= blockGenomeStartPositive[exCount-1]) && (prevGBEndPos >= blockGenomeStartPositive[0])) { showPrevGBPos = FALSE; } } else { if ((prevGBStartPos <= blockGenomeStartPositive[0]) && (prevGBEndPos >= blockGenomeStartPositive[exCount-1])) { showPrevGBPos = FALSE; } } if ((cgiOptionalString("aaOrigOffset") != NULL) && scaleButtonPushed) { trackOrigOffset = atoi(cgiOptionalString("aaOrigOffset"))*pbScale; } pixWidth = 160+ protSeqLen*pbScale; if (pixWidth > MAX_PB_PIXWIDTH) { pixWidth = MAX_PB_PIXWIDTH; } if ((protSeqLen*pbScale - trackOrigOffset) < MAX_PB_PIXWIDTH) { pixWidth = protSeqLen*pbScale - trackOrigOffset + 160; } if (pixWidth < 550) pixWidth = 550; insideWidth = pixWidth-gfxBorder; if (proteinInSupportedGenome) { pixHeight = 250; } else { pixHeight = 215; } if (sfCount > 0) pixHeight = pixHeight + 20; /* make room for individual residues display */ if (pbScale >=6) pixHeight = pixHeight + 20; if (pbScale >=18) pixHeight = pixHeight + 30; if (psOutput) { vg = vgOpenPostScript(pixWidth, pixHeight, psOutput); suppressHtml = TRUE; hideControls = TRUE; } else { trashDirFile(&gifTn, "pbt", "pbt", ".png"); vg = vgOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE); } /* Put up horizontal scroll controls. */ hWrites("Move "); hButton("pbt.left3", "<<<"); hButton("pbt.left2", " <<"); hButton("pbt.left1", " < "); hButton("pbt.right1", " > "); hButton("pbt.right2", ">> "); hButton("pbt.right3", ">>>"); hPrintf("     "); /* Put up scaling controls. */ hPrintf("Current scale: "); if (pbScale == 1) hPrintf("1/6 "); if (pbScale == 3) hPrintf("1/2 "); if (pbScale == 6) hPrintf("FULL "); if (pbScale == 22) hPrintf("DNA "); hPrintf("    Rescale to "); hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"1/6\">\n"); hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"1/2\">\n"); hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"FULL\">\n"); if (kgVersion == KG_III) { /* for KG III, the protein has to exist in the kgProtMap2 table (which will turn on doExonTrack flag) to provide the genomic position data needed for DNA sequence display */ if ((proteinInSupportedGenome) && (doExonTrack)) hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"DNA\">\n"); } else { if (proteinInSupportedGenome) hPrintf("<INPUT TYPE=SUBMIT NAME=\"pbScale\" VALUE=\"DNA\">\n"); } hPrintf("<FONT SIZE=1><BR><BR></FONT>\n"); g_vg = vg; pbRed = vgFindColorIx(g_vg, 0xf9, 0x51, 0x59); pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0); bkgColor = vgFindColorIx(vg, 255, 254, 232); vgBox(vg, 0, 0, insideWidth, pixHeight, bkgColor); /* Start up client side map. */ hPrintf("<MAP Name=%s>\n", mapName); vgSetClip(vg, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder); /* start drawing indivisual tracks */ doAAScale(l, yOffp, 1); if (pbScale >= 6) doResidues(aa, l, yOffp); if (pbScale >= 18) doDnaTrack(chrom, strand, exCount, l, yOffp); if ((mrnaID != NULL) && showPrevGBPos) { doPrevGB(exCount, chrom, strand, l, yOffp, proteinID, mrnaID); } if (mrnaID != NULL) { if (doExonTrack) doExon(exCount, chrom, l, yOffp, proteinID, mrnaID); } doCharge(aa, l, yOffp); doHydrophobicity(aa, l, yOffp); doCysteines(aa, l, yOffp); if (sfCount > 0) doSuperfamily(ensPepName, sfCount, yOffp); if (hasResFreq) doAnomalies(aa, l, yOffp); doAAScale(l, yOffp, -1); vgClose(&vg); /* Finish map and save out picture and tell html file about it. */ hPrintf("</MAP>\n"); /* put tracks image here */ hPrintf( "\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>", gifTn.forCgi, pixWidth, pixHeight, mapName); if (proteinInSupportedGenome) { hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#tracks\" TARGET=_blank>"); } else { if (hIsGsidServer()) { hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbGsid/pbTracksHelp.shtml#tracks\" TARGET=_blank>"); } else { hPrintf("<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#tracks\" TARGET=_blank>"); } } hPrintf("Explanation of Protein Tracks</A><br>"); safef(trackOffset, sizeof(trackOffset), "%d", trackOrigOffset); cgiMakeHiddenVar("trackOffset", trackOffset); /* remember where the AA base origin is so that it can be passed to next PB page */ aaOrigOffset = trackOrigOffset/pbScale; safef(aaOrigOffsetStr, sizeof(aaOrigOffsetStr), "%d", aaOrigOffset); cgiMakeHiddenVar("aaOrigOffset", aaOrigOffsetStr); /* save the following state variables, to be used by PDF/Postcript processing */ cartSetString(cart,"pbt.pbScaleStr", pbScaleStr); cartSetString(cart,"pbt.trackOffset", trackOffset); cartSaveSession(cart); fflush(stdout); }