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 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 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 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 hLine(double fx, double fy, double fw, double ih, int color)
/* draw a horizontal line based on data coordinates */
{
int x, y, w, h;
calStampXY(stampPictPtr, fx, fy, &x, &y);
w = (int)(fw * xScale);
h = ih;
vgBox(g_vg, x, y-h, w+1, h, color);
}
void vLineM(double fx, double fy, double fh, int iw, int color)
/* draw a vertical line based on data coordinates, for Marker lines */
{
int x, y, w, h;
calStampXY(stampPictPtr, fx, fy, &x, &y);
w = iw,
h = (int)(fh * yScale);
vgBox(g_vg, x, y-h-1, w, h-1, color);
}
void pbBox(double fx, double fy, double fw, double fh, int color)
/* draw a box based on data coordinates */
{
int x, y, w, h;
calStampXY(stampPictPtr, fx, fy, &x, &y);
w = (int)(fw * xScale);
h = (int)(fh * yScale);
vgBox(g_vg, x, y-h, w+1, h, color);
}
void hLine2(double fx, double fy, double fw, double ih, int color)
/* draw a horizontal line based on data coordinates,
this function extend 1 pixel more to the right,
useful for picture fine tuning of slight difference due to rounding.
*/
{
int x, y, w, h;
calStampXY(stampPictPtr, fx, fy, &x, &y);
w = (int)(fw * xScale);
h = ih;
/* 1 pixel more to the width */
vgBox(g_vg, x, y-h, w+1+1, h, color);
}
void vgDrawRulerBumpText(struct vGfx *vg, int xOff, int yOff,
int height, int width,
Color color, MgFont *font,
int startNum, int range, int bumpX, int bumpY)
/* Draw a ruler inside the indicated part of mg with numbers that start at
* startNum and span range. Bump text positions slightly. */
{
int tickSpan;
int tickPos;
double scale;
int firstTick;
int remainder;
int end = startNum + range;
int x;
char tbuf[14];
int numWid;
int goodNumTicks;
int niceNumTicks = width/35;
numLabelString(startNum+range, tbuf);
numWid = mgFontStringWidth(font, tbuf)+4+bumpX;
goodNumTicks = width/numWid;
if (goodNumTicks < 1) goodNumTicks = 1;
if (goodNumTicks > niceNumTicks) goodNumTicks = niceNumTicks;
tickSpan = figureTickSpan(range, goodNumTicks);
scale = (double)width / range;
firstTick = startNum + tickSpan;
remainder = firstTick % tickSpan;
firstTick -= remainder;
for (tickPos=firstTick; tickPos<end; tickPos += tickSpan)
{
numLabelString(tickPos, tbuf);
numWid = mgFontStringWidth(font, tbuf)+4;
x = (int)((tickPos-startNum) * scale) + xOff;
vgBox(vg, x, yOff, 1, height, color);
if (x - numWid >= xOff)
{
vgTextCentered(vg, x-numWid + bumpX, yOff + bumpY, numWid,
height, color, font, tbuf);
}
}
}
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 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;
}
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 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 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);
}
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]);
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 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);
kgId = sqlGetField(database, "kgXref", "kgId", cond_str);
if (kgId != NULL)
{
sqlSafefFrag(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);
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);
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);
}
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 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;
}
}
