static void cytoBandDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw cytoBand items. */
{
struct cytoBand *band = item;
int heightPer = tg->heightPer;
int x1,x2,w;
x1 = round((double)((int)tg->itemStart(tg,band) - winStart)*scale) + xOff;
x2 = round((double)((int)tg->itemEnd(tg,band) - winStart)*scale) + xOff;
/* Clip here so that text will tend to be more visible... */
if (x1 < xOff)
x1 = xOff;
if (x2 > insideX + insideWidth)
x2 = insideX + insideWidth;
w = x2-x1;
if (w < 1)
w = 1;
hCytoBandDrawAt(band, hvg, x1, y, w, heightPer, hCytoBandDbIsDmel(database), font,
mgFontPixelHeight(font), tg->ixColor, tg->ixAltColor,
shadesOfGray, maxShade);
if(tg->mapsSelf)
tg->mapItem(tg, hvg, band, band->name, band->name, band->chromStart, band->chromEnd,
x1, y, w, heightPer);
else
mapBoxHc(hvg, band->chromStart, band->chromEnd, x1,y,w,heightPer, tg->track,
band->name, band->name);
}
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);
}
void genoLayDrawChromLabels(struct genoLay *gl, struct hvGfx *hvg, int color)
/* Draw chromosomes labels in image */
{
struct slRef *ref;
struct genoLayChrom *chrom;
int pixelHeight = mgFontPixelHeight(gl->font);
if (gl->allOneLine)
{
int yOffset = gl->chromOffsetY + gl->chromHeight + 1;
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
hvGfxTextCentered(hvg, chrom->x, yOffset, chrom->width, pixelHeight, color, gl->font,
chrom->shortName);
}
}
else
{
int yOffset = gl->chromOffsetY + gl->chromHeight - pixelHeight;
/* Draw chromosome labels. */
for (ref = gl->leftList; ref != NULL; ref = ref->next)
leftLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
for (ref = gl->rightList; ref != NULL; ref = ref->next)
rightLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
if (ref == gl->bottomList)
leftLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
else if (ref->next == NULL)
rightLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
else
midLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
}
}
}
void genoLayDrawBandedChroms(struct genoLay *gl, struct hvGfx *hvg, char *db,
struct sqlConnection *conn, Color *shadesOfGray, int maxShade,
int defaultColor)
/* Draw chromosomes with centromere and band glyphs.
* Get the band data from the database. If the data isn't
* there then draw simple chroms in default color instead */
{
char *bandTable = "cytoBandIdeo";
int yOffset = gl->chromOffsetY;
genoLayDrawSimpleChroms(gl, hvg, defaultColor);
if (sqlTableExists(conn, bandTable) && !gl->allOneLine)
{
int centromereColor = hCytoBandCentromereColor(hvg);
double pixelsPerBase = 1.0/gl->basesPerPixel;
int height = gl->chromHeight;
int innerHeight = gl->chromHeight-2;
struct genoLayChrom *chrom;
boolean isDmel = hCytoBandDbIsDmel(db);
boolean bColor = hvGfxFindColorIx(hvg, 200, 150, 150);
int fontPixelHeight = mgFontPixelHeight(gl->font);
for (chrom = gl->chromList; chrom != NULL; chrom = chrom->next)
{
boolean gotAny = FALSE;
struct sqlResult *sr;
char **row;
char query[256];
int cenX1=BIGNUM, cenX2=0;
int y = chrom->y + yOffset;
/* Fetch bands from database and draw them. */
safef(query, sizeof(query), "select * from %s where chrom='%s'",
bandTable, chrom->fullName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct cytoBand band;
int x1, x2;
cytoBandStaticLoad(row, &band);
x1 = pixelsPerBase*band.chromStart;
x2 = pixelsPerBase*band.chromEnd;
if (sameString(band.gieStain, "acen"))
{
/* Centromere is represented as two adjacent bands.
* We'll just record the extents of it here, and draw it
* in one piece later. */
if (x1 < cenX1)
cenX1 = x1;
if (x2 > cenX2)
cenX2 = x2;
}
else
{
/* Draw band */
hCytoBandDrawAt(&band, hvg, x1+chrom->x, y+1, x2-x1, innerHeight,
isDmel, gl->font, fontPixelHeight, MG_BLACK, bColor,
shadesOfGray, maxShade);
gotAny = TRUE;
}
}
sqlFreeResult(&sr);
/* Draw box around chromosome */
hvGfxBox(hvg, chrom->x, y, chrom->width, 1, MG_BLACK);
hvGfxBox(hvg, chrom->x, y+height-1, chrom->width, 1, MG_BLACK);
hvGfxBox(hvg, chrom->x, y, 1, height, MG_BLACK);
hvGfxBox(hvg, chrom->x+chrom->width-1, y, 1, height, MG_BLACK);
/* Draw centromere if we found one. */
if (cenX2 > cenX1)
{
hCytoBandDrawCentromere(hvg, cenX1+chrom->x, y, cenX2-cenX1, height,
MG_WHITE, centromereColor);
}
}
}
}
