import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
-import jalview.bin.Jalview;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
private FontMetrics fm;
- private final boolean MAC = Platform.isAMac();
+ private final boolean USE_FILL_ROUND_RECT = Platform.isAMacAndNotJS();
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
return null;
}
- boolean rna = false;
-
/**
* Render the annotation rows associated with an alignment.
*
.getAlignmentStrucConsensusAnnotation();
final AlignmentAnnotation complementConsensusAnnot = av
.getComplementConsensusAnnotation();
- boolean renderHistogram = true, renderProfile = true,
- normaliseProfile = false, isRNA = rna;
BitSet graphGroupDrawn = new BitSet();
int charOffset = 0; // offset for a label
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
- isRNA = row.isRNA();
+ boolean renderHistogram = true;
+ boolean renderProfile = false;
+ boolean normaliseProfile = false;
+ boolean isRNA = row.isRNA();
+
+ // check if this is a consensus annotation row and set the display
+ // settings appropriately
+ // TODO: generalise this to have render styles for consensus/profile
+ // data
+ if (row.groupRef != null && row == row.groupRef.getConsensus())
{
- // check if this is a consensus annotation row and set the display
- // settings appropriately
- // TODO: generalise this to have render styles for consensus/profile
- // data
- if (row.groupRef != null && row == row.groupRef.getConsensus())
- {
- renderHistogram = row.groupRef.isShowConsensusHistogram();
- renderProfile = row.groupRef.isShowSequenceLogo();
- normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
- }
- else if (row == consensusAnnot || row == structConsensusAnnot
- || row == complementConsensusAnnot)
- {
- renderHistogram = av_renderHistogram;
- renderProfile = av_renderProfile;
- normaliseProfile = av_normaliseProfile;
- }
- else
- {
- renderHistogram = true;
- // don't need to set render/normaliseProfile since they are not
- // currently used in any other annotation track renderer
- }
+ renderHistogram = row.groupRef.isShowConsensusHistogram();
+ renderProfile = row.groupRef.isShowSequenceLogo();
+ normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
+ }
+ else if (row == consensusAnnot || row == structConsensusAnnot
+ || row == complementConsensusAnnot)
+ {
+ renderHistogram = av_renderHistogram;
+ renderProfile = av_renderProfile;
+ normaliseProfile = av_normaliseProfile;
}
+
Annotation[] row_annotations = row.annotations;
if (!row.visible)
{
&& (displayChar.length() > 0))
{
Graphics2D gg = ((Graphics2D) g);
- AffineTransform oldTransform = gg.getTransform();
float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
displayChar.length());
*/
final int xPos = (x * charWidth) + charOffset;
final int yPos = y + iconOffset;
+
+ /*
+ * translate to drawing position _before_ applying any scaling
+ */
gg.translate(xPos, yPos);
if (scaledToFit)
{
{
gg.drawString(displayChar, 0, 0);
}
+ if (scaledToFit)
+ {
+ /*
+ * undo scaling before translating back
+ * (restoring saved transform does NOT work in JS PDFGraphics!)
+ */
+ gg.transform(AffineTransform
+ .getScaleInstance(1D / fmScaling, 1.0));
+ }
gg.translate(-xPos, -yPos);
- gg.setTransform(oldTransform);
}
}
if (row.hasIcons)
int x1 = lastSSX;
int x2 = (x * charWidth);
- if (MAC)
+ if (USE_FILL_ROUND_RECT)
{
int ofs = charWidth / 2;
// Off by 1 offset when drawing rects and ovals
boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
float ht = normaliseProfile ? y - _aa.graphHeight : y1;
- double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
+ final double normaliseFactor = normaliseProfile ? _aa.graphHeight
+ : (y2 - y1);
/**
* Render a single base for a sequence profile, a base pair for
s = new String(dc);
}
// next profl[] position is profile % for the character(s)
-
- double newHeight = htn * scale * profl[c++];
+
+ int percent = profl[c++];
+ if (percent == 0)
+ {
+ // failsafe in case a count rounds down to 0%
+ continue;
+ }
+ double newHeight = normaliseFactor * scale * percent;
/*
* Set character colour as per alignment colour scheme; use the
// (int)(scl));
// g.setColor(profcolour.findColour(dc[0]).darker());
- double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
+ double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
double sy = newHeight / asc;
- double newAsc = asc * sy;
+ double newAsc = asc * sy;
double newDec = dec * sy;
// it is not necessary to recalculate lm for the new font.
// note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0
// int hght = (int) (ht + (newAsc - newDec);
// - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
- if (Jalview.isJS())
+ if (Platform.isJS())
{
/*
* SwingJS does not implement font.deriveFont()
* this is off by a very small amount
*/
final int hght = (int) (ht2 + (newAsc - newDec));
- Graphics2D gg = (Graphics2D) g.create();
- gg.setFont(ofont);
- int xShift = (int) (x * charWidth / sx);
- int yShift = (int) (hght / sy);
+ Graphics2D gg = (Graphics2D) g;
+ int xShift = (int) Math.round(x * charWidth / sx);
+ int yShift = (int) Math.round(hght / sy);
gg.transform(AffineTransform.getScaleInstance(sx, sy));
gg.drawString(s, xShift, yShift);
- gg.dispose();
+ gg.transform(
+ AffineTransform.getScaleInstance(1D / sx, 1D / sy));
ht2 += newHeight;
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
+ // Java ('normal') method is to scale the font to fit
+
final int hght = (int) (ht + (newAsc - newDec));
Font font = ofont
.deriveFont(AffineTransform.getScaleInstance(sx, sy));
ht += newHeight;
}
}
- g.setFont(ofont);
}
}
x++;
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ { 5f, 3f }, 0f));
y2 = (int) (y
- ((_aa.threshold.value - min) / range) * _aa.graphHeight);
git://source.jalview.org / jalview.git / blobdiff