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JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations...
[jalview.git]
/
src
/
jalview
/
renderer
/
seqfeatures
/
FeatureColourFinder.java
diff --git
a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
index
00cbd2c
..
d5784b0
100644
(file)
--- a/
src/jalview/renderer/seqfeatures/FeatureColourFinder.java
+++ b/
src/jalview/renderer/seqfeatures/FeatureColourFinder.java
@@
-20,6
+20,7
@@
*/
package jalview.renderer.seqfeatures;
*/
package jalview.renderer.seqfeatures;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.SequenceI;
import jalview.api.FeatureRenderer;
import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.SequenceI;
@@
-75,7
+76,7
@@
public class FeatureColourFinder
* @param defaultColour
* @param seq
* @param column
* @param defaultColour
* @param seq
* @param column
- * alignment column position (base zero)
+ * alignment column position (0..)
* @return
*/
public Color findFeatureColour(Color defaultColour, SequenceI seq,
* @return
*/
public Color findFeatureColour(Color defaultColour, SequenceI seq,
@@
-101,7
+102,7
@@
public class FeatureColourFinder
}
}
}
}
- Color c = featureRenderer.findFeatureColour(seq, column, g);
+ Color c = featureRenderer.findFeatureColour(seq, column + 1, g);
if (c == null)
{
return defaultColour;
if (c == null)
{
return defaultColour;
@@
-122,8
+123,16
@@
public class FeatureColourFinder
*/
boolean noFeaturesDisplayed()
{
*/
boolean noFeaturesDisplayed()
{
- if (featureRenderer == null
- || !featureRenderer.getViewport().isShowSequenceFeatures())
+ if (featureRenderer == null)
+ {
+ return true;
+ }
+ AlignViewportI av = featureRenderer.getViewport();
+ if (av.isShowComplementFeatures())
+ {
+ return false;
+ }
+ if (!av.isShowSequenceFeatures())
{
return true;
}
{
return true;
}