import java.awt.geom.AffineTransform;
import java.awt.image.ImageObserver;
import java.util.BitSet;
+import java.util.Collections;
+import java.util.HashMap;
import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
import org.jfree.graphics2d.svg.SVGGraphics2D;
import org.jibble.epsgraphics.EpsGraphics2D;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.ProfilesI;
+import jalview.datamodel.annotations.AnnotationColouringI;
import jalview.renderer.api.AnnotationRendererFactoryI;
import jalview.renderer.api.AnnotationRowRendererI;
import jalview.schemes.ColourSchemeI;
*/
private boolean canClip = false;
+ /**
+ * Property to set text antialiasing method
+ */
+ private static final String TEXT_ANTIALIAS_METHOD = "TEXT_ANTIALIAS_METHOD";
+
+ private static final Object textAntialiasMethod;
+
+ static
+ {
+ final String textAntialiasMethodPref = Cache
+ .getDefault(TEXT_ANTIALIAS_METHOD, "GASP");
+ switch (textAntialiasMethodPref)
+ {
+ case "ON":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_ON;
+ break;
+ case "GASP":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_GASP;
+ break;
+ case "LCD_HBGR":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HBGR;
+ break;
+ case "LCD_HRGB":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB;
+ break;
+ case "LCD_VBGR":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_VBGR;
+ break;
+ case "LCD_VRGB":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_VRGB;
+ break;
+ case "OFF":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_OFF;
+ break;
+ case "DEFAULT":
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_DEFAULT;
+ break;
+ default:
+ jalview.bin.Console.warn(TEXT_ANTIALIAS_METHOD + " value '"
+ + textAntialiasMethodPref
+ + "' not recognised, defaulting to 'GASP'. See https://docs.oracle.com/javase/8/docs/api/java/awt/RenderingHints.html#KEY_TEXT_ANTIALIASING");
+ textAntialiasMethod = RenderingHints.VALUE_TEXT_ANTIALIAS_GASP;
+ }
+ }
+
public AnnotationRenderer()
{
this(false);
int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
- g.setColor(STEM_COLOUR);
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
: row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || dc != row_annotations[sCol - 1].secondaryStructure || !validEnd;
+ || dc != row_annotations[sCol - 1].secondaryStructure
+ || !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| dc != row_annotations[column].secondaryStructure;
+ if (diffupstream || diffdownstream)
+ {
+ // draw glyphline under arrow
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
+ g.setColor(STEM_COLOUR);
+
if (column > 0 && Rna.isClosingParenthesis(dc))
{
if (diffupstream)
*/
fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
- { y + iconOffset, y + 13 + iconOffset, y + 7 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x1 += 5;
}
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
- fillPolygon(g, new int[] { x2 - 5, x2 - 5, x2 },
+ fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 },
new int[]
- { y + iconOffset, y + 13 + iconOffset, y + 7 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x2 -= 5;
}
}
}
// draw arrow body
+ unsetAntialias(g);
fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
: row_annotations[column - 1].displayCharacter;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter) || !validEnd;
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter)
+ || !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
AlignViewportI av, Graphics g, int activeRow, int startRes,
int endRes)
{
+ return drawComponent(annotPanel, av, g, activeRow, startRes, endRes,
+ false);
+ }
+
+ public boolean drawComponent(AwtRenderPanelI annotPanel,
+ AlignViewportI av, Graphics g, int activeRow, int startRes,
+ int endRes, boolean forExport)
+ {
if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D)
{
this.setVectorRendering(true);
.getComplementConsensusAnnotation();
BitSet graphGroupDrawn = new BitSet();
- int charOffset = 0; // offset for a label
// \u03B2 \u03B1
// debug ints
int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
// flag used for vector rendition
this.glyphLineDrawn = false;
x = (startRes == 0) ? 0 : -1;
+
while (x < endRes - startRes)
{
if (hasHiddenColumns)
if (validCharWidth && validRes && displayChar != null
&& (displayChar.length() > 0))
{
- // Graphics2D gg = (g);
- float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
- displayChar.length());
+ float fmWidth = fm.stringWidth(displayChar);
/*
* shrink label width to fit in column, if that is
if (scaleColLabel && fmWidth > charWidth)
{
scaledToFit = true;
- fmScaling = charWidth;
- fmScaling /= fmWidth;
+ fmScaling = (float) charWidth / fmWidth;
// and update the label's width to reflect the scaling.
fmWidth = charWidth;
}
- charOffset = (int) ((charWidth - fmWidth) / 2f);
+ float charOffset = (charWidth - fmWidth) / 2f;
if (row_annotations[column].colour == null)
{
* draw the label, unless it is the same secondary structure
* symbol (excluding RNA Helix) as the previous column
*/
- final int xPos = (x * charWidth) + charOffset;
- final int yPos = y + iconOffset;
-
+ final float xPos = (x * charWidth) + charOffset;
+ final float yPos = y + iconOffset;
+
+ // Act on a copy of the Graphics2d object
+ Graphics2D g2dCopy = (Graphics2D) g2d.create();
+ // Clip to this annotation line (particularly width).
+ // This removes artifacts from text when side scrolling
+ // (particularly in wrap format), but can result in clipped
+ // characters until a full paint is drawn.
+ // Add charHeight allowance above and below annotation for
+ // character overhang.
+ // If we're in an image export, set the clip width to be the
+ // entire width of the annotation.
+
+ int clipWidth = forExport
+ ? row_annotations.length * charWidth - 1
+ : imgWidth - 1;
+ g2dCopy.setClip(0, (int) yPos - 2 * charHeight, clipWidth,
+ charHeight * 3);
/*
* translate to drawing position _before_ applying any scaling
*/
- g2d.translate(xPos, yPos);
+ g2dCopy.translate(xPos, yPos);
if (scaledToFit)
{
/*
* use a scaling transform to make the label narrower
* (JalviewJS doesn't have Font.deriveFont(AffineTransform))
*/
- g2d.transform(
+ g2dCopy.transform(
AffineTransform.getScaleInstance(fmScaling, 1.0));
}
- setAntialias(g);
+ setAntialias(g2dCopy, true);
if (column == 0 || row.graph > 0)
{
- g2d.drawString(displayChar, 0, 0);
+ g2dCopy.drawString(displayChar, 0, 0);
}
else if (row_annotations[column - 1] == null || (labelAllCols
|| !displayChar.equals(
|| (displayChar.length() < 2
&& row_annotations[column].secondaryStructure == ' ')))
{
- g2d.drawString(displayChar, 0, 0);
- }
- if (scaledToFit)
- {
- /*
- * undo scaling before translating back
- * (restoring saved transform does NOT work in JS PDFGraphics!)
- */
- g2d.transform(AffineTransform
- .getScaleInstance(1D / fmScaling, 1.0));
+ g2dCopy.drawString(displayChar, 0, 0);
}
- g2d.translate(-xPos, -yPos);
+ g2dCopy.dispose();
}
}
if (row.hasIcons)
if (!validRes || (ss != lastSS))
{
- if (x > -1)
+ if (x > 0)
{
// int nb_annot = x - temp;
renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns,
av, hiddenColumns, columnSelection, row,
row_annotations, startRes, endRes, row.graphMin,
- row.graphMax, y);
+ row.graphMax, y, isVectorRendering());
}
if (debugRedraw)
{
}
else
{
- // g.setColor(Color.orange);
fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
0);
}
}
else
{
- // g.setColor(Color.magenta);
fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
8, 0, 0);
}
eRes = Math.min(eRes, aa_annotations.length);
- if (sRes == 0)
- {
- x++;
- }
-
int y1 = y, y2 = y;
float range = max - min;
}
g.setColor(Color.gray);
- drawLine(g, squareStroke, x * charWidth - charWidth, y2,
- (eRes - sRes) * charWidth, y2);
+ drawLine(g, squareStroke, x * charWidth, y2, (eRes - sRes) * charWidth,
+ y2);
+
+ if (sRes == 0)
+ {
+ x++;
+ }
eRes = Math.min(eRes, aa_annotations.length);
int column;
int aaMax = aa_annotations.length - 1;
- while (x < eRes - sRes)
+ while (x <= eRes - sRes)
{
column = sRes + x;
if (hasHiddenColumns)
continue;
}
+ boolean individualColour = false;
if (aa_annotations[column].colour == null)
{
g.setColor(Color.black);
else
{
g.setColor(aa_annotations[column].colour);
+ individualColour = true;
+ }
+
+ boolean value1Exists = column > 0
+ && aa_annotations[column - 1] != null;
+ float value1 = 0f;
+ Color color1 = null;
+ if (value1Exists)
+ {
+ value1 = aa_annotations[column - 1].value;
+ color1 = aa_annotations[column - 1].colour;
}
+ float value2 = aa_annotations[column].value;
+ boolean nextValueExists = aa_annotations.length > column + 1
+ && aa_annotations[column + 1] != null;
- if (aa_annotations[column - 1] == null
- && aa_annotations.length > column + 1
- && aa_annotations[column + 1] == null)
+ // check for standalone value
+ if (!value1Exists && !nextValueExists)
{
- // standalone value
- y1 = y - (int) (((aa_annotations[column].value - min) / range)
- * graphHeight);
- drawLine(g, x * charWidth + charWidth / 4, y1,
- x * charWidth + 3 * charWidth / 4, y1);
+ y2 = y - yValueToPixelHeight(value2, min, range, graphHeight);
+ drawLine(g, x * charWidth + charWidth / 4, y2,
+ x * charWidth + 3 * charWidth / 4, y2);
x++;
continue;
}
- if (aa_annotations[column - 1] == null)
+ if (!value1Exists)
{
x++;
continue;
}
- y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
- * graphHeight);
- y2 = y - (int) (((aa_annotations[column].value - min) / range)
- * graphHeight);
+ y1 = y - yValueToPixelHeight(value1, min, range, graphHeight);
+ y2 = y - yValueToPixelHeight(value2, min, range, graphHeight);
- drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
- x * charWidth + charWidth / 2, y2);
+ float v1 = value1;
+ float v2 = value2;
+ int a1 = (x - 1) * charWidth + charWidth / 2;
+ int b1 = y1;
+ int a2 = x * charWidth + charWidth / 2;
+ int b2 = y2;
+ if (x == 0)
+ {
+ // only draw an initial half-line
+ a1 = x * charWidth;
+ b1 = y1 + (y2 - y1) / 2;
+ v1 = value1 + (value2 - value1) / 2;
+ }
+ else if (x == eRes - sRes)
+ {
+ // this is one past the end to draw -- only draw the first half of the
+ // line
+ a2 = x * charWidth - 1;
+ b2 = y1 + (y2 - y1) / 2;
+ v2 = value1 + (value2 - value1) / 2;
+ }
+ else
+ {
+ }
+ AnnotationColouringI ac = aa_annotations[column]
+ .getAnnotationColouring();
+ List<Map.Entry<Float, Color>> valCols = ac == null ? null
+ : ac.rangeColours(v1, v2);
+ if (valCols != null)
+ {
+ drawSegmentedLine(g, valCols, a1, b1, a2, b2);
+ }
+ else
+ {
+ drawLine(g, a1, b1, a2, b2);
+ }
x++;
}
{
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
- Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f);
-
y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
- drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
+ drawLine(g, dashedLine(charWidth), 0, y2, (eRes - sRes) * charWidth,
+ y2);
}
g2d.setStroke(prevStroke);
}
+ private static double log2 = Math.log(2);
+
+ // Cached dashed line Strokes
+ private static Map<Integer, Stroke> dashedLineLookup = new HashMap<>();
+
+ /**
+ * Returns a dashed line stroke as close to 6-4 pixels as fits within the
+ * charWidth. This allows translations of multiples of charWidth without
+ * disrupting the dashed line. The exact values are 0.6-0.4 proportions of
+ * charWidth for charWidth under 16. For charWidth 16 or over, the number of
+ * dashes doubles as charWidth doubles.
+ *
+ * @param charWidth
+ * @return Stroke with appropriate dashed line fitting exactly within the
+ * charWidth
+ */
+ private static Stroke dashedLine(int charWidth)
+ {
+ if (!dashedLineLookup.containsKey(charWidth))
+ {
+ int power2 = charWidth >= 8 ? (int) (Math.log(charWidth) / log2) : 2;
+ float width = ((float) charWidth) / ((float) Math.pow(2, power2 - 3));
+ float segment1 = width * 0.6f;
+ float segment2 = width - segment1;
+ dashedLineLookup.put(charWidth, new BasicStroke(1,
+ BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]
+ { segment1, segment2 }, 0f));
+ }
+ return dashedLineLookup.get(charWidth);
+ }
+
+ private void drawSegmentedLine(Graphics g,
+ List<Map.Entry<Float, Color>> valCols, int x1, int y1, int x2,
+ int y2)
+ {
+ if (valCols == null || valCols.size() == 0)
+ {
+ return;
+ }
+ // let's only go forwards+up|down -- try and avoid providing right to left
+ // x values
+ if (x2 < x1)
+ {
+ int tmp = y2;
+ y2 = y1;
+ y1 = tmp;
+ tmp = x2;
+ x2 = x1;
+ x1 = tmp;
+ Collections.reverse(valCols);
+ }
+ Graphics2D g2d = (Graphics2D) g.create();
+ float yd = y2 - y1;
+ boolean reverse = yd > 0; // reverse => line going DOWN (y increasing)
+ Map.Entry<Float, Color> firstValCol = valCols.remove(0);
+ float firstVal = firstValCol.getKey();
+ Color firstCol = firstValCol.getValue();
+ int yy1 = 0;
+ yy1 = reverse ? (int) Math.ceil(y1 + firstVal * yd)
+ : (int) Math.floor(y1 + firstVal * yd);
+ Color thisCol = firstCol;
+ for (int i = 0; i < valCols.size(); i++)
+ {
+ Map.Entry<Float, Color> valCol = valCols.get(i);
+ float val = valCol.getKey();
+ Color col = valCol.getValue();
+ int clipX = x1 - 1;
+ int clipW = x2 - x1 + 2;
+ int clipY = 0;
+ int clipH = 0;
+ int yy2 = 0;
+ if (reverse) // line going down
+ {
+ yy2 = (int) Math.ceil(y1 + val * yd);
+ g2d.setColor(thisCol);
+ clipY = yy1 - 1;
+ clipH = yy2 - yy1;
+ if (i == 0)
+ {
+ // highest segment, don't clip at the top
+ clipY -= 2;
+ clipH += 2;
+ }
+ if (i == valCols.size() - 1)
+ {
+ // lowest segment, don't clip at the bottom
+ clipH += 2;
+ }
+ }
+ else // line going up (or level)
+ {
+ yy2 = (int) Math.floor(y1 + val * yd);
+ // g2d.setColor(Color.cyan); g2d.drawRect(x1 - 1, yy1, x2 - x1 + 1, yy2
+ // -
+ // yy1 + 1);
+ g2d.setColor(col);
+ clipY = yy2;
+ clipH = yy1 - yy2;
+ if (i == 0)
+ {
+ // lowest segment, don't clip at the bottom
+ clipH += 2;
+ }
+ if (i == valCols.size() - 1)
+ {
+ // highest segment, don't clip at the top
+ clipY -= 2;
+ clipH += 2;
+ }
+ }
+ g2d.setClip(clipX, clipY, clipW, clipH);
+ drawLine(g2d, x1, y1, x2, y2);
+ yy1 = yy2;
+ thisCol = col;
+ }
+ g2d.dispose();
+ }
+
+ private static int yValueToPixelHeight(float value, float min,
+ float range, int graphHeight)
+ {
+ return (int) (((value - min) / range) * graphHeight);
+ }
+
@SuppressWarnings("unused")
void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
}
g.setColor(colour == Color.white ? Color.lightGray : colour);
- // Debug - render boxes around characters
- // g.setColor(Color.red);
- // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
- // (int)(scl));
- // g.setColor(profcolour.findColour(dc[0]).darker());
-
double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
double sy = newHeight / asc;
double newAsc = asc * sy;
g2d.setStroke(p);
}
- private void drawLine(Graphics g, int a, int b, int c, int d)
+ private void drawLine(Graphics g, int x1, int y1, int x2, int y2)
{
setAntialias(g);
- g.drawLine(a, b, c, d);
+ g.drawLine(x1, y1, x2, y2);
}
private void setAntialias(Graphics g)
{
+ setAntialias(g, false);
+ }
+
+ private void setAntialias(Graphics g, boolean text)
+ {
if (isVectorRendering())
{
// no need to antialias vector drawings
if (Cache.getDefault("ANTI_ALIAS", true))
{
Graphics2D g2d = (Graphics2D) g;
- g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ if (text)
+ {
+ g2d.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
+ this.textAntialiasMethod);
+ }
+ else
+ {
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff