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package jalview.gui; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.Dimension; |
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import java.awt.Font; |
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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.awt.RenderingHints; |
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import java.awt.image.BufferedImage; |
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import java.beans.PropertyChangeEvent; |
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import java.util.List; |
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import javax.swing.JPanel; |
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import jalview.datamodel.SequenceI; |
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import jalview.viewmodel.ViewportListenerI; |
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import jalview.viewmodel.ViewportRanges; |
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@author |
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@version |
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| 0% |
Uncovered Elements: 285 (285) |
Complexity: 73 |
Complexity Density: 0.39 |
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public class IdCanvas extends JPanel implements ViewportListenerI |
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{ |
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protected AlignViewport av; |
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protected boolean showScores = true; |
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protected int maxIdLength = -1; |
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protected String maxIdStr = null; |
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BufferedImage image; |
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int imgHeight = 0; |
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boolean fastPaint = false; |
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List<SequenceI> searchResults; |
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AnnotationPanel ap; |
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private Font idfont; |
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@param |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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public IdCanvas(AlignViewport av)... |
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{ |
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setLayout(new BorderLayout()); |
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this.av = av; |
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PaintRefresher.Register(this, av.getSequenceSetId()); |
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av.getRanges().addPropertyChangeListener(this); |
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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: 28 (28) |
Complexity: 8 |
Complexity Density: 0.4 |
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public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s,... |
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int i, int starty, int ypos) |
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{ |
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int xPos = 0; |
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int panelWidth = getWidth(); |
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int charHeight = av.getCharHeight(); |
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if ((searchResults != null) && searchResults.contains(s)) |
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{ |
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g.setColor(Color.black); |
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g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), |
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charHeight); |
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g.setColor(Color.white); |
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} |
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else if ((av.getSelectionGroup() != null) |
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&& av.getSelectionGroup().getSequences(null).contains(s)) |
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{ |
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g.setColor(Color.lightGray); |
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g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), |
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charHeight); |
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g.setColor(Color.white); |
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} |
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else |
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{ |
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g.setColor(av.getSequenceColour(s)); |
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g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), |
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charHeight); |
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g.setColor(Color.black); |
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} |
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if (av.isRightAlignIds()) |
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{ |
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FontMetrics fm = g.getFontMetrics(); |
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xPos = panelWidth |
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- fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4; |
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} |
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g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, |
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(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); |
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if (hiddenRows && av.getShowHiddenMarkers()) |
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{ |
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drawMarker(g, av, i, starty, ypos); |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 34 (34) |
Complexity: 7 |
Complexity Density: 0.29 |
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public void fastPaint(int vertical)... |
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{ |
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if (image == null || av.getWrapAlignment()) |
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{ |
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repaint(); |
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return; |
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} |
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ViewportRanges ranges = av.getRanges(); |
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Graphics2D gg = image.createGraphics(); |
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gg.copyArea(0, 0, getWidth(), imgHeight, 0, |
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-vertical * av.getCharHeight()); |
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int ss = ranges.getStartSeq(); |
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int es = ranges.getEndSeq(); |
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int transY = 0; |
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if (vertical > 0) |
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{ |
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ss = es - vertical; |
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if (ss < ranges.getStartSeq()) |
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{ |
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ss = ranges.getStartSeq(); |
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} |
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else |
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{ |
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transY = imgHeight - ((vertical + 1) * av.getCharHeight()); |
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} |
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} |
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else if (vertical < 0) |
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{ |
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es = ss - vertical; |
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if (es > ranges.getEndSeq()) |
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{ |
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es = ranges.getEndSeq(); |
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} |
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} |
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gg.translate(0, transY); |
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drawIds(gg, av, ss, es, searchResults, true, getWidth()); |
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gg.translate(0, -transY); |
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gg.dispose(); |
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fastPaint = true; |
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av.getAlignPanel().repaint(); |
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} |
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@param |
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| 0% |
Uncovered Elements: 25 (25) |
Complexity: 5 |
Complexity Density: 0.26 |
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@Override... |
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public void paintComponent(Graphics g) |
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{ |
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g.setColor(Color.white); |
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g.fillRect(0, 0, getWidth(), getHeight()); |
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if (fastPaint) |
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{ |
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fastPaint = false; |
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g.drawImage(image, 0, 0, this); |
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return; |
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} |
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int oldHeight = imgHeight; |
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imgHeight = getHeight(); |
239 |
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imgHeight -= (imgHeight % av.getCharHeight()); |
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if (imgHeight < 1) |
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{ |
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return; |
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} |
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if (oldHeight != imgHeight || image.getWidth(this) != getWidth()) |
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{ |
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image = new BufferedImage(getWidth(), imgHeight, |
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BufferedImage.TYPE_INT_RGB); |
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} |
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Graphics2D gg = image.createGraphics(); |
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gg.setColor(Color.white); |
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gg.fillRect(0, 0, getWidth(), imgHeight); |
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drawIds(gg, av, av.getRanges().getStartSeq(), |
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av.getRanges().getEndSeq(), searchResults, true, getWidth()); |
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gg.dispose(); |
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g.drawImage(image, 0, 0, this); |
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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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279 |
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@param |
280 |
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282 |
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283 |
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| 0% |
Uncovered Elements: 62 (62) |
Complexity: 16 |
Complexity Density: 0.4 |
|
284 |
0 |
void drawIds(Graphics2D g, AlignViewport alignViewport,... |
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final int startSeq, final int endSeq, List<SequenceI> selection, |
286 |
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boolean forGUI, int panelWidth) |
287 |
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{ |
288 |
0 |
Font font = alignViewport.getFont(); |
289 |
0 |
if (alignViewport.isSeqNameItalics()) |
290 |
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{ |
291 |
0 |
setIdfont(new Font(font.getName(), Font.ITALIC, font.getSize())); |
292 |
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} |
293 |
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else |
294 |
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{ |
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setIdfont(font); |
296 |
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} |
297 |
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298 |
0 |
g.setFont(getIdfont()); |
299 |
0 |
FontMetrics fm = g.getFontMetrics(); |
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301 |
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if (alignViewport.antiAlias) |
302 |
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{ |
303 |
0 |
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, |
304 |
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RenderingHints.VALUE_ANTIALIAS_ON); |
305 |
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} |
306 |
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307 |
0 |
Color currentColor = Color.white; |
308 |
0 |
Color currentTextColor = Color.black; |
309 |
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310 |
0 |
boolean hasHiddenRows = alignViewport.hasHiddenRows(); |
311 |
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312 |
0 |
if (alignViewport.getWrapAlignment()) |
313 |
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{ |
314 |
0 |
drawIdsWrapped(g, alignViewport, startSeq, getHeight(), |
315 |
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isManuallyAdjusted() ? panelWidth : -1, forGUI); |
316 |
0 |
return; |
317 |
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} |
318 |
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319 |
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320 |
0 |
int xPos = 0; |
321 |
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322 |
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323 |
0 |
for (int i = startSeq; i <= endSeq; i++) |
324 |
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{ |
325 |
0 |
SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i); |
326 |
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327 |
0 |
if (sequence == null) |
328 |
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{ |
329 |
0 |
continue; |
330 |
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} |
331 |
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332 |
0 |
if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) |
333 |
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{ |
334 |
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g.setFont(getHiddenFont(sequence, alignViewport)); |
335 |
0 |
fm = g.getFontMetrics(); |
336 |
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} |
337 |
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338 |
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339 |
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if (selection != null && selection.contains(sequence)) |
340 |
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{ |
341 |
0 |
currentColor = Color.black; |
342 |
0 |
currentTextColor = Color.white; |
343 |
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} |
344 |
0 |
else if ((alignViewport.getSelectionGroup() != null) && alignViewport |
345 |
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.getSelectionGroup().getSequences(null).contains(sequence)) |
346 |
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{ |
347 |
0 |
currentColor = Color.lightGray; |
348 |
0 |
currentTextColor = Color.black; |
349 |
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} |
350 |
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else |
351 |
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{ |
352 |
0 |
currentColor = alignViewport.getSequenceColour(sequence); |
353 |
0 |
currentTextColor = Color.black; |
354 |
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} |
355 |
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356 |
0 |
g.setColor(currentColor); |
357 |
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358 |
0 |
int charHeight = alignViewport.getCharHeight(); |
359 |
0 |
g.fillRect(0, (i - startSeq) * charHeight, getWidth(), charHeight); |
360 |
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361 |
0 |
g.setColor(currentTextColor); |
362 |
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363 |
0 |
String string = sequence |
364 |
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.getDisplayId(alignViewport.getShowJVSuffix()); |
365 |
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366 |
0 |
if (alignViewport.isRightAlignIds()) |
367 |
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{ |
368 |
0 |
xPos = panelWidth - fm.stringWidth(string) - 4; |
369 |
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} |
370 |
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371 |
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g.drawString(string, xPos, |
372 |
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(((i - startSeq) * charHeight) + charHeight) |
373 |
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- (charHeight / 5)); |
374 |
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375 |
0 |
if (hasHiddenRows && av.getShowHiddenMarkers()) |
376 |
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{ |
377 |
0 |
drawMarker(g, alignViewport, i, startSeq, 0); |
378 |
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} |
379 |
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} |
380 |
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} |
381 |
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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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@param |
387 |
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@param |
388 |
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@param |
389 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
390 |
0 |
void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,... |
391 |
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int startSeq, int pageHeight) |
392 |
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{ |
393 |
0 |
drawIdsWrapped(g, alignViewport, startSeq, pageHeight, -1, true); |
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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@param |
400 |
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@param |
401 |
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@param |
402 |
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@param |
403 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
404 |
0 |
public void drawIdsWrappedNoGUI(Graphics2D g, AlignViewport av2,... |
405 |
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int startSeq, int totalHeight) |
406 |
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{ |
407 |
0 |
drawIdsWrapped(g, av2, startSeq, totalHeight, -1, false); |
408 |
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} |
409 |
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| 0% |
Uncovered Elements: 50 (50) |
Complexity: 12 |
Complexity Density: 0.35 |
|
410 |
0 |
public void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,... |
411 |
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int startSeq, int pageHeight, int idWidth, boolean forGUI) |
412 |
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{ |
413 |
0 |
int alignmentWidth = alignViewport.getAlignment().getWidth(); |
414 |
0 |
final int alheight = alignViewport.getAlignment().getHeight(); |
415 |
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416 |
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417 |
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418 |
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|
419 |
0 |
SeqCanvas seqCanvas = alignViewport.getAlignPanel() |
420 |
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.getSeqPanel().seqCanvas; |
421 |
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422 |
0 |
final int charHeight = alignViewport.getCharHeight(); |
423 |
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|
424 |
0 |
AnnotationLabels labels = null; |
425 |
0 |
if (alignViewport.isShowAnnotation()) |
426 |
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{ |
427 |
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428 |
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429 |
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430 |
0 |
labels = new AnnotationLabels(alignViewport); |
431 |
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} |
432 |
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|
433 |
0 |
ViewportRanges ranges = alignViewport.getRanges(); |
434 |
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435 |
0 |
int rowSize = ranges.getViewportWidth(); |
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 |
0 |
boolean hasHiddenRows = alignViewport.hasHiddenRows(); |
442 |
0 |
int ypos = seqCanvas.wrappedSpaceAboveAlignment; |
443 |
0 |
int rowStartRes = ranges.getStartRes(); |
444 |
0 |
while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth)) |
445 |
|
{ |
446 |
0 |
for (int i = startSeq; i < alheight; i++) |
447 |
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{ |
448 |
0 |
SequenceI s = alignViewport.getAlignment().getSequenceAt(i); |
449 |
0 |
if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) |
450 |
|
{ |
451 |
0 |
g.setFont(getHiddenFont(s, alignViewport)); |
452 |
|
} |
453 |
|
else |
454 |
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{ |
455 |
0 |
g.setFont(getIdfont()); |
456 |
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} |
457 |
0 |
drawIdString(g, hasHiddenRows, s, i, 0, ypos); |
458 |
|
} |
459 |
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|
460 |
0 |
if (labels != null && alignViewport.isShowAnnotation()) |
461 |
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{ |
462 |
0 |
int getWidth = getWidth(); |
463 |
0 |
int thisIdWidth = getWidth; |
464 |
0 |
g.translate(0, ypos + (alheight * charHeight)); |
465 |
0 |
if (!isManuallyAdjusted()) |
466 |
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{ |
467 |
0 |
int getAnnotationsIdWidth = labels.drawLabels(g, false, -1, false, |
468 |
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forGUI, null, false); |
469 |
0 |
thisIdWidth = idWidth < 0 ? getAnnotationsIdWidth : idWidth; |
470 |
0 |
if (thisIdWidth > getWidth) |
471 |
|
{ |
472 |
0 |
this.setPreferredSize( |
473 |
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new Dimension(thisIdWidth, this.getHeight())); |
474 |
0 |
this.repaint(); |
475 |
0 |
alignViewport.setIdWidth(thisIdWidth); |
476 |
|
} |
477 |
|
} |
478 |
0 |
labels.drawComponent(g, false, thisIdWidth, forGUI); |
479 |
0 |
g.translate(0, -ypos - (alheight * charHeight)); |
480 |
|
} |
481 |
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|
482 |
0 |
ypos += seqCanvas.wrappedRepeatHeightPx; |
483 |
0 |
rowStartRes += rowSize; |
484 |
|
} |
485 |
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} |
486 |
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487 |
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488 |
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489 |
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490 |
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491 |
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@param |
492 |
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@param |
493 |
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@param |
494 |
|
@param |
495 |
|
@param |
496 |
|
|
|
|
| 0% |
Uncovered Elements: 40 (40) |
Complexity: 8 |
Complexity Density: 0.31 |
|
497 |
0 |
void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex,... |
498 |
|
int starty, int yoffset) |
499 |
|
{ |
500 |
0 |
SequenceI[] hseqs = alignViewport.getAlignment() |
501 |
|
.getHiddenSequences().hiddenSequences; |
502 |
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|
503 |
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|
504 |
0 |
int hSize = hseqs.length; |
505 |
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|
506 |
0 |
int hiddenIndex = seqIndex; |
507 |
0 |
int lastIndex = seqIndex - 1; |
508 |
0 |
int nextIndex = seqIndex + 1; |
509 |
|
|
510 |
0 |
for (int j = 0; j < hSize; j++) |
511 |
|
{ |
512 |
0 |
if (hseqs[j] != null) |
513 |
|
{ |
514 |
0 |
if (j - 1 < hiddenIndex) |
515 |
|
{ |
516 |
0 |
hiddenIndex++; |
517 |
|
} |
518 |
0 |
if (j - 1 < lastIndex) |
519 |
|
{ |
520 |
0 |
lastIndex++; |
521 |
|
} |
522 |
0 |
if (j - 1 < nextIndex) |
523 |
|
{ |
524 |
0 |
nextIndex++; |
525 |
|
} |
526 |
|
} |
527 |
|
} |
528 |
|
|
529 |
|
|
530 |
|
|
531 |
|
|
532 |
0 |
boolean below = (hiddenIndex > lastIndex + 1); |
533 |
0 |
boolean above = (nextIndex > hiddenIndex + 1); |
534 |
|
|
535 |
0 |
g.setColor(Color.blue); |
536 |
0 |
int charHeight = av.getCharHeight(); |
537 |
|
|
538 |
|
|
539 |
|
|
540 |
|
|
541 |
0 |
int[] xPoints = new int[] { getWidth() - charHeight, |
542 |
|
getWidth() - charHeight, getWidth() }; |
543 |
0 |
int yShift = seqIndex - starty; |
544 |
|
|
545 |
0 |
if (below) |
546 |
|
{ |
547 |
0 |
int[] yPoints = new int[] { yShift * charHeight + yoffset, |
548 |
|
yShift * charHeight + yoffset + charHeight / 4, |
549 |
|
yShift * charHeight + yoffset }; |
550 |
0 |
g.fillPolygon(xPoints, yPoints, 3); |
551 |
|
} |
552 |
0 |
if (above) |
553 |
|
{ |
554 |
0 |
yShift++; |
555 |
0 |
int[] yPoints = new int[] { yShift * charHeight + yoffset, |
556 |
|
yShift * charHeight + yoffset - charHeight / 4, |
557 |
|
yShift * charHeight + yoffset }; |
558 |
0 |
g.fillPolygon(xPoints, yPoints, 3); |
559 |
|
} |
560 |
|
} |
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
|
565 |
|
|
566 |
|
@param |
567 |
|
@param |
568 |
|
@return |
569 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
570 |
0 |
private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport)... |
571 |
|
{ |
572 |
0 |
if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq)) |
573 |
|
{ |
574 |
0 |
return new Font(av.getFont().getName(), Font.BOLD, |
575 |
|
av.getFont().getSize()); |
576 |
|
} |
577 |
0 |
return getIdfont(); |
578 |
|
} |
579 |
|
|
580 |
|
|
581 |
|
|
582 |
|
|
583 |
|
@param |
584 |
|
|
585 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
586 |
0 |
public void setHighlighted(List<SequenceI> list)... |
587 |
|
{ |
588 |
0 |
searchResults = list; |
589 |
0 |
repaint(); |
590 |
|
} |
591 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
592 |
0 |
public Font getIdfont()... |
593 |
|
{ |
594 |
0 |
return idfont; |
595 |
|
} |
596 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
597 |
0 |
public void setIdfont(Font idfont)... |
598 |
|
{ |
599 |
0 |
this.idfont = idfont; |
600 |
|
} |
601 |
|
|
602 |
|
|
603 |
|
|
604 |
|
|
605 |
|
|
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 6 |
Complexity Density: 0.86 |
|
614 |
0 |
@Override... |
615 |
|
public void propertyChange(PropertyChangeEvent evt) |
616 |
|
{ |
617 |
0 |
String propertyName = evt.getPropertyName(); |
618 |
0 |
if (propertyName.equals(ViewportRanges.STARTSEQ) |
619 |
|
|| (av.getWrapAlignment() |
620 |
|
&& propertyName.equals(ViewportRanges.STARTRES))) |
621 |
|
{ |
622 |
0 |
fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); |
623 |
|
} |
624 |
0 |
else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ)) |
625 |
|
{ |
626 |
0 |
fastPaint(((int[]) evt.getNewValue())[1] |
627 |
|
- ((int[]) evt.getOldValue())[1]); |
628 |
|
} |
629 |
0 |
else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT)) |
630 |
|
{ |
631 |
0 |
repaint(); |
632 |
|
} |
633 |
|
} |
634 |
|
|
635 |
|
private boolean manuallyAdjusted = false; |
636 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
637 |
0 |
public boolean isManuallyAdjusted()... |
638 |
|
{ |
639 |
0 |
return manuallyAdjusted; |
640 |
|
} |
641 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
642 |
0 |
public void setManuallyAdjusted(boolean b)... |
643 |
|
{ |
644 |
0 |
manuallyAdjusted = b; |
645 |
|
} |
646 |
|
|
647 |
|
} |