+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer.seqfeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
-public class FeatureRenderer extends
- jalview.viewmodel.seqfeatures.FeatureRendererModel
+public class FeatureRenderer extends FeatureRendererModel
{
FontMetrics fm;
boolean av_validCharWidth, av_isShowSeqFeatureHeight;
+ private Integer currentColour;
+
protected void updateAvConfig()
{
av_charHeight = av.getCharHeight();
charOffset = (av_charWidth - fm.charWidth(s)) / 2;
g.drawString(String.valueOf(s), charOffset
+ (av_charWidth * (i - start)), pady);
+
}
}
}
BufferedImage offscreenImage;
+ @Override
public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
{
return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
}
/**
- * This is used by the Molecule Viewer and Overview to get the accurate
- * colourof the rendered sequence
+ * This is used by the Molecule Viewer and Overview to get the accurate colour
+ * of the rendered sequence
*/
- public synchronized int findFeatureColour(int initialCol, final SequenceI seq,
- int column)
+ public synchronized int findFeatureColour(int initialCol,
+ final SequenceI seq, int column)
{
if (!av.isShowSequenceFeatures())
{
}
else
{
- return ((Integer) currentColour).intValue();
+ return currentColour.intValue();
}
}
else if (showFeature(sequenceFeature))
{
if (av_isShowSeqFeatureHeight
- && sequenceFeature.score != Float.NaN)
+ && !Float.isNaN(sequenceFeature.score))
{
renderScoreFeature(g, seq,
seq.findIndex(sequenceFeature.begin) - 1,
}
- if (transparency != 1.0f && g != null && transparencyAvailable)
+ if (transparency != 1.0f && g != null)
{
Graphics2D g2 = (Graphics2D) g;
g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
}
}
- boolean transparencyAvailable = true;
-
- protected void setTransparencyAvailable(boolean isTransparencyAvailable)
- {
- transparencyAvailable = isTransparencyAvailable;
- }
-
- @Override
- public boolean isTransparencyAvailable()
- {
- return transparencyAvailable;
- }
-
/**
* Called when alignment in associated view has new/modified features to
* discover and display.
*
*/
+ @Override
public void featuresAdded()
{
lastSeq = null;