+/*
+ * 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.api.AlignViewportI;
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;
+
+ /**
+ * Constructor given a viewport
+ *
+ * @param viewport
+ */
+ public FeatureRenderer(AlignViewportI viewport)
+ {
+ this.av = viewport;
+ }
+
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 Structure Viewers and the Overview Window to get the
+ * feature colour of the rendered sequence, returned as an RGB value
+ *
+ * @param defaultColour
+ * @param seq
+ * @param column
+ * @return
*/
- public synchronized int findFeatureColour(int initialCol, final SequenceI seq,
- int column)
+ public synchronized int findFeatureColour(int defaultColour,
+ final SequenceI seq, int column)
{
if (!av.isShowSequenceFeatures())
{
- return initialCol;
+ return defaultColour;
}
SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
if (lastSequenceFeatures == null || sfSize == 0)
{
- return initialCol;
+ return defaultColour;
}
if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
if (offscreenImage != null)
{
- offscreenImage.setRGB(0, 0, initialCol);
+ offscreenImage.setRGB(0, 0, defaultColour);
drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
return offscreenImage.getRGB(0, 0);
if (currentColour == null)
{
- return initialCol;
+ return defaultColour;
}
else
{
- return ((Integer) currentColour).intValue();
+ return currentColour.intValue();
}
}
int epos;
+ /**
+ * Draws the sequence on the graphics context, or just determines the colour
+ * that would be drawn (if flag offscreenrender is true).
+ *
+ * @param g
+ * @param seq
+ * @param start
+ * start column (or sequence position in offscreenrender mode)
+ * @param end
+ * end column (not used in offscreenrender mode)
+ * @param y1
+ * vertical offset at which to draw on the graphics
+ */
public synchronized void drawSequence(Graphics g, final SequenceI seq,
int start, int end, int y1)
{
}
sfSize = lastSequenceFeatures.length;
- String type;
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
{
- type = renderOrder[renderIndex];
-
- if (type == null || !showFeatureOfType(type))
+ String type = renderOrder[renderIndex];
+ if (!showFeatureOfType(type))
{
continue;
}
continue;
}
- if (featureGroups != null
- && sequenceFeature.featureGroup != null
- && sequenceFeature.featureGroup.length() != 0
- && featureGroups.containsKey(sequenceFeature.featureGroup)
- && !featureGroups.get(sequenceFeature.featureGroup)
- .booleanValue())
+ if (featureGroupNotShown(sequenceFeature))
{
continue;
}
+ /*
+ * check feature overlaps the visible part of the alignment,
+ * unless doing offscreenRender (to the Overview window or a
+ * structure viewer) which is not limited
+ */
if (!offscreenRender
&& (sequenceFeature.getBegin() > epos || sequenceFeature
.getEnd() < spos))
continue;
}
+ Color featureColour = getColour(sequenceFeature);
+ boolean isContactFeature = sequenceFeature.isContactFeature();
+
if (offscreenRender && offscreenImage == null)
{
- if (sequenceFeature.begin <= start
- && sequenceFeature.end >= start)
+ /*
+ * offscreen mode with no image (image is only needed if transparency
+ * is applied to feature colours) - just check feature is rendered at
+ * the requested position (start == sequence position in this mode)
+ */
+ boolean featureIsAtPosition = sequenceFeature.begin <= start
+ && sequenceFeature.end >= start;
+ if (isContactFeature)
+ {
+ featureIsAtPosition = sequenceFeature.begin == start
+ || sequenceFeature.end == start;
+ }
+ if (featureIsAtPosition)
{
// this is passed out to the overview and other sequence renderers
// (e.g. molecule viewer) to get displayed colour for rendered
// sequence
- currentColour = new Integer(getColour(sequenceFeature).getRGB());
+ currentColour = new Integer(featureColour.getRGB());
// used to be retreived from av.featuresDisplayed
// currentColour = av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type);
}
}
- else if (sequenceFeature.type.equals("disulfide bond"))
+ else if (isContactFeature)
{
renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.begin) - 1,
- getColour(sequenceFeature)
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
+ seq.findIndex(sequenceFeature.begin) - 1, featureColour,
+ start, end, y1);
renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
- seq.findIndex(sequenceFeature.end) - 1,
- getColour(sequenceFeature)
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
+ seq.findIndex(sequenceFeature.end) - 1, featureColour,
+ start, end, y1);
}
else if (showFeature(sequenceFeature))
{
if (av_isShowSeqFeatureHeight
- && sequenceFeature.score != Float.NaN)
+ && !Float.isNaN(sequenceFeature.score))
{
renderScoreFeature(g, seq,
seq.findIndex(sequenceFeature.begin) - 1,
seq.findIndex(sequenceFeature.end) - 1,
- getColour(sequenceFeature), start, end, y1,
+ featureColour, start, end, y1,
normaliseScore(sequenceFeature));
}
else
{
renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
seq.findIndex(sequenceFeature.end) - 1,
- getColour(sequenceFeature), start, end, y1);
+ featureColour, start, end, y1);
}
}
-
}
-
}
- 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()
+ /**
+ * Answers true if the feature belongs to a feature group which is not
+ * currently displayed, else false
+ *
+ * @param sequenceFeature
+ * @return
+ */
+ protected boolean featureGroupNotShown(
+ final SequenceFeature sequenceFeature)
{
- return transparencyAvailable;
+ return featureGroups != null
+ && sequenceFeature.featureGroup != null
+ && sequenceFeature.featureGroup.length() != 0
+ && featureGroups.containsKey(sequenceFeature.featureGroup)
+ && !featureGroups.get(sequenceFeature.featureGroup)
+ .booleanValue();
}
/**
* discover and display.
*
*/
+ @Override
public void featuresAdded()
{
lastSeq = null;