/**
* Draws a rectangle symbolizing a variant
*
* @param g graphics object
* @param height height of the graphics
* @param variantDisplay the variant
* @param color the color of the stripe
* @param genomeWindow the displayed genome window
*/
private void drawVariant(
Graphics g,
int height,
VariantDisplay variantDisplay,
Color color,
GenomeWindow genomeWindow) {
Variant variant = variantDisplay.getVariant();
// Get start and stop position
int start = variant.getStart();
int stop = variant.getStop();
// Fits the start and stop position to the screen
if ((start < genomeWindow.getStart())
&& (stop
> genomeWindow
.getStart())) { // if the variant starts before the left edge of the track but stop
// after
start = genomeWindow.getStart(); // the drawing must start from the left edge of the track
}
if ((start < genomeWindow.getStop())
&& (stop
> genomeWindow
.getStop())) { // if the variant start before the right edge of the track and ends
// up further,
stop = genomeWindow.getStop(); // the drawing must stop at the right edge of the track
}
// Transform the start and stop position to screen coordinates
int x =
projectWindow.genomeToScreenPosition(start); // get the position where the variant starts
int width =
projectWindow.genomeToScreenWidth(
stop - start); // get the width of the variant on the screen
if (width == 0) { // if the width is 0 pixel,
width = 1; // we set it to 1 in order to be seen
}
// Get the height of the clip and of the stripe
int variantHeight =
getVariantHeight(variant, height); // Instantiate the int for the height of the variant
// Sets the stripe color
Color newColor;
if ((drawer.getVariantUnderMouse() != null)
&& drawer.getVariantUnderMouse().equals(variant)) { // if there is a variant under the mouse
newColor = Colors.stripeFilter(color); // we change the color of the variant
} else { // if not
newColor =
new Color(
color.getRed(),
color.getGreen(),
color.getBlue(),
variantOpacity); // we use the defined color taking into account the opacity
}
g.setColor(newColor); // we set the graphic object color
// if it is not a blank of synchronization
int y =
height
- variantHeight; // y represents the top left corner of the stripes, the axis goes down
// to the bottom
// Draws the variant
int nucleotideNumber;
if (variant
instanceof
ReferenceVariant) { // drawing a reference stripe requires a different method (shorter and
// more simple)
if (color != null) { // if color is null, it means we don't want to draw the reference
drawReference(g, x, width, height);
}
} else {
g.fillRect(x, y, width, variantHeight); // draw the stripe
// Draws the edge line of stripes
if (variant.getType()
== VariantType.INSERTION) { // the edge of an insertion and a deletion are different
drawInsertion(g, x, y, width, variantHeight);
} else if (variant.getType() == VariantType.DELETION) {
drawDeletion(g, x, y, width, variantHeight);
}
}
if (variantDisplay.getDisplay() == VariantDisplayList.SHOW_FILTER) {
drawFilterPattern(g, x, y, width, variantHeight);
}
nucleotideNumber = stop - start;
if (nucleotideNumber == 0) {
nucleotideNumber = 1;
}
// Draw the variant letters
if (variant.getType() != VariantType.MIX) {
drawLetters(
g,
height,
x,
width,
variantHeight,
variantDisplay,
nucleotideNumber); // draw the letters (nucleotides) over the stripe
}
}
/**
* Draws the letters (nucleotides) over the stripe.
*
* @param g graphics object
* @param graphicsHeigth height of the graphics object
* @param x x coordinate
* @param width width of the stripe
* @param height height of the stripe
* @param variantDisplay variant
* @param nucleotideNumber number of nucleotide to display
*/
private void drawLetters(
Graphics g,
int graphicsHeigth,
int x,
int width,
int height,
VariantDisplay variantDisplay,
int nucleotideNumber) {
Variant variant = variantDisplay.getVariant();
VariantType variantType = variant.getType(); // gets the variant type
if (((variantType == VariantType.INSERTION)
&& (MGDisplaySettings.DRAW_INSERTION_LETTERS == MGDisplaySettings.YES_MG_OPTION))
|| // checks all options in order to determine if the letters must be drawn
((variantType == VariantType.DELETION)
&& (MGDisplaySettings.DRAW_DELETION_LETTERS == MGDisplaySettings.YES_MG_OPTION))
|| ((variantType == VariantType.SNPS)
&& (MGDisplaySettings.DRAW_SNP_LETTERS == MGDisplaySettings.YES_MG_OPTION))
|| ((variant instanceof ReferenceVariant)
&& (MGDisplaySettings.DRAW_REFERENCE_LETTERS == MGDisplaySettings.YES_MG_OPTION))) {
// if the letters must be drawn
double windowWidth =
width
/ nucleotideNumber; // calculate the size of window (here, the window is the width of
// a nucleotide on the screen)
FontMetrics fm = g.getFontMetrics(); // get the font metrics
if ((fm.getHeight() < height)
&& (fm.stringWidth("A")
< windowWidth)) { // verifies if the height of the font is smaller than the height of
// the stripe AND if the width of a reference letter (A) is smaller
// than a window size
String letters = variantDisplay.getVariantSequence();
g.setColor(Colors.BLACK); // set the color of the letters
int letterY =
(int)
(graphicsHeigth - (height / 2d)); // define where the draw will start on the Y axis
Graphics2D g2d =
(Graphics2D)
g.create(); // we reverse all coordinates to display the letter on the right way
if (currentDrawingAllele == AlleleType.ALLELE02) {
g2d.scale(1, -1);
letterY *= -1;
// letterY -= fm.getHeight() / 2d; // commented because it was buggy on windows
} else {
// letterY += fm.getHeight() / 2d; // commented because it was buggy on windows
}
int firstNucleotide =
projectWindow.screenToGenomePosition(x)
- variant
.getStart(); // retrieve the position of the first displayed nucleotide in the
// variant
firstNucleotide = Math.max(0, firstNucleotide);
for (int i = 0;
i < nucleotideNumber;
i++) { // for all the nucleotide that are supposed to be displayed
String letter = "-"; // the default letter is the question mark
if ((letters != "-")
&& ((i + firstNucleotide)
< letters
.length())) { // if the letters are different to the question mark and if the
// current index is smaller than the string length
letter = letters.charAt(i + firstNucleotide) + ""; // we get the current character
}
// int xC = (int) Math.round(x + (i * windowWidth) + ((windowWidth -
// fm.stringWidth(letter)) * 0.5)); // the horizontal position from where the draw starts:
// x (of the stripe) + size of a window * current window number + (windows width - letter
// width) / 2 (for the middle)
int xC = projectWindow.genomeToScreenPosition(variant.getStart() + i + firstNucleotide);
g2d.drawString(letter, xC, letterY); // we draw the letter
}
}
}
}