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Merge branch 'develop' into trialMerge
[jalview.git]
/
src
/
jalview
/
renderer
/
seqfeatures
/
FeatureRenderer.java
diff --git
a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index
d580f2c
..
a1980c7
100644
(file)
--- a/
src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/
src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@
-22,8
+22,8
@@
package jalview.renderer.seqfeatures;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.MappedFeatures;
-import jalview.datamodel.Range;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
@@
-276,9
+276,9
@@
public class FeatureRenderer extends FeatureRendererModel
/*
* if columns are all gapped, or sequence has no features, nothing to do
*/
/*
* if columns are all gapped, or sequence has no features, nothing to do
*/
- Range visiblePositions = seq.findPositions(start+1, end+1);
- if (visiblePositions == null || (!seq.getFeatures().hasFeatures()
- && !av.isShowComplementFeatures()))
+ ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
+ if (visiblePositions == null || !seq.getFeatures().hasFeatures()
+ && !av.isShowComplementFeatures())
{
return null;
}
{
return null;
}
@@
-447,12
+447,16
@@
public class FeatureRenderer extends FeatureRendererModel
*/
Color drawComplementFeatures(final Graphics g, final SequenceI seq,
int start, int end, int y1, boolean colourOnly,
*/
Color drawComplementFeatures(final Graphics g, final SequenceI seq,
int start, int end, int y1, boolean colourOnly,
- Range visiblePositions, Color drawnColour)
+ ContiguousI visiblePositions, Color drawnColour)
{
AlignViewportI comp = av.getCodingComplement();
FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
.getFeatureRenderer();
{
AlignViewportI comp = av.getCodingComplement();
FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
.getFeatureRenderer();
- for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++)
+
+ final int visibleStart = visiblePositions.getBegin();
+ final int visibleEnd = visiblePositions.getEnd();
+
+ for (int pos = visibleStart; pos <= visibleEnd; pos++)
{
int column = seq.findIndex(pos);
MappedFeatures mf = fr2
{
int column = seq.findIndex(pos);
MappedFeatures mf = fr2