void chkGlue(char *bacAcc, char *finBac, char *unfinBac, char *gluedBac, int trim, char *repeatMask)
/* Display glued and unglued form of BAC. */
{
int trackCount = 1;
int pixWidth, pixHeight;
int x, y;
struct memGfx *mg;
struct tempName gifTn, mapTn;
FILE *mapFile;
printf("See picture at bottom for overview of where contigs align.\n\n");
/* Figure out basic dimensions and allocate picture. */
font = mgSmallFont();
trackWidth = 700;
trackHeight = mgFontPixelHeight(font) + 4;
pixWidth = trackWidth + 2*border;
pixHeight = trackCount * (trackHeight+border) + border;
x = y = border;
mg = mgNew(pixWidth, pixHeight);
mgClearPixels(mg);
makeBlockColors(mg);
/* Create map file. */
makeTempName(&mapTn, "glu", ".map");
mapFile = mustOpen(mapTn.forCgi, "wb");
mapWriteHead(mapFile, pixWidth, pixHeight, bacAcc, trim, repeatMask);
/* Write out tracks onto picture. */
aliTrack(bacAcc, finBac, unfinBac, mg, x, y, mapFile, trim, repeatMask);
/* Save pic and tell html file about it. */
makeTempName(&gifTn, "glu", ".gif");
mgSaveGif(mg, gifTn.forCgi);
printf("<INPUT TYPE=HIDDEN NAME=map VALUE=\"%s\">\n", mapTn.forCgi);
printf(
"<P><INPUT TYPE=IMAGE SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d NAME = \"clickMe\" ALIGN=BOTTOM><BR>\n",
gifTn.forHtml, pixWidth, pixHeight);
printf("Click on contig for detailed alignment\n");
/* Write end of map */
mapWriteBox(mapFile, mtNone, 0, 0, pixWidth, pixHeight, NULL, 0, 0, 0, 0, 0);
mapWriteBox(mapFile, mtEnd, 0, 0, pixWidth, pixHeight, NULL, 0, 0, 0, 0, 0);
/* Clean up. */
fclose(mapFile);
mgFree(&mg);
}
char *altGraphXMakeImage(struct altGraphX *ag)
/* create a drawing of splicing pattern */
{
MgFont *font = mgSmallFont();
int fontHeight = mgFontLineHeight(font);
struct spaceSaver *ssList = NULL;
struct hash *heightHash = NULL;
int rowCount = 0;
struct tempName gifTn;
int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));
int pixHeight = 0;
struct hvGfx *hvg;
int lineHeight = 0;
double scale = 0;
Color shadesOfGray[9];
int maxShade = ArraySize(shadesOfGray)-1;
scale = (double)pixWidth/(ag->tEnd - ag->tStart);
lineHeight = 2 * fontHeight +1;
altGraphXLayout(ag, ag->tStart, ag->tEnd, scale, 100, &ssList, &heightHash, &rowCount);
hashFree(&heightHash);
pixHeight = rowCount * lineHeight;
makeTempName(&gifTn, "hgc", ".png");
hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
makeGrayShades(hvg, maxShade, shadesOfGray);
hvGfxSetClip(hvg, 0, 0, pixWidth, pixHeight);
altGraphXDrawPack(ag, ssList, hvg, 0, 0, pixWidth, lineHeight, lineHeight-1,
ag->tStart, ag->tEnd, scale,
font, MG_BLACK, shadesOfGray, "Dummy", NULL);
hvGfxUnclip(hvg);
hvGfxClose(&hvg);
printf(
"<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
gifTn.forHtml, pixWidth, pixHeight);
return cloneString(gifTn.forHtml);
}
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 agpVsMap(char *agpName, char *infoName, char *gifName)
/* agpVsMap - Plot clones in agp vs. map coordinates. */
{
struct mapPos *mapList, *mp;
struct agpFrag *agpList, *bp;
struct hash *cloneHash = newHash(14);
struct hashEl *hel;
struct cloneInfo *cloneList = NULL, *clone;
struct memGfx *mg = NULL;
int pixWidth = 600;
int pixHeight = 600;
int rulerHeight = 20;
int maxMapPos = 0, maxAgpPos = 0;
double scaleMap, scaleAgp;
Color orange, green;
mapList = readInfoFile(infoName);
agpList = readAgpFile(agpName);
for (mp = mapList; mp != NULL; mp = mp->next)
{
if (mp->phase > 0)
{
AllocVar(clone);
hel = hashAddUnique(cloneHash, mp->cloneName, clone);
clone->name = hel->name;
clone->mp = mp;
slAddHead(&cloneList, clone);
if (mp->pos > maxMapPos) maxMapPos = mp->pos;
}
}
slReverse(&cloneList);
for (bp = agpList; bp != NULL; bp = bp->next)
{
if (bp->chromStart > maxAgpPos) maxAgpPos = bp->chromStart;
}
/* Draw scatterplot on bitmap. */
mg = mgNew(pixWidth, pixHeight);
mgClearPixels(mg);
orange = mgFindColor(mg, 210, 150, 0);
green = mgFindColor(mg, 0, 200, 0);
mgDrawRuler(mg, 0, pixHeight-rulerHeight, rulerHeight, pixWidth, MG_BLACK,
mgSmallFont(), 0, maxMapPos+1);
scaleMap = (double)pixWidth/(double)(maxMapPos+1.0);
scaleAgp = (double)(pixHeight)/(double)(maxAgpPos+1.0);
for (bp = agpList; bp != NULL; bp = bp->next)
{
char cloneName[128];
fragToCloneName(bp->frag, cloneName);
clone = hashFindVal(cloneHash, cloneName);
if (clone == NULL)
warn("%s is in %s but not %s", cloneName,
agpName, infoName);
else
{
int x = round(scaleMap*clone->mp->pos);
int y = pixHeight - round(scaleAgp*bp->chromStart);
int phase = clone->mp->phase;
int back;
if (phase <= 1) back = green;
else if (phase == 2) back = orange;
else back = MG_RED;
drawPlus(mg, x, y, back);
}
}
mgSaveGif(mg, gifName);
}
void makePlot(struct clonePos *xList, struct clonePos *yList, struct hash *yHash)
/* Write out graphics for plot. */
{
struct memGfx *mg = NULL;
struct tempName gifTn;
char *mapName = "map";
struct clonePos *xp, *yp;
int i, j, x, y, nextX, nextY;
int divisions = 10;
double invZoom = 1.0/zoom;
double magnify = 2.0;
double newZoom = zoom*magnify;
double invNewZoom = 1.0/newZoom;
int xCount = slCount(xList);
plotName = (xCount/zoom < 50);
if (xList == NULL || yList == NULL)
return;
font = mgSmallFont();
posSpan(xList, &xStart, &xEnd);
posSpan(yList, &yStart, &yEnd);
if (pix < 50 || pix > 5000)
errAbort("Pixels out of range - must be between 50 an 5000");
mg = mgNew(pix, pix);
mgClearPixels(mg);
/* Plot dots. */
for (xp = xList; xp != NULL; xp = xp->next)
{
if ((yp = hashFindVal(yHash, xp->name)) != NULL)
{
zoomScale(xp->pos, yp->pos, &x, &y);
plot(mg, x, y, xp->name, MG_BLACK);
}
}
/* Make zooming image map. */
printf("<MAP Name=%s>\n", mapName);
for (i=0; i<divisions; ++i)
{
double cenX = xOff + (i + 0.5) * (invZoom / divisions);
double sx = cenX - invNewZoom/2;
x = i*pix/divisions;
nextX = (i+1)*pix/divisions;
for (j=0; j<divisions; ++j)
{
double cenY = yOff + (j + 0.5) * (invZoom / divisions);
double sy = cenY - invNewZoom/2;
y = j*pix/divisions;
nextY = (j+1)*pix/divisions;
mapZoomIn(x, y, nextX - x, nextY - y, sx, sy, zoom*magnify);
}
}
printf("</MAP>\n");
/* Save image in temp dir. */
makeTempName(&gifTn, "wikPic", ".gif");
mgSaveGif(mg, gifTn.forCgi, FALSE);
printf(
"<P><IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>\n",
gifTn.forHtml, pix, pix, mapName);
mgFree(&mg);
/* Print some extra info. */
printf("X has %d elements ranging from %d to %d<BR>\n", slCount(xList), xStart, xEnd);
printf("Y has %d elements ranging from %d to %d<BR>\n", slCount(yList), yStart, yEnd);
}
