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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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| 0% |
Uncovered Elements: 208 (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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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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public SequenceRenderer(AlignViewportI viewport)... |
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{ |
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this.av = viewport; |
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resColourFinder = new ResidueColourFinder(); |
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} |
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@param |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
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@Override... |
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public void prepare(Graphics g, boolean renderGaps) |
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{ |
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graphics = g; |
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fm = g.getFontMetrics(); |
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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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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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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@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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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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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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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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allGroups = sg; |
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drawBoxes(seq, start, end, y1); |
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if (av.isValidCharWidth()) |
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{ |
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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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@param |
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| 0% |
Uncovered Elements: 43 (43) |
Complexity: 9 |
Complexity Density: 0.33 |
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public synchronized void drawBoxes(SequenceI seq, int start, int end,... |
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int y1) |
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{ |
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Color resBoxColour = Color.white; |
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if (seq == null) |
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{ |
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return; |
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} |
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int i = start; |
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int length = seq.getLength(); |
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int curStart = -1; |
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int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), |
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avHeight = av.getCharHeight(); |
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Color tempColour = null; |
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while (i <= end) |
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{ |
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resBoxColour = Color.white; |
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if (i < length) |
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{ |
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SequenceGroup currentSequenceGroup = resColourFinder |
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.getCurrentSequenceGroup(allGroups, i); |
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if (currentSequenceGroup != null) |
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{ |
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if (currentSequenceGroup.getDisplayBoxes()) |
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{ |
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resBoxColour = resColourFinder.getBoxColour( |
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currentSequenceGroup.getGroupColourScheme(), seq, i); |
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} |
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} |
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else if (av.getShowBoxes()) |
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{ |
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resBoxColour = resColourFinder |
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.getBoxColour(av.getResidueShading(), seq, i); |
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} |
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} |
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if (resBoxColour != tempColour) |
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{ |
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if (tempColour != null) |
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{ |
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graphics.fillRect(avWidth * (curStart - start), y1, curWidth, |
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avHeight); |
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} |
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graphics.setColor(resBoxColour); |
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curStart = i; |
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curWidth = avWidth; |
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tempColour = resBoxColour; |
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} |
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else |
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{ |
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curWidth += avWidth; |
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} |
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i++; |
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} |
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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 |
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| 0% |
Uncovered Elements: 99 (99) |
Complexity: 28 |
Complexity Density: 0.49 |
|
245 |
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public void drawText(SequenceI seq, int start, int end, int y1)... |
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{ |
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y1 += av.getCharHeight() - av.getCharHeight() / 5; |
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int charOffset = 0; |
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char s; |
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if (end + 1 >= seq.getLength()) |
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{ |
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end = seq.getLength() - 1; |
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} |
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graphics.setColor(av.getTextColour()); |
256 |
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boolean drawAllText = monospacedFont && av.getShowText() |
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&& allGroups.length == 0 && !av.getColourText() |
259 |
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&& av.getThresholdTextColour() == 0; |
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263 |
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264 |
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265 |
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if (graphics instanceof EpsGraphics2D |
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|| graphics instanceof SVGGraphics2D) |
267 |
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{ |
268 |
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drawAllText = false; |
269 |
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} |
270 |
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if (drawAllText) |
271 |
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{ |
272 |
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if (av.isRenderGaps()) |
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{ |
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graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1); |
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} |
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else |
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{ |
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char gap = av.getGapCharacter(); |
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graphics.drawString( |
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seq.getSequenceAsString(start, end + 1).replace(gap, ' '), |
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0, y1); |
282 |
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} |
283 |
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} |
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else |
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{ |
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boolean srep = av.isDisplayReferenceSeq(); |
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boolean getboxColour = false; |
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boolean isarep = av.getAlignment().getSeqrep() == seq; |
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0 |
Color resBoxColour = Color.white; |
290 |
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291 |
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for (int i = start; i <= end; i++) |
292 |
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{ |
293 |
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294 |
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graphics.setColor(av.getTextColour()); |
295 |
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getboxColour = false; |
296 |
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s = seq.getCharAt(i); |
297 |
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|
298 |
0 |
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 |
0 |
SequenceGroup currentSequenceGroup = resColourFinder |
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.getCurrentSequenceGroup(allGroups, i); |
305 |
0 |
if (currentSequenceGroup != null) |
306 |
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{ |
307 |
0 |
if (!currentSequenceGroup.getDisplayText()) |
308 |
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{ |
309 |
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continue; |
310 |
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} |
311 |
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312 |
0 |
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 |
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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 |
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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 |
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graphics.setColor(currentSequenceGroup.textColour); |
337 |
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} |
338 |
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boolean isgrep = currentSequenceGroup != null |
339 |
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? currentSequenceGroup.getSeqrep() == seq |
340 |
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: false; |
341 |
0 |
if (!isarep && !isgrep |
342 |
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&& currentSequenceGroup.getShowNonconserved()) |
343 |
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344 |
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{ |
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s = getDisplayChar(srep, i, s, '.', currentSequenceGroup); |
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348 |
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} |
349 |
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350 |
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} |
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else |
352 |
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{ |
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0 |
if (!av.getShowText()) |
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{ |
355 |
0 |
continue; |
356 |
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} |
357 |
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358 |
0 |
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 |
|
} |
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 |
0 |
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 |
|
+ resBoxColour.getGreen() < av.getThresholdTextColour()) |
384 |
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{ |
385 |
0 |
graphics.setColor(av.getTextColour2()); |
386 |
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} |
387 |
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} |
388 |
0 |
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 |
0 |
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; |
397 |
0 |
graphics.drawString(String.valueOf(s), |
398 |
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charOffset + av.getCharWidth() * (i - start), y1); |
399 |
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400 |
|
} |
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 |
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@param |
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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 |
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|| position < currentGroup.getStartRes() |
422 |
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|| 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 |
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@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 |
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@param |
461 |
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462 |
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@param |
463 |
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464 |
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|
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| 0% |
Uncovered Elements: 18 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
|
465 |
0 |
public void drawHighlightedText(SequenceI seq, int start, int end, int x1,... |
466 |
|
int y1) |
467 |
|
{ |
468 |
0 |
int pady = av.getCharHeight() / 5; |
469 |
0 |
int charOffset = 0; |
470 |
0 |
graphics.setColor(Color.BLACK); |
471 |
0 |
graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1), |
472 |
|
av.getCharHeight()); |
473 |
0 |
graphics.setColor(Color.white); |
474 |
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|
475 |
0 |
char s = '~'; |
476 |
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|
477 |
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|
478 |
0 |
if (av.isValidCharWidth()) |
479 |
|
{ |
480 |
0 |
for (int i = start; i <= end; i++) |
481 |
|
{ |
482 |
0 |
if (i < seq.getLength()) |
483 |
|
{ |
484 |
0 |
s = seq.getCharAt(i); |
485 |
|
} |
486 |
|
|
487 |
0 |
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; |
488 |
0 |
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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@param |
499 |
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@param |
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@param |
503 |
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504 |
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@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 |
|
} |