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package jalview.gui; |
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import jalview.api.AlignViewportI; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.renderer.ResidueColourFinder; |
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import jalview.renderer.seqfeatures.FeatureColourFinder; |
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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 org.jfree.graphics2d.svg.SVGGraphics2D; |
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import org.jibble.epsgraphics.EpsGraphics2D; |
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| 60.6% |
Uncovered Elements: 82 (208) |
Complexity: 62 |
Complexity Density: 0.51 |
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public class SequenceRenderer implements jalview.api.SequenceRenderer |
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{ |
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final static int CHAR_TO_UPPER = 'A' - 'a'; |
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AlignViewportI av; |
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FontMetrics fm; |
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boolean renderGaps = true; |
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SequenceGroup[] allGroups = null; |
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Graphics graphics; |
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boolean monospacedFont; |
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ResidueColourFinder resColourFinder; |
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@param |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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839 |
public SequenceRenderer(AlignViewportI viewport)... |
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{ |
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839 |
this.av = viewport; |
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839 |
resColourFinder = new ResidueColourFinder(); |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
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3512 |
@Override... |
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public void prepare(Graphics g, boolean renderGaps) |
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{ |
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3512 |
graphics = g; |
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3512 |
fm = g.getFontMetrics(); |
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3512 |
double dwidth = fm.getStringBounds("M", g).getWidth(); |
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monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() |
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&& av.getCharWidth() == dwidth); |
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3512 |
this.renderGaps = renderGaps; |
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} |
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@param |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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32779 |
@Override... |
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public Color getResidueColour(final SequenceI seq, int position, |
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FeatureColourFinder finder) |
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{ |
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32779 |
allGroups = av.getAlignment().findAllGroups(seq); |
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return resColourFinder.getResidueColour(av.getShowBoxes(), |
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av.getResidueShading(), allGroups, seq, position, finder); |
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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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| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
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17139 |
public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,... |
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int end, int y1) |
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{ |
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17139 |
allGroups = sg; |
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17139 |
drawBoxes(seq, start, end, y1); |
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if (av.isValidCharWidth()) |
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{ |
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17139 |
drawText(seq, start, end, y1); |
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} |
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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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| 90.7% |
Uncovered Elements: 4 (43) |
Complexity: 9 |
Complexity Density: 0.33 |
|
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17139 |
public synchronized void drawBoxes(SequenceI seq, int start, int end,... |
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int y1) |
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{ |
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17139 |
Color resBoxColour = Color.white; |
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17139 |
if (seq == null) |
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{ |
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return; |
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} |
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17139 |
int i = start; |
170 |
17139 |
int length = seq.getLength(); |
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|
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17139 |
int curStart = -1; |
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17139 |
int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), |
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avHeight = av.getCharHeight(); |
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17139 |
Color tempColour = null; |
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965288 |
while (i <= end) |
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{ |
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948149 |
resBoxColour = Color.white; |
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948154 |
if (i < length) |
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{ |
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946361 |
SequenceGroup currentSequenceGroup = resColourFinder |
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.getCurrentSequenceGroup(allGroups, i); |
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946362 |
if (currentSequenceGroup != null) |
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{ |
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530536 |
if (currentSequenceGroup.getDisplayBoxes()) |
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{ |
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530536 |
resBoxColour = resColourFinder.getBoxColour( |
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currentSequenceGroup.getGroupColourScheme(), seq, i); |
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} |
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} |
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415824 |
else if (av.getShowBoxes()) |
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{ |
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415825 |
resBoxColour = resColourFinder |
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.getBoxColour(av.getResidueShading(), seq, i); |
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} |
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} |
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948151 |
if (resBoxColour != tempColour) |
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{ |
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474542 |
if (tempColour != null) |
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{ |
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457403 |
graphics.fillRect(avWidth * (curStart - start), y1, curWidth, |
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avHeight); |
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} |
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474542 |
graphics.setColor(resBoxColour); |
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474542 |
curStart = i; |
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474542 |
curWidth = avWidth; |
213 |
474542 |
tempColour = resBoxColour; |
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} |
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else |
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{ |
217 |
473609 |
curWidth += avWidth; |
218 |
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} |
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220 |
948149 |
i++; |
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} |
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223 |
17139 |
graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight); |
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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 |
243 |
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244 |
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| 50.5% |
Uncovered Elements: 49 (99) |
Complexity: 28 |
Complexity Density: 0.49 |
|
245 |
17139 |
public void drawText(SequenceI seq, int start, int end, int y1)... |
246 |
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{ |
247 |
17139 |
y1 += av.getCharHeight() - av.getCharHeight() / 5; |
248 |
17139 |
int charOffset = 0; |
249 |
17139 |
char s; |
250 |
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|
251 |
17139 |
if (end + 1 >= seq.getLength()) |
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{ |
253 |
1568 |
end = seq.getLength() - 1; |
254 |
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} |
255 |
17139 |
graphics.setColor(av.getTextColour()); |
256 |
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|
257 |
17139 |
boolean drawAllText = monospacedFont && av.getShowText() |
258 |
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&& allGroups.length == 0 && !av.getColourText() |
259 |
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&& av.getThresholdTextColour() == 0; |
260 |
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261 |
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262 |
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263 |
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264 |
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|
265 |
17139 |
if (graphics instanceof EpsGraphics2D |
266 |
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|| graphics instanceof SVGGraphics2D) |
267 |
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{ |
268 |
210 |
drawAllText = false; |
269 |
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} |
270 |
17139 |
if (drawAllText) |
271 |
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{ |
272 |
0 |
if (av.isRenderGaps()) |
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{ |
274 |
0 |
graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1); |
275 |
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} |
276 |
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else |
277 |
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{ |
278 |
0 |
char gap = av.getGapCharacter(); |
279 |
0 |
graphics.drawString( |
280 |
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seq.getSequenceAsString(start, end + 1).replace(gap, ' '), |
281 |
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0, y1); |
282 |
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} |
283 |
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} |
284 |
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else |
285 |
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{ |
286 |
17139 |
boolean srep = av.isDisplayReferenceSeq(); |
287 |
17139 |
boolean getboxColour = false; |
288 |
17139 |
boolean isarep = av.getAlignment().getSeqrep() == seq; |
289 |
17139 |
Color resBoxColour = Color.white; |
290 |
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|
291 |
963498 |
for (int i = start; i <= end; i++) |
292 |
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{ |
293 |
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|
294 |
946359 |
graphics.setColor(av.getTextColour()); |
295 |
946359 |
getboxColour = false; |
296 |
946359 |
s = seq.getCharAt(i); |
297 |
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|
298 |
946359 |
if (!renderGaps && jalview.util.Comparison.isGap(s)) |
299 |
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{ |
300 |
0 |
continue; |
301 |
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} |
302 |
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|
303 |
946361 |
SequenceGroup currentSequenceGroup = resColourFinder |
304 |
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.getCurrentSequenceGroup(allGroups, i); |
305 |
946362 |
if (currentSequenceGroup != null) |
306 |
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{ |
307 |
530536 |
if (!currentSequenceGroup.getDisplayText()) |
308 |
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{ |
309 |
0 |
continue; |
310 |
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} |
311 |
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|
312 |
530536 |
if (currentSequenceGroup.thresholdTextColour > 0 |
313 |
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|| currentSequenceGroup.getColourText()) |
314 |
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{ |
315 |
0 |
getboxColour = true; |
316 |
0 |
resBoxColour = resColourFinder.getBoxColour( |
317 |
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currentSequenceGroup.getGroupColourScheme(), seq, i); |
318 |
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|
319 |
0 |
if (currentSequenceGroup.getColourText()) |
320 |
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{ |
321 |
0 |
graphics.setColor(resBoxColour.darker()); |
322 |
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} |
323 |
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|
324 |
0 |
if (currentSequenceGroup.thresholdTextColour > 0) |
325 |
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{ |
326 |
0 |
if (resBoxColour.getRed() + resBoxColour.getBlue() |
327 |
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+ resBoxColour |
328 |
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.getGreen() < currentSequenceGroup.thresholdTextColour) |
329 |
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{ |
330 |
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graphics.setColor(currentSequenceGroup.textColour2); |
331 |
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} |
332 |
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} |
333 |
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} |
334 |
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else |
335 |
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{ |
336 |
530536 |
graphics.setColor(currentSequenceGroup.textColour); |
337 |
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} |
338 |
530536 |
boolean isgrep = currentSequenceGroup != null |
339 |
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? currentSequenceGroup.getSeqrep() == seq |
340 |
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: false; |
341 |
530536 |
if (!isarep && !isgrep |
342 |
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&& currentSequenceGroup.getShowNonconserved()) |
343 |
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344 |
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{ |
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346 |
0 |
s = getDisplayChar(srep, i, s, '.', currentSequenceGroup); |
347 |
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348 |
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} |
349 |
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|
350 |
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} |
351 |
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else |
352 |
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{ |
353 |
415826 |
if (!av.getShowText()) |
354 |
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{ |
355 |
0 |
continue; |
356 |
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} |
357 |
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|
358 |
415825 |
if (av.getColourText()) |
359 |
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{ |
360 |
0 |
getboxColour = true; |
361 |
0 |
resBoxColour = resColourFinder |
362 |
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.getBoxColour(av.getResidueShading(), seq, i); |
363 |
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|
364 |
0 |
if (av.getShowBoxes()) |
365 |
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{ |
366 |
0 |
graphics.setColor(resBoxColour.darker()); |
367 |
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} |
368 |
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else |
369 |
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{ |
370 |
0 |
graphics.setColor(resBoxColour); |
371 |
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} |
372 |
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} |
373 |
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|
374 |
415825 |
if (av.getThresholdTextColour() > 0) |
375 |
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{ |
376 |
0 |
if (!getboxColour) |
377 |
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{ |
378 |
0 |
resBoxColour = resColourFinder |
379 |
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.getBoxColour(av.getResidueShading(), seq, i); |
380 |
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} |
381 |
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|
382 |
0 |
if (resBoxColour.getRed() + resBoxColour.getBlue() |
383 |
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+ resBoxColour.getGreen() < av.getThresholdTextColour()) |
384 |
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{ |
385 |
0 |
graphics.setColor(av.getTextColour2()); |
386 |
|
} |
387 |
|
} |
388 |
415825 |
if (!isarep && av.getShowUnconserved()) |
389 |
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{ |
390 |
0 |
s = getDisplayChar(srep, i, s, '.', null); |
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 |
946362 |
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; |
397 |
946363 |
graphics.drawString(String.valueOf(s), |
398 |
|
charOffset + av.getCharWidth() * (i - start), y1); |
399 |
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|
400 |
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} |
401 |
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} |
402 |
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} |
403 |
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404 |
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405 |
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406 |
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407 |
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408 |
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409 |
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@param |
410 |
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@param |
411 |
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@param |
412 |
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@param |
413 |
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@return |
414 |
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|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 14 |
Complexity Density: 3.5 |
|
415 |
0 |
private char getDisplayChar(final boolean usesrep, int position,... |
416 |
|
char sequenceChar, char conservedChar, SequenceGroup currentGroup) |
417 |
|
{ |
418 |
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|
419 |
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|
420 |
0 |
char conschar = (usesrep) ? (currentGroup == null |
421 |
|
|| position < currentGroup.getStartRes() |
422 |
|
|| position > currentGroup.getEndRes() |
423 |
|
? av.getAlignment().getSeqrep().getCharAt(position) |
424 |
0 |
: (currentGroup.getSeqrep() != null |
425 |
|
? currentGroup.getSeqrep().getCharAt(position) |
426 |
|
: av.getAlignment().getSeqrep() |
427 |
|
.getCharAt(position))) |
428 |
0 |
: (currentGroup != null && currentGroup.getConsensus() != null |
429 |
|
&& position >= currentGroup.getStartRes() |
430 |
|
&& position <= currentGroup.getEndRes() |
431 |
|
&& currentGroup |
432 |
|
.getConsensus().annotations.length > position) |
433 |
|
? currentGroup |
434 |
|
.getConsensus().annotations[position].displayCharacter |
435 |
|
.charAt(0) |
436 |
|
: av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter |
437 |
|
.charAt(0); |
438 |
0 |
if (!jalview.util.Comparison.isGap(conschar) |
439 |
|
&& (sequenceChar == conschar |
440 |
|
|| sequenceChar + CHAR_TO_UPPER == conschar)) |
441 |
|
{ |
442 |
0 |
sequenceChar = conservedChar; |
443 |
|
} |
444 |
0 |
return sequenceChar; |
445 |
|
} |
446 |
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|
447 |
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|
448 |
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449 |
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|
450 |
|
@param |
451 |
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452 |
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@param |
453 |
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454 |
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@param |
455 |
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456 |
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@param |
457 |
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458 |
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@param |
459 |
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460 |
|
@param |
461 |
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462 |
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@param |
463 |
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|
464 |
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|
|
|
| 88.9% |
Uncovered Elements: 2 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
|
465 |
18 |
public void drawHighlightedText(SequenceI seq, int start, int end, int x1,... |
466 |
|
int y1) |
467 |
|
{ |
468 |
18 |
int pady = av.getCharHeight() / 5; |
469 |
18 |
int charOffset = 0; |
470 |
18 |
graphics.setColor(Color.BLACK); |
471 |
18 |
graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1), |
472 |
|
av.getCharHeight()); |
473 |
18 |
graphics.setColor(Color.white); |
474 |
|
|
475 |
18 |
char s = '~'; |
476 |
|
|
477 |
|
|
478 |
18 |
if (av.isValidCharWidth()) |
479 |
|
{ |
480 |
72 |
for (int i = start; i <= end; i++) |
481 |
|
{ |
482 |
54 |
if (i < seq.getLength()) |
483 |
|
{ |
484 |
54 |
s = seq.getCharAt(i); |
485 |
|
} |
486 |
|
|
487 |
54 |
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; |
488 |
54 |
graphics.drawString(String.valueOf(s), |
489 |
|
charOffset + x1 + (av.getCharWidth() * (i - start)), |
490 |
|
(y1 + av.getCharHeight()) - pady); |
491 |
|
} |
492 |
|
} |
493 |
|
} |
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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@param |
499 |
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500 |
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@param |
501 |
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502 |
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@param |
503 |
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|
504 |
|
@param |
505 |
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|
506 |
|
|
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|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
507 |
0 |
public void drawCursor(Graphics g, char s, int x1, int y1)... |
508 |
|
{ |
509 |
0 |
int pady = av.getCharHeight() / 5; |
510 |
0 |
int charOffset = 0; |
511 |
0 |
g.setColor(Color.black); |
512 |
0 |
g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); |
513 |
|
|
514 |
0 |
if (av.isValidCharWidth()) |
515 |
|
{ |
516 |
0 |
g.setColor(Color.white); |
517 |
0 |
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; |
518 |
0 |
g.drawString(String.valueOf(s), charOffset + x1, |
519 |
|
(y1 + av.getCharHeight()) - pady); |
520 |
|
} |
521 |
|
|
522 |
|
} |
523 |
|
} |