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package jalview.renderer.seqfeatures; |
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import java.awt.AlphaComposite; |
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import java.awt.Color; |
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import java.awt.FontMetrics; |
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import java.awt.Graphics; |
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import java.awt.Graphics2D; |
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import java.util.List; |
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import jalview.api.AlignViewportI; |
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import jalview.api.FeatureColourI; |
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import jalview.datamodel.ContiguousI; |
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import jalview.datamodel.MappedFeatures; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.Desktop; |
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import jalview.util.Comparison; |
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import jalview.util.ReverseListIterator; |
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import jalview.viewmodel.seqfeatures.FeatureRendererModel; |
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| 53.2% |
Uncovered Elements: 124 (265) |
Complexity: 70 |
Complexity Density: 0.44 |
|
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public class FeatureRenderer extends FeatureRendererModel |
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{ |
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private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite |
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.getInstance(AlphaComposite.SRC_OVER, 1.0f); |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public FeatureRenderer(AlignViewportI viewport)... |
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{ |
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this.av = viewport; |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@return |
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| 82.9% |
Uncovered Elements: 6 (35) |
Complexity: 9 |
Complexity Density: 0.39 |
|
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21808 |
boolean renderFeature(Graphics g, SequenceI seq, int featureStart,... |
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int featureEnd, Color featureColour, int start, int end, int y1, |
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boolean colourOnly) |
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{ |
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21808 |
int charHeight = av.getCharHeight(); |
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21808 |
int charWidth = av.getCharWidth(); |
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21808 |
boolean validCharWidth = av.isValidCharWidth(); |
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21808 |
if (featureStart > end || featureEnd < start) |
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{ |
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return false; |
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} |
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21808 |
if (featureStart < start) |
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{ |
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featureStart = start; |
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} |
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21808 |
if (featureEnd >= end) |
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{ |
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featureEnd = end; |
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} |
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21808 |
int pady = (y1 + charHeight) - charHeight / 5; |
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|
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21808 |
FontMetrics fm = g.getFontMetrics(); |
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58339 |
for (int i = featureStart; i <= featureEnd; i++) |
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{ |
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36531 |
char s = seq.getCharAt(i); |
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36531 |
if (Comparison.isGap(s)) |
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{ |
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continue; |
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} |
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36531 |
g.setColor(featureColour); |
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36531 |
g.fillRect((i - start) * charWidth, y1, charWidth, charHeight); |
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36531 |
if (colourOnly || !validCharWidth) |
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{ |
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continue; |
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} |
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g.setColor(Color.white); |
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int charOffset = (charWidth - fm.charWidth(s)) / 2; |
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g.drawString(String.valueOf(s), |
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charOffset + (charWidth * (i - start)), pady); |
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} |
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return true; |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 49 (49) |
Complexity: 11 |
Complexity Density: 0.33 |
|
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0 |
boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart,... |
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int fend, Color featureColour, int start, int end, int y1, |
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byte[] bs, boolean colourOnly) |
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{ |
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if (fstart > end || fend < start) |
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{ |
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return false; |
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} |
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if (fstart < start) |
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{ |
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fstart = start; |
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} |
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if (fend >= end) |
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{ |
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fend = end; |
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} |
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int charHeight = av.getCharHeight(); |
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int pady = (y1 + charHeight) - charHeight / 5; |
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int ystrt = 0, yend = charHeight; |
165 |
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if (bs[0] != 0) |
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{ |
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168 |
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if (bs[1] < 128) |
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{ |
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yend = charHeight * (128 - bs[1]) / 512; |
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ystrt = charHeight - yend / 2; |
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} |
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else |
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{ |
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ystrt = charHeight / 2; |
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yend = charHeight * (bs[1] - 128) / 512; |
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} |
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} |
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else |
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{ |
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yend = charHeight * bs[1] / 255; |
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ystrt = charHeight - yend; |
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} |
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FontMetrics fm = g.getFontMetrics(); |
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int charWidth = av.getCharWidth(); |
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for (int i = fstart; i <= fend; i++) |
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{ |
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char s = seq.getCharAt(i); |
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if (Comparison.isGap(s)) |
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{ |
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continue; |
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} |
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g.setColor(featureColour); |
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int x = (i - start) * charWidth; |
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g.drawRect(x, y1, charWidth, charHeight); |
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g.fillRect(x, y1 + ystrt, charWidth, yend); |
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if (colourOnly || !av.isValidCharWidth()) |
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{ |
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continue; |
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} |
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g.setColor(Color.black); |
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int charOffset = (charWidth - fm.charWidth(s)) / 2; |
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g.drawString(String.valueOf(s), |
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charOffset + (charWidth * (i - start)), pady); |
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} |
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0 |
return true; |
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} |
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@inheritDoc |
218 |
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| 86.7% |
Uncovered Elements: 2 (15) |
Complexity: 4 |
Complexity Density: 0.44 |
|
219 |
20704 |
@Override... |
220 |
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public Color findFeatureColour(SequenceI seq, int column, Graphics g) |
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{ |
222 |
20704 |
if (!av.isShowSequenceFeatures()) |
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{ |
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0 |
return null; |
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} |
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20704 |
if (Comparison.isGap(seq.getCharAt(column - 1))) |
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{ |
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234 |
2651 |
return null; |
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} |
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237 |
18053 |
Color renderedColour = null; |
238 |
18053 |
if (transparency == 1.0f) |
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{ |
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243 |
18049 |
renderedColour = findFeatureColour(seq, column); |
244 |
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} |
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else |
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{ |
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251 |
4 |
renderedColour = drawSequence(g, seq, column, column, 0, true); |
252 |
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} |
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18051 |
return renderedColour; |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@return |
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| 79.7% |
Uncovered Elements: 16 (79) |
Complexity: 25 |
Complexity Density: 0.56 |
|
276 |
1383 |
public synchronized Color drawSequence(final Graphics g,... |
277 |
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final SequenceI seq, int start, int end, int y1, |
278 |
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boolean colourOnly) |
279 |
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{ |
280 |
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281 |
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282 |
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|
283 |
1383 |
ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1); |
284 |
1383 |
if (visiblePositions == null || !seq.getFeatures().hasFeatures() |
285 |
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&& !av.isShowComplementFeatures()) |
286 |
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{ |
287 |
217 |
return null; |
288 |
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} |
289 |
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|
290 |
1166 |
updateFeatures(); |
291 |
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|
292 |
1166 |
if (transparency != 1f && g != null) |
293 |
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{ |
294 |
4 |
Graphics2D g2 = (Graphics2D) g; |
295 |
4 |
g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, |
296 |
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transparency)); |
297 |
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} |
298 |
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299 |
1166 |
Color drawnColour = null; |
300 |
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301 |
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302 |
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303 |
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304 |
1166 |
if (av.isShowComplementFeatures() |
305 |
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&& !av.isShowComplementFeaturesOnTop()) |
306 |
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{ |
307 |
0 |
drawnColour = drawComplementFeatures(g, seq, start, end, y1, |
308 |
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colourOnly, visiblePositions, drawnColour); |
309 |
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} |
310 |
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311 |
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312 |
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313 |
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314 |
33011 |
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) |
315 |
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{ |
316 |
31845 |
String type = renderOrder[renderIndex]; |
317 |
31845 |
if (!showFeatureOfType(type)) |
318 |
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{ |
319 |
23405 |
continue; |
320 |
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} |
321 |
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|
322 |
8440 |
FeatureColourI fc = getFeatureStyle(type); |
323 |
8440 |
List<SequenceFeature> overlaps = seq.getFeatures().findFeatures( |
324 |
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visiblePositions.getBegin(), visiblePositions.getEnd(), type); |
325 |
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|
326 |
8440 |
if (overlaps.size() > 1 && fc.isSimpleColour()) |
327 |
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{ |
328 |
1755 |
filterFeaturesForDisplay(overlaps); |
329 |
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} |
330 |
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|
331 |
8440 |
for (SequenceFeature sf : overlaps) |
332 |
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{ |
333 |
21808 |
Color featureColour = getColor(sf, fc); |
334 |
21808 |
if (featureColour == null) |
335 |
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{ |
336 |
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337 |
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338 |
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|
339 |
0 |
continue; |
340 |
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} |
341 |
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342 |
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343 |
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344 |
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345 |
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346 |
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|
347 |
21808 |
int visibleStart = sf.getBegin(); |
348 |
21808 |
if (visibleStart < visiblePositions.getBegin()) |
349 |
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{ |
350 |
129 |
visibleStart = sf.isContactFeature() ? sf.getEnd() |
351 |
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: visiblePositions.getBegin(); |
352 |
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} |
353 |
21808 |
int visibleEnd = sf.getEnd(); |
354 |
21808 |
if (visibleEnd > visiblePositions.getEnd()) |
355 |
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{ |
356 |
19 |
visibleEnd = sf.isContactFeature() ? sf.getBegin() |
357 |
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: visiblePositions.getEnd(); |
358 |
|
} |
359 |
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|
360 |
21808 |
int featureStartCol = seq.findIndex(visibleStart); |
361 |
21808 |
int featureEndCol = sf.begin == sf.end ? featureStartCol |
362 |
|
: seq.findIndex(visibleEnd); |
363 |
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|
364 |
|
|
365 |
|
|
366 |
21808 |
boolean isContactFeature = sf.isContactFeature(); |
367 |
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|
368 |
21808 |
if (isContactFeature) |
369 |
|
{ |
370 |
0 |
boolean drawn = renderFeature(g, seq, featureStartCol - 1, |
371 |
|
featureStartCol - 1, featureColour, start, end, y1, |
372 |
|
colourOnly); |
373 |
0 |
drawn |= renderFeature(g, seq, featureEndCol - 1, |
374 |
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featureEndCol - 1, featureColour, start, end, y1, |
375 |
|
colourOnly); |
376 |
0 |
if (drawn) |
377 |
|
{ |
378 |
0 |
drawnColour = featureColour; |
379 |
|
} |
380 |
|
} |
381 |
|
else |
382 |
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{ |
383 |
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|
384 |
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|
385 |
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|
386 |
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387 |
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388 |
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389 |
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|
390 |
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|
391 |
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392 |
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393 |
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394 |
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395 |
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396 |
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397 |
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398 |
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399 |
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400 |
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401 |
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402 |
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|
403 |
21808 |
boolean drawn = renderFeature(g, seq, featureStartCol - 1, |
404 |
|
featureEndCol - 1, featureColour, start, end, y1, |
405 |
|
colourOnly); |
406 |
21808 |
if (drawn) |
407 |
|
{ |
408 |
21808 |
drawnColour = featureColour; |
409 |
|
} |
410 |
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|
411 |
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} |
412 |
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} |
413 |
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} |
414 |
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415 |
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416 |
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417 |
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|
418 |
1166 |
if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop()) |
419 |
|
{ |
420 |
0 |
drawnColour = drawComplementFeatures(g, seq, start, end, y1, |
421 |
|
colourOnly, visiblePositions, drawnColour); |
422 |
|
} |
423 |
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|
424 |
1166 |
if (transparency != 1.0f && g != null) |
425 |
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{ |
426 |
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|
427 |
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|
428 |
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|
429 |
4 |
Graphics2D g2 = (Graphics2D) g; |
430 |
4 |
g2.setComposite(NO_TRANSPARENCY); |
431 |
|
} |
432 |
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|
433 |
1166 |
return drawnColour; |
434 |
|
} |
435 |
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436 |
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437 |
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438 |
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439 |
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440 |
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441 |
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@param |
442 |
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@param |
443 |
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@param |
444 |
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@param |
445 |
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@param |
446 |
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@param |
447 |
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@param |
448 |
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@param |
449 |
|
@return |
450 |
|
|
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|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 3 |
Complexity Density: 0.21 |
|
451 |
0 |
Color drawComplementFeatures(final Graphics g, final SequenceI seq,... |
452 |
|
int start, int end, int y1, boolean colourOnly, |
453 |
|
ContiguousI visiblePositions, Color drawnColour) |
454 |
|
{ |
455 |
0 |
AlignViewportI comp = av.getCodingComplement(); |
456 |
0 |
FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp) |
457 |
|
.getFeatureRenderer(); |
458 |
|
|
459 |
0 |
final int visibleStart = visiblePositions.getBegin(); |
460 |
0 |
final int visibleEnd = visiblePositions.getEnd(); |
461 |
|
|
462 |
0 |
for (int pos = visibleStart; pos <= visibleEnd; pos++) |
463 |
|
{ |
464 |
0 |
int column = seq.findIndex(pos); |
465 |
0 |
MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos); |
466 |
0 |
if (mf != null) |
467 |
|
{ |
468 |
0 |
for (SequenceFeature sf : mf.features) |
469 |
|
{ |
470 |
0 |
FeatureColourI fc = fr2.getFeatureStyle(sf.getType()); |
471 |
0 |
Color featureColour = fr2.getColor(sf, fc); |
472 |
0 |
renderFeature(g, seq, column - 1, column - 1, featureColour, |
473 |
|
start, end, y1, colourOnly); |
474 |
0 |
drawnColour = featureColour; |
475 |
|
} |
476 |
|
} |
477 |
|
} |
478 |
0 |
return drawnColour; |
479 |
|
} |
480 |
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|
481 |
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|
482 |
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|
483 |
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|
484 |
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|
485 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
486 |
19 |
@Override... |
487 |
|
public void featuresAdded() |
488 |
|
{ |
489 |
19 |
findAllFeatures(); |
490 |
|
} |
491 |
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|
492 |
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493 |
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494 |
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495 |
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496 |
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497 |
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498 |
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499 |
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500 |
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501 |
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502 |
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503 |
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@param |
504 |
|
@param |
505 |
|
|
506 |
|
@return |
507 |
|
|
|
|
| 77.8% |
Uncovered Elements: 8 (36) |
Complexity: 11 |
Complexity Density: 0.55 |
|
508 |
18049 |
Color findFeatureColour(SequenceI seq, int column)... |
509 |
|
{ |
510 |
|
|
511 |
|
|
512 |
|
|
513 |
18049 |
updateFeatures(); |
514 |
|
|
515 |
|
|
516 |
|
|
517 |
|
|
518 |
18049 |
if (av.isShowComplementFeatures() && av.isShowComplementFeaturesOnTop()) |
519 |
|
{ |
520 |
0 |
Color col = findComplementFeatureColour(seq, column); |
521 |
0 |
if (col != null) |
522 |
|
{ |
523 |
0 |
return col; |
524 |
|
} |
525 |
|
} |
526 |
|
|
527 |
|
|
528 |
|
|
529 |
|
|
530 |
|
|
531 |
18049 |
for (int renderIndex = renderOrder.length |
532 |
524479 |
- 1; renderIndex >= 0; renderIndex--) |
533 |
|
{ |
534 |
513352 |
String type = renderOrder[renderIndex]; |
535 |
514310 |
if (!showFeatureOfType(type)) |
536 |
|
{ |
537 |
338455 |
continue; |
538 |
|
} |
539 |
|
|
540 |
|
|
541 |
|
|
542 |
|
|
543 |
|
|
544 |
175853 |
List<SequenceFeature> overlaps = seq.findFeatures(column, column, |
545 |
|
type); |
546 |
175683 |
for (int i = overlaps.size() - 1; i >= 0; i--) |
547 |
|
{ |
548 |
6720 |
SequenceFeature sequenceFeature = overlaps.get(i); |
549 |
6720 |
if (!featureGroupNotShown(sequenceFeature)) |
550 |
|
{ |
551 |
6719 |
Color col = getColour(sequenceFeature); |
552 |
6719 |
if (col != null) |
553 |
|
{ |
554 |
6715 |
return col; |
555 |
|
} |
556 |
|
} |
557 |
|
} |
558 |
|
} |
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
11334 |
Color col = null; |
564 |
11334 |
if (av.isShowComplementFeatures() |
565 |
|
&& !av.isShowComplementFeaturesOnTop()) |
566 |
|
{ |
567 |
0 |
col = findComplementFeatureColour(seq, column); |
568 |
|
} |
569 |
|
|
570 |
11334 |
return col; |
571 |
|
} |
572 |
|
|
|
|
| 0% |
Uncovered Elements: 22 (22) |
Complexity: 5 |
Complexity Density: 0.36 |
|
573 |
0 |
Color findComplementFeatureColour(SequenceI seq, int column)... |
574 |
|
{ |
575 |
0 |
AlignViewportI complement = av.getCodingComplement(); |
576 |
0 |
AlignFrame af = Desktop.getAlignFrameFor(complement); |
577 |
0 |
FeatureRendererModel fr2 = af.getFeatureRenderer(); |
578 |
0 |
MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, |
579 |
|
seq.findPosition(column - 1)); |
580 |
0 |
if (mf == null) |
581 |
|
{ |
582 |
0 |
return null; |
583 |
|
} |
584 |
0 |
ReverseListIterator<SequenceFeature> it = new ReverseListIterator<>( |
585 |
|
mf.features); |
586 |
0 |
while (it.hasNext()) |
587 |
|
{ |
588 |
0 |
SequenceFeature sf = it.next(); |
589 |
0 |
if (!fr2.featureGroupNotShown(sf)) |
590 |
|
{ |
591 |
0 |
Color col = fr2.getColour(sf); |
592 |
0 |
if (col != null) |
593 |
|
{ |
594 |
0 |
return col; |
595 |
|
} |
596 |
|
} |
597 |
|
} |
598 |
0 |
return null; |
599 |
|
} |
600 |
|
} |